bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractSummary: 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.govSupplementary 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

Abstract
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

Abstract
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

Abstract
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
Seminal influences: Drosophila Acps and the molecular interplay between males and females during reproduction
Authors: Ravi Ram K. , Wolfner Mariana F. 
Published: June 2007

AbstractSuccessful 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.
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

AbstractDuring 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

AbstractDrought 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

AbstractThe 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

SummaryStrong 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

SummaryCentral 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

Summary

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 habitat fragmentation reduce fