bluuebunny/crossref_metadata_2025 huggingface dataset:
Stabilitätsbedingungen für parametererregte Schwingungssysteme mit schmalbandigen Zufallserregungen
Authors: Wedig W.
Published: June 2007

Für ein parametererregtes Schwingungssystem mit einem Freiheitsgrad, das durch gefiltertes weißes Rauschen erregt wird, werden die Gleichungen für die quadratischen Momente über die Fokker‐Planck‐Gleichung hergeleitet und mit Hilfe der Störungsrechnung näherungsweise gelöst. Die angegebene Momentenstabilitätsbedingung zeigt, daß stochastische Erregungen mit einer schmalen, um eine mittlere Erregerfrequenz konzentrierten Spektraldichteverteilung ähnlich stabilitätsgefährdend für die Ruhelage des Systems sind wie periodische Parametererregungen. Mit breiter werdendem Frequenzband der Erregerspektraldichte nimmt die destabilisierende Wirkung ab.
Über nichtlineare Parameterresonanzen
Authors: Schmidt G. , Heinrich W.
Published: June 2007

Es wird gezeigt, daß Nichtlinearitäten mit periodischen Koeffizienten in Schwingungssystemen zu Resonanzen führen, die wesentlich von nichtlinearen Dämpfungskräften beeinflußt werden.
The Behaviour of an Edge Dislocation in Non‐Homogeneous Anisotropic Body with Cracks
Authors: Kurihara T.
Published: June 2007

The forces of interaction between a stationary edge dislocation and a partially bonded bimetallic interface is discussed in the framework of the elastic continuum approximation. Here, each of two semi‐infinite media, bonded together, is assumed to be anisotropic. The method of solution is based on the reduction to a type of dual nonhomogeneous Hilbert problem for two functions. Some numerical calculations are carried out for the simple case where the direction of the Burgers vector of dislocation is perpendicular to the interface. It is assumed that both of two materials are orthotropic and have the same elastic coefficients. The effect of mismatch of the axes of elastic symmetry on the glide force and the equilibrium position of dislocation is discussed in detail.
An Extension of the Vector Potential Concept to the Case of a Three‐Dimensional Unsteady Boundary Layer
Authors: Schreier St.
Published: June 2007

A method is given for finding a first order solution of the laminar boundary layer equations for a cone whose angle of attack may be changing with time and whose pitch rate may not be zero. The angle of attack and its time derivatives, as well as the pitch rate and its time derivatives, are assumed small. The solution is presented in the form of a power series in x, the distance from the nose of the body. It approaches the solution of Brong for the inviscid case at the outer edge of the boundary layer, and the solution of Moore for the boundary layer in steady flow as the time derivatives go to zero. Viscous interaction is neglected and the gas is assumed ideal. The boundary layer equations are reduced to a series of ordinary differential equations which may readily be solved by computer. Sample numerical solutions are presented for the case: Mach number 10, cone half angle 10°, insulated wall.
Existenz und numerische Erfaßbarkeit verallgemeinerter Lösungen halblinearer Anfangswertaufgaben
Authors: Ansorge R. , Geiger C. , Hass R.
Published: June 2007

Gelegentlich lassen sich bei linearen Anfangswertaufgaben mit partiellen Differentialgleichungen neben den echten Lösungen auch die sogenannten verallgemeinerten Lösungen mittels Differenzenverfahren erfassen. Eine Abschätzung des globalen Verfahrensfehlers gelang erstmals 1967 durch J. Peetre und V. Thomée. In der vorliegenden Arbeit werden zunächst Bedingungen angegeben, unter denen auch halblineare Anfangswertaufgaben verallgemeinerte Lösungen besitzen. Es wird gezeigt, daß auch hier die numerische Erfaßbarkeit der verallgemeinerten Lösungen durch Differenzenverfahren gewährleistet werden kann, und eine auf approximationstheoretischen Hilfsmitteln beruhende Abschätzung des hierbei auftretenden globalen Verfahrensfehlers wird für gewisse Klassen von Anfangswertaufgaben hergeleitet. Die Abschätzung ist hinsichtlich der Konvergenzordnung nicht verbesserbar.
Minimum Principles for Viscoelastic Solids with Vanishing Poisson Ratio
Authors: Breuer S.
Published: June 2007

Four minimum principles are presented, governing the quasistatic deformations of viscoelastic solids with vanishing Poisson Ratio. The positive‐definiteness of the work energy is not required for the principles to hold.
Cereal aphid populations in non‐crop habitats show strong density dependence
Authors: BOMMARCO RICCARDO , WETTERLIND SIMON , SIGVALD ROLAND
Published: June 2007

Few studies have addressed how density‐dependent and density‐independent regulation of population growth and abundance varies among habitats for a species that requires multiple habitat types to complete its life cycle. Understanding such relationships, however, are of direct relevance to the control of crop pest insects that regularly move between crop and non‐crop habitats.

We used autoregressive models to analyse a series of seasonal catches of the cereal aphid Rhopalosiphum padi. The data were collected from regional suction traps and egg counts on the overwintering host, over a period of 14–31 years, at four locations in Sweden. R. padi is an obligate host‐alternating species in Sweden and seasonal catches reflect habitat use in a year: the primary woody host in winter and spring, the cereal crops in summer, and the perennial grasslands in the autumn.

Strong direct density dependence acting within the year was found, but the strength varied between seasons depending on habitat use by the aphids during the year. Only a weak indication or no indication at all of density dependence was found during the period of residency on the primary host in the winter and spring periods.

Density dependence occurred when R. padi utilized summer cereals (42% of the variation was explained), and even stronger density dependence occurred in the perennial grasslands in the autumn (70% variation explained). Stochastic fluctuations in the winter and spring were balanced by a strong density dependence in the cereal and grassland habitats in the summer and autumn periods, which reduced variability in population fluctuations.

Weather, measured as seasonal average temperature and accumulated precipitation, did not affect aphid abundance fluctuations much, explaining only 1–9% of the variability.

Synthesis and applications. Our results suggest that density‐dependent regulation of R. padi occurs in late summer grasslands and early summer cereals. The mechanisms causing these patterns are not understood, making it difficult to provide specific pest management recommendations at this stage. The results do indicate, however, that pest management needs to involve a landscape‐level approach, taking into account mechanistic information about the plant, herbivore and predator interactions in multiple habitats visited by the herbivorous pest.
Dopaminergic modulation of short-term synaptic plasticity at striatal inhibitory synapses
Authors: Tecuapetla Fatuel , Carrillo-Reid Luis , Bargas José , Galarraga Elvira
Published: June 2007

Circuit properties, such as the selection of motor synergies, have been posited as relevant tasks for the recurrent inhibitory synapses between spiny projection neurons of the neostriatum, a nucleus of the basal ganglia participating in procedural learning and voluntary motor control. Here we show how the dopaminergic system regulates short-term plasticity (STP) in these synapses. STP is thought to endow neuronal circuits with computational powers such as gain control, filtering, and the emergence of transitory net states. But little is known about STP regulation. Employing unitary and population synaptic recordings, we observed that activation of dopamine receptors can modulate STP between spiny neurons. A D
1
-class agonist enhances, whereas a D
2
-class agonist decreases, short-term depression most probably by synaptic redistribution. Presynaptic receptors appear to be responsible for this modulation. In contrast, STP between fast-spiking interneurons and spiny projection neurons is largely unregulated despite expressing presynaptic receptors. Thus, the present experiments provide an explanation for dopamine actions at the circuit level: the control of STP between lateral connections of output neurons and the reorganization of the balance between different forms of inhibitory transmission. Theoretically, D
1
receptors would promote a sensitive, responsive state for temporal precision (dynamic component), whereas D
2
receptors would sense background activity (static component).
Long-range structural effects of a Charcot–Marie–Tooth disease-causing mutation in human glycyl-tRNA synthetase
Authors: Xie Wei , Nangle Leslie A. , Zhang Wei , Schimmel Paul , Yang Xiang-Lei
Published: June 2007

Functional expansion of specific tRNA synthetases in higher organisms is well documented. These additional functions may explain why dominant mutations in glycyl-tRNA synthetase (GlyRS) and tyrosyl-tRNA synthetase cause Charcot–Marie–Tooth (CMT) disease, the most common heritable disease of the peripheral nervous system. At least 10 disease-causing mutant alleles of GlyRS have been annotated. These mutations scatter broadly across the primary sequence and have no apparent unifying connection. Here we report the structure of wild type and a CMT-causing mutant (G526R) of homodimeric human GlyRS. The mutation is at the site for synthesis of glycyl-adenylate, but the rest of the two structures are closely similar. Significantly, the mutant form diffracts to a higher resolution and has a greater dimer interface. The extra dimer interactions are located ≈30 Å away from the G526R mutation. Direct experiments confirm the tighter dimer interaction of the G526R protein. The results suggest the possible importance of subtle, long-range structural effects of CMT-causing mutations at the dimer interface. From analysis of a third crystal, an appended motif, found in higher eukaryote GlyRSs, seems not to have a role in these long-range effects.
Collaboration between the ClpB AAA+ remodeling protein and the DnaK chaperone system
Authors: Doyle Shannon M. , Hoskins Joel R. , Wickner Sue
Published: June 2007

ClpB and Hsp104, members of the AAA+ superfamily of proteins, protect cells from the devastating effects of protein inactivation and aggregation that arise after extreme heat stress. They exist as a hexameric ring and contain two nucleotide-binding sites per monomer. ClpB and Hsp104 are able to dissolve protein aggregates in conjunction with the DnaK/Hsp70 chaperone system, although the roles of the individual chaperones in disaggregation are not well understood. In the absence of the DnaK/Hsp70 system, ClpB and Hsp104 alone are able to perform protein remodeling when their ATPase activity is asymmetrically slowed either by providing a mixture of ATP and ATPγS, a nonphysiological and slowly hydrolyzed ATP analog, or by inactivating one of the two nucleotide-binding domains by mutation. To gain insight into the roles of ClpB and the DnaK system in protein remodeling, we tested whether there was a further stimulation by the DnaK chaperone system under conditions that elicited remodeling activity by ClpB alone. Our results demonstrate that ClpB and the DnaK system act synergistically to remodel proteins and dissolve aggregates. The results further show that ATP is required and that both nucleotide-binding sites of ClpB must be able to hydrolyze ATP to permit functional collaboration between ClpB and the DnaK system.
OBO-Edit—an ontology editor for biologists
Authors: Day-Richter John , Harris Midori A. , Haendel Melissa ,   The Gene Ontology OBO-Edit Working Group, Lewis Suzanna
Published: June 2007

Summary: OBO-Edit is an open source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. Implemented in Java, OBO-Edit uses a graph-oriented approach to display and edit ontologies. OBO-Edit is particularly valuable for viewing and editing biomedical ontologies.

Availability:  https://sourceforge.net/project/showfiles.php?group_id=36855

Contact:  gohelp@geneontology.org
VIPER: an advanced software package to support high-throughput LC-MS peptide identification
Authors: Monroe Matthew E. , Tolić Nikola , Jaitly Navdeep , Shaw Jason L. , Adkins Joshua N. , Smith Richard D.
Published: June 2007

Summary: The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these LC-MS features to a database of peptides previously identified in LC-MS/MS analyses, and identify and quantify pairs of isotopically labeled peptides.

Availability: VIPER may be downloaded free of charge at http://ncrr.pnl.gov/software/

Contact:  rds@pnl.gov or proteomics@pnl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
Edge-based scoring and searching method for identifying condition-responsive protein–protein interaction sub-network
Authors: Guo Zheng , Li Yongjin , Gong Xue , Yao Chen , Ma Wencai , Wang Dong , Li Yanhui , Zhu Jing , Zhang Min , Yang Da , Wang Jing
Published: June 2007

Motivation: Current high-throughput protein–protein interaction (PPI) data do not provide information about the condition(s) under which the interactions occur. Thus, the identification of condition-responsive PPI sub-networks is of great importance for investigating how a living cell adapts to changing environments.

Results: In this article, we propose a novel edge-based scoring and searching approach to extract a PPI sub-network responsive to conditions related to some investigated gene expression profiles. Using this approach, what we constructed is a sub-network connected by the selected edges (interactions), instead of only a set of vertices (proteins) as in previous works. Furthermore, we suggest a systematic approach to evaluate the biological relevance of the identified responsive sub-network by its ability of capturing condition-relevant functional modules. We apply the proposed method to analyze a human prostate cancer dataset and a yeast cell cycle dataset. The results demonstrate that the edge-based method is able to efficiently capture relevant protein interaction behaviors under the investigated conditions.

Contact:  guoz@ems.hrbmu.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
PIP: a database of potential intron polymorphism markers
Authors: Yang Long , Jin Gulei , Zhao Xiangqian , Zheng Yan , Xu Zhaohua , Wu Weiren
Published: June 2007

Motivation: With the recent progress made in large-scale plant functional genome sequencing projects, a great amount of EST (express sequence tag) data is becoming available. With the help of complete genomic sequence information of model plants (rice and Arabidopsis), it is possible to predict the joints between adjacent exons after splicing (or termed ‘intron positions’ for short) in homologous ESTs of other plants. This would allow developing potential intron polymorphism (PIP) markers in these plants by designing primers in exons flanking the target intron.

Results: We have extracted a total of 57 658 PIP markers in 59 plant species and created a web-based database platform named PIP to provide detailed information of these PIP markers and homologous relationships among PIP markers from different species. The platform also provides a function of online designing of PIP markers based on cDNA/EST sequences submitted by users. With evaluations performed in silico, we have found that the intron position prediction is highly reliable and the polymorphism level of PIP markers is high enough for practical need.

Availability:  http://ibi.zju.edu.cn/pgl/pip/

Contact:  wuwr@zju.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
BioText Search Engine: beyond abstract search
Authors: Hearst Marti A. , Divoli Anna , Guturu Harendra , Ksikes Alex , Nakov Preslav , Wooldridge Michael A. , Ye Jerry
Published: June 2007

Summary: The BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. One novel feature is the ability to search and browse article figures and their captions. A grid view juxtaposes many different figures associated with the same keywords, providing new insight into the literature. An abstract/title search and list view shows at a glance many of the figures associated with each article. The interface is carefully designed according to usability principles and techniques. The search engine is a work in progress, and more functionality will be added over time.

Availability:  http://biosearch.berkeley.edu

Contact:  divoli@ischool.berkeley.edu and hearst@ischool.berkeley.edu
Extraction Not Creation: The History of Offshore Petroleum in the Gulf of Mexico
Authors: Priest Tyler
Published: June 2007

Offshore development is one of the most important but least analyzed chapters in the history of the petroleum industry, and the Gulf of Mexico is the most explored, drilled, and developed offshore petroleum province in the world. This essay examines offshore oil and gas development in the Gulf of Mexico, highlighting the importance of access and how the unique geology and geography of the Gulf shaped both access and technology. Interactions between technology, capital, geology, and the political structure of access in the Gulf of Mexico generated a functionally and regionally complex extractive industry that repeatedly resolved the material and economic contradictions of expanding into deeper water. This was not achieved, however, simply through technological miracles or increased mastery over the environment, as industry experts and popular accounts often imply. The industry moved deeper only by more profoundly adapting to the environment, not by transcending its limits. This essay diverges from celebratory narratives about offshore development and from interpretations that emphasize the social construction of the environment. It challenges the storyline of market-driven technology and its miraculous ability to expand and create petroleum abundance in the Gulf.
Seminal influences: Drosophila Acps and the molecular interplay between males and females during reproduction
Authors: Ravi Ram K. , Wolfner Mariana F.
Published: June 2007

Successful reproduction requires contributions from both the male and the female. In Drosophila, contributions from the male include accessory gland proteins (Acps) that are components of the seminal fluid. Upon their transfer to the female, Acps affect the female's physiology and behavior. Although primary sequences of Acp genes exhibit variation among species and genera, the conservation of protein biochemical classes in the seminal fluid suggests a conservation of functions. Bioinformatics coupled with molecular and genetic tools available for Drosophila melanogaster has expanded the functional analysis of Acps in recent years to the genomic/proteomic scale. Molecular interplay between Acps and the female enhances her egg production, reduces her receptivity to remating, alters her immune response and feeding behavior, facilitates storage and utilization of sperm in the female and affects her longevity. Here, we provide an overview of the D. melanogaster Acps and integrate the results from several studies that bring the current number of known D. melanogaster Acps to 112. We then discuss several examples of how the female's physiological processes and behaviors are mediated by interactions between Acps and the female. Understanding how Acps elicit particular female responses will provide insights into reproductive biology and chemical communication, tools for analyzing models of sexual cooperation and/or sexual conflict, and information potentially useful for strategies for managing insect pests.
The Physiology of Obese-Hyperglycemic Mice [ob/obMice]
Authors: Lindström Per
Published: June 2007

This review summarizes key aspects of what has been learned about the physiology of leptin deficiency as it can be observed in obese-hyperglycemicob/obmice. These mice lack functional leptin. They are grossly overweight and hyperphagic, particularly at young ages, and develop severe insulin resistance. They have been used as a model for obesity and as a rich source of pancreatic islets with high insulin release capacity. The leptin deficiency manifests also with regard to immune function, the cardiovascular system including angiogenesis, supportive tissue function, malignancies, and reproductive function.ob/obMice are well suited for studies on the interaction between leptin and insulin, and for studies on initial aspects of metabolic disturbances leading to type-2diabetes.
WT1 Peptide Cancer Vaccine for Patients with Hematopoietic Malignancies and Solid Cancers
Authors: Oka Yoshihiro , Tsuboi Akihiro , Elisseeva Olga A. , Nakajima Hiroko , Fujiki Fumihiro , Kawakami Manabu , Shirakata Toshiaki , Nishida Sumiyuki , Hosen Naoki , Oji Yusuke , Kawase Ichiro , Sugiyama Haruo
Published: June 2007

Wild-type Wilms' tumor geneWT1is expressed at a high level in hematopoietic malignancies including acute leukemia, chronic myelogenous leukemia, and myelodysplastic syndromes, as well as in various kinds of solid cancers. Human cytotoxic T lymphocytes (CTLs), which could specifically lyseWT1-expressing tumor cells with HLA class I restriction, were generatedin vitro. It was also demonstrated that mice immunized with the WT1 peptide rejected challenges byWT1-expressing cancer cells and survived with no signs of autoaggression to normal organs that physiologically expressedWT1. Furthermore, we and others detected IgM and IgG WT1 antibodies in patients with hematopoietic malignancies, indicating that the WT1 protein was highly immunogenic, and that immunoglobulin class-switch-inducing, WT1-specific, cellular immune responses were elicited in these patients. CD8+WT1-specific CTLs were also detected in peripheral blood or tumor-draining lymph nodes of cancer patients. These results provided us with the rationale for elicitation of CTL responses targeting the WT1 product for cancer immunotherapy. On the basis of these findings, we performed a phase I clinical trial of a WT1 peptide cancer vaccine for the patients with malignant neoplasms. These results strongly suggested that the WT1 peptide cancer vaccine had efficacy in the clinical setting because clinical responses, including reduction of leukemic blast cells or regression of tumor masses, were observed after the WT1 vaccination in patients with hematopoietic malignancies or solid cancers. The power of a tumor-associated-antigen (TAA)-derived cancer vaccine may be enhanced in combination with stronger adjuvants, helper peptide, molecular-target-based drugs, or some chemotherapy drugs, such as gemcitabine, which has been revealed to suppress regulartory T-cell function. In contrast, reduction of WT1 peptide dose may be needed for the treatment of patients with hematological stem cell diseases, because rapid and strong destruction of malignant cell-sustained hematopoiesis before recovery of normal hematopoiesis may lead to pancytopenia in these patients.
Soil Water Availability Modulation Over Estimated Relative Yield Losses in Wheat (Triticum aestivumL.) Due to Ozone Exposure
Authors: De la Torre Daniel , Sierra Maria Jose
Published: June 2007

The approach developed by Fuhrer in 1995 to estimate wheat yield losses induced by ozone and modulated by the soil water content (SWC) was applied to the data on Catalonian wheat yields. The aim of our work was to apply this approach and adjust it to Mediterranean environmental conditions by means of the necessary corrections. The main objective pursued was to prove the importance of soil water availability in the estimation of relative wheat yield losses as a factor that modifies the effects of tropospheric ozone on wheat, and to develop the algorithms required for the estimation of relative yield losses, adapted to the Mediterranean environmental conditions. The results show that this is an easy way to estimate relative yield losses just using meteorological data, without using ozone fluxes, which are much more difficult to calculate. Soil water availability is very important as a modulating factor of the effects of ozone on wheat; when soil water availability decreases, almost twice the amount of accumulated exposure to ozone is required to induce the same percentage of yield loss as in years when soil water availability is high.
Reward, Context, and Human Behaviour
Authors: Blaukopf Clare L. , DiGirolamo Gregory J.
Published: June 2007

Animal models of reward processing have revealed an extensive network of brain areas that process different aspects of reward, from expectation and prediction to calculation of relative value. These results have been confirmed and extended in human neuroimaging to encompass secondary rewards more unique to humans, such as money. The majority of the extant literature covers the brain areas associated with rewards whilst neglecting analysis of the actual behaviours that these rewards generate. This review strives to redress this imbalance by illustrating the importance of looking at the behavioural outcome of rewards and the context in which they are produced. Following a brief review of the literature of reward-related activity in the brain, we examine the effect of reward context on actions. These studies reveal how the presence of reward vs. rewardandpunishment, or being conscious vs. unconscious of reward-related actions, differentially influence behaviour. The latter finding is of particular importance given the extent to which animal models are used in understanding the reward systems of the human mind. It is clear that further studies are needed to learn about the human reaction to reward in its entirety, including any distinctions between conscious and unconscious behaviours. We propose that studies of reward entail a measure of the animal's (human or nonhuman) knowledge of the reward and knowledge of its own behavioural outcome to achieve that reward.
Subjective Outcome Evaluation of the Project P.A.T.H.S.: Qualitative Findings Based on the Experiences of Program Participants
Authors: Shek Daniel T. L. , Sun Rachel C. F.
Published: June 2007

A total of 52 schools participated in the Experimental Implementation Phase of the Project P.A.T.H.S. After completion of the Tier 1 Program, 8,057 students responded to a Subjective Outcome Evaluation Form (Form A) to assess their views of the program, instructors, and perceived effectiveness of the program. Based on the schools' evaluation reports, results of secondary data analyses on four open-ended questions showed that: (a) students felt that they had learned things at the personal, interpersonal, familial, and societal levels; (b) they appreciated the program design, instructors' performance, learning process, and program effectiveness; (c) they generally had positive comments on instructors attitude and teaching process; and (d) they made some suggestions on how the program and its implementation could be improved. The present study, based on qualitative data of subjective outcome evaluation, provides additional support for the effectiveness of the Tier 1 Program of the Project P.A.T.H.S. in Hong Kong.
Alternative Therapeutic Intervention for Individuals with Rett Syndrome
Authors: Lotan Meir
Published: June 2007

The individual with Rett syndrome (RS) displays an array of challenging difficulties in all areas of daily living. Since there is no cure for the disorder at this moment, parents of the individual with Rett search for different interventional modalities that will improve the condition and quality of life for their child. During the last few years, many individuals with RS have experienced different kinds of interventions. This paper presents these methods with relevant case stories for others to share the possibilities. This paper reviews the following interventions: animal-assisted therapy, such as dolphin therapy and dog-assisted therapy; auditory integration training; hyperbaric chamber; manual therapy, such as acupuncture/acupressure, aromatherapy, craniosacral therapy, Mayo facial release, Treager massage, chiropractor, and Reiki; mental modification techniques, such as Lovas and cognitive rehabilitation; motoric interventions, such as advanced biomechanical rehabilitation, patterning/Doman-DeLacato approach, and yoga. The present paper is not a recommendation for any of the above-mentioned techniques, but merely a review of different interventions available for the inquisitive parent of the individual with RS.
HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
Authors: Wang Gary P. , Ciuffi Angela , Leipzig Jeremy , Berry Charles C. , Bushman Frederic D.
Published: June 2007

Integration of retroviral DNA into host cell DNA is a defining feature of retroviral replication. HIV integration is known to be favored in active transcription units, which promotes efficient transcription of the viral genes, but the molecular mechanisms responsible for targeting are not fully clarified. Here we used pyrosequencing to map 40,569 unique sites of HIV integration. Computational prediction of nucleosome positions in target DNA indicated that integration sites are periodically distributed on the nucleosome surface, consistent with favored integration into outward-facing DNA major grooves in chromatin. Analysis of integration site positions in the densely annotated ENCODE regions revealed a wealth of new associations between integration frequency and genomic features. Integration was particularly favored near transcription-associated histone modifications, including H3 acetylation, H4 acetylation, and H3 K4 methylation, but was disfavored in regions rich in transcription-inhibiting modifications, which include H3 K27 trimethylation and DNA CpG methylation. Statistical modeling indicated that effects of histone modification on HIV integration were partially independent of other genomic features influencing integration. The pyrosequencing and bioinformatic methods described here should be useful for investigating many aspects of retroviral DNA integration.
Synergid Cell Death in Arabidopsis Is Triggered following Direct Interaction with the Pollen Tube
Authors: Sandaklie-Nikolova Linda , Palanivelu Ravishankar , King Edward J. , Copenhaver Gregory P. , Drews Gary N.
Published: June 2007

During angiosperm reproduction, one of the two synergid cells within the female gametophyte undergoes cell death prior to fertilization. The pollen tube enters the female gametophyte by growing into the synergid cell that undergoes cell death and releases its two sperm cells within the degenerating synergid cytoplasm to effect double fertilization. In Arabidopsis (Arabidopsis thaliana) and many other species, synergid cell death is dependent upon pollination. However, the mechanism by which the pollen tube causes synergid cell death is not understood. As a first step toward understanding this mechanism, we defined the temporal relationship between pollen tube arrival at the female gametophyte and synergid cell death in Arabidopsis. Using confocal laser scanning microscopy, light microscopy, transmission electron microscopy, and real-time observation of these two events in vitro, we demonstrate that synergid cell death initiates after the pollen tube arrives at the female gametophyte but before pollen tube discharge. Our results support a model in which a signaling cascade triggered by pollen tube-synergid cell contact induces synergid cell death in Arabidopsis.
Medicago truncatulaRoot Nodule Proteome Analysis Reveals Differential Plant and Bacteroid Responses to Drought Stress
Authors: Larrainzar Estíbaliz , Wienkoop Stefanie , Weckwerth Wolfram , Ladrera Rubén , Arrese-Igor Cesar , González Esther M.
Published: June 2007

Drought is one of the environmental factors most affecting crop production. Under drought, symbiotic nitrogen fixation is one of the physiological processes to first show stress responses in nodulated legumes. This inhibition process involves a number of factors whose interactions are not yet understood. This work aims to further understand changes occurring in nodules under drought stress from a proteomic perspective. Drought was imposed on Medicago truncatula ‘Jemalong A17’ plants grown in symbiosis with Sinorhizobium meliloti strain 2011. Changes at the protein level were analyzed using a nongel approach based on liquid chromatography coupled to tandem mass spectrometry. Due to the complexity of nodule tissue, the separation of plant and bacteroid fractions in M. truncatula root nodules was first checked with the aim of minimizing cross contamination between the fractions. Second, the protein plant fraction of M. truncatula nodules was profiled, leading to the identification of 377 plant proteins, the largest description of the plant nodule proteome so far. Third, both symbiotic partners were independently analyzed for quantitative differences at the protein level during drought stress. Multivariate data mining allowed for the classification of proteins sets that were involved in drought stress responses. The isolation of the nodule plant and bacteroid protein fractions enabled the independent analysis of the response of both counterparts, gaining further understanding of how each symbiotic member is distinctly affected at the protein level under a water-deficit situation.
The Knysna elephants: a population study conducted using faecal DNA
Authors: Eggert Lori S. , Patterson Gareth , Maldonado Jesús E.
Published: June 2007

The elephants of the Knysna region continue to survive, despite fears that there was only a single surviving female. Their range is larger than previously believed, and includes the Afromontane forest and mountain fynbos. The five individuals detected in this study were all females, and share a single mitochondrial DNA control region haplotype with individuals from Addo Elephant National Park. At least two of these elephants appear to be first‐order relatives, and the others may be part of a single matrilineal group. The genetic diversity detected is lower than that found in most African savanna populations, but is higher than that found at Addo, where individuals represent the descendents of a severe population size bottleneck. Levels of genetic diversity are more similar to those detected at Kruger National Park, suggesting that the Knysna elephants represent a remnant of the once widespread populations of South Africa.
Neotyphodiuminteractions with a wild grass are driven mainly by endophyte haplotype
Authors: MORSE L. J. , FAETH S. H. , DAY T. A.
Published: June 2007

Strong mutualistic associations are expected to arise between host and microbial symbionts when symbionts lose sexuality, and rely strictly on their host for reproduction via vertical transmission. TheNeotyphodiumendophyte is a vertically transmitted, asexual symbiont of pooid grasses. In agronomic grasses,Neotyphodiumtypically interacts mutualistically with its host by increasing drought resistance and other properties. However, the interaction likely depends on host and endophyte genotypic variation, yet little is known how this variation influences host physiological and morphological responses, especially in wild grasses.

We used four differentNeotyphodium‐infected maternal lines of a wild grass, Arizona fescue (Festuca arizonica). Two lines harboured one haplotype and two lines harboured a different haplotype. We experimentally removed the endophyte from some ramets of the four lines. We grew infected (E+) and uninfected (E−) plants in a greenhouse under varying water availability.

We examined the effect of endophyte infection, endophyte and host plant maternal genotype, and water availability on traditional growth parameters. We also measured leaf net photosynthesis and dark respiration, leaf conductance to water vapour, leaf water potential, leaf rolling and stomatal density to provide explanations for differences in biomass production and relative growth rates (RGR).

Our general findings show thatNeotyphodiuminfection,Neotyphodiumhaplotype and its interaction with host maternal genotype, and varying water availability influence Arizona fescue physiology, growth and biomass production. Based only on infection status, the direction of interaction between endophyte and host is not mutualistic in terms of host growth. Overall, endophyte haplotype and its interaction with host maternal genotype is the most critical, and consistent factor in influencing host growth and physiological outcomes. Variation due to endophyte haplotype in terms of growth and physiological parameters is often greater than that between infected and uninfected hosts.

Endophyte–host interactions are likely to be enormously complex because of the genetic and environmental variation that exists in natural populations. The outcome of these interactions in natural grass–endophyte systems is exceedingly difficult to predict based simply on the presence or absence of the endophyte.
A performance based approach to distinguish indices from handicaps in sexual selection studies
Authors: VANHOOYDONCK B. , VAN DAMME R. , HERREL A. , IRSCHICK D. J.
Published: June 2007

Central to theories of the evolution of conspicuous secondary sexual traits is that sexual traits honestly reflect at least one aspect of an individual's quality. In general, the reliability of sexual traits can be explained in two ways. Either sexual traits are reliable indicators of individual quality because they are costly and the costs in terms of survival are higher for an individual of low quality as compared to an individual of high quality (i.e. handicap principle) or sexual traits are reliable because of physical constraints and thus cost‐free (reliability by design).

The distinction between indices and handicaps thus centres on whether the sexual signal under consideration entails costs in terms of survival for its bearer. Although measuring survival directly is still the most accurate way to determine whether this is indeed the case, it is often practically impossible. We propose to introduce performance measurements because one may detect potential costs at the whole‐organismal level by quantifying performance traits relevant in terms of survival and reproductive success.

We present some examples of sexual signals that can be classified as indices or handicaps by using our performance‐based approach. We also discuss some well‐cited examples which could fit the model of a handicap and propose that measurements of performance could be a feasible test of this idea.
Searching efficiency and the functional response of a pause‐travel forager
Authors: POOLE A. E. , STILLMAN R. A. , WATSON H. K. , NORRIS K. J.
Published: June 2007

The feeding rates of many predators and parasitoids exhibit type II functional responses, with a decelerating rate of increase to reach an asymptotic value as the density of their prey or hosts increases. Holling's disc equation describes such relationships and predicts that the asymptotic feeding rate at high prey densities is set by handling time, while the rate at which feeding rate increases with increased prey density is determined by searching efficiency. Searching efficiency and handling time are also parameters in other models which describe the functional response. Models which incorporate functional responses in order to make predictions of the effects of food shortage thus rely upon a clear understanding and accurate quantification of searching efficiency and handling time.

Blackbird Turdus merula exhibit a type II functional response and use pause‐travel foraging, a foraging technique in which animals search for prey while stationary and then move to capture prey. Pause‐travel foraging allows accurate direct measurement of feeding rate and both searching efficiency and handling time. We use Blackbirds as a model species to: (i) compare observed measures of both searching efficiency and handling time with those estimated by statistically fitting the disc equation to the observed functional response; and (ii) investigate alternative measures of searching efficiency derived by the established method where search area is assumed to be circular and a new method that we propose where it is not.

We find that the disc equation can adequately explain the functional response of blackbirds feeding on artificial prey. However, this depends critically upon how searching efficiency is measured. Two variations on the previous method of measuring search area (a component of searching efficiency) overestimated searching efficiency, and hence predicted feeding rates higher than those observed. Two variations of our alternative approach produced lower estimates of searching efficiency, closer to that estimated by fitting the disc equation, and hence more accurately predicted feeding rate. Our study shows the limitations of the previous method of measuring searching efficiency, and describes a new method for measuring searching efficiency more accurately.
Squamous cell carcinoma arising in mature cystic teratoma of the ovary: an immunohistochemical analysis of its tumorigenesis
Authors: Iwasa A , Oda Y , Kaneki E , Ohishi Y , Kurihara S , Yamada T , Hirakawa T , Wake N , Tsuneyoshi M
Published: June 2007

Aims:  Squamous cell carcinoma (SCC) is the most common form of malignant transformation in mature cystic teratoma (MCT) of the ovary. Some investigators have suggested the possibility of origin from columnar epithelium. The aim of this study was to analyse such tumours immunohistochemically to elucidate their histogenesis.

Methods and results:  The expression of cytokeratin (CK) 10 and CK18 was examined in 21 samples of SCC arising in MCT. The expression of CK10 and CK18 was also assessed in SCCs arising in different organs (skin, vulva, lung and uterine cervix) for the purpose of comparison. SCC in MCT expressed CK10 in 7/21 cases [33.3%, 95% confidence interval (CI) 0.12–0.53] and CK18 in 14/21 cases (66.7%, 95% CI 0.46–0.87). SCC in MCT expressed CK10 less frequently, but CK18 more frequently, as is the case in SCCs of the uterine cervix (CK10, 20%; CK18, 70%) and the lung (CK10, 5%; CK18, 90%), both of which are derived from columnar epithelium by squamous metaplasia.

Conclusions:  SCC in MCT may be derived from metaplastic squamous epithelium.
COX‐2 expression in lobular in situ neoplasia of the breast: correlation with histopathological grading system according to the Tavassoli classification
Authors: Perrone G , Zagami M , Santini D , Vincenzi B , Gullotta G , Morini S , Battista C , Guerriero G , Altomare V , Tonini G , Rabitti C
Published: June 2007

Aims:  There is considerable evidence to link cyclooxygenase (COX)‐2 to the development of cancer. The aim of this study was to assess COX‐2 expression and its subcellular localization in lobular in situ neoplasia (LIN) of the breast and to verify differences in COX‐2 expression between different grades of lesions according to the Tavassoli classification.

Methods and results:  We analysed the expression of COX‐2 protein by immunohistochemistry in tissue samples of 51 LIN lesions classified into three grades according to the Tavassoli classification. COX‐2 immunostaining was observed in 78.4% of LIN samples and showed a prevalent membranous rather than cytoplasmic pattern. COX‐2 was expressed in 16/17 (94.1%) LIN1, 22/25 (88%) LIN2 and 2/9 (22.2%) LIN3. As regards COX‐2 expression, a statistically significant difference was found between LIN1 and LIN3 (P = 0.001) and between LIN2 and LIN3 (P =0.001). No difference was found between LIN1 and LIN2. Moreover, a significant negative correlation was found between LIN grade and COX‐2 expression (P < 0.0001).

Conclusions:  COX‐2 is highly expressed in LIN, supporting a role for this protein in the early stage of breast carcinogenesis, representing the rationale for using COX‐2 selective inhibitors in the earliest stages of breast cancer.
Does a Melatonin‐Dependent Circadian Oscillator in the Pars Tuberalis Drive Prolactin Seasonal Rhythmicity?
Authors: Dardente H.
Published: June 2007

The pars tuberalis (PT) of the adenohypophysis expresses a high density of melatonin receptors and is thought to be a crucial relay for the actions of melatonin on seasonal rhythmicity of prolactin secretion by the pars distalis (PD). In common with the suprachiasmatic nucleus of the hypothalamus and most other peripheral tissues, the PT rhythmically expresses a range of ‘clock genes’. Interestingly, this expression is highly dependent upon melatonin/photoperiod, with several aspects unique to the PT. These observations led to the establishment of a conceptual framework for the encoding of seasonal timing in this tissue. This review summarises current knowledge of the morphological, functional and molecular aspects of the PT and considers its role in seasonal timing. The strengths and weaknesses of current hypotheses that link melatonin action in the PT to its seasonal effect on lactotrophs of the PD are discussed and alternative working hypotheses are suggested.
Region‐Specific Expression and Hormonal Regulation of the First Exon Variants of Rat Prolactin Receptor mRNA in Rat Brain and Anterior Pituitary Gland
Authors: Nogami H. , Hoshino R. , Ogasawara K. , Miyamoto S. , Hisano S.
Published: June 2007

Recent studies have revealed the occurrence of five first exon variants of the rat prolactin receptor mRNA, suggesting that multiple promoters direct prolactin receptor transcription in response to different regulatory factors. In the present study, regional expression of these first exon variants, as well as two prolactin receptor subtypes generated by alternative splicing, was examined in the brains and anterior pituitary glands of female rats. Expression of the long‐form was detected in the choroid plexus, hypothalamus, hippocampus, cerebral cortex and anterior pituitary gland, whereas the short form was detected only in the choroid plexus. E1‐3 mRNA, a first exon variant, was detected in the choroid plexus, hypothalamus, and anterior pituitary gland, whereas E1‐4 was detected only in the choroid plexus. Other variants were not detectable by the polymerase chain reaction protocol employed in this study. Ovariectomy increased the short form in the choroid plexus and the E1‐3 expression in the choroid plexus and pituitary gland, but changes in the long‐form and E1‐4 expression were minimal. Replacement of oestrogens and prolactin suggest that oestrogens down‐regulate E1‐3 expression in the choroid plexus and pituitary gland, and that the negative effect of oestrogen is mediated by prolactin in the pituitary gland. The present results revealed the region‐specific promoter usage in prolactin receptor mRNA transcription, as well as the involvement of oestrogens in the regulation of E1‐3 mRNA expression in the brain and pituitary gland.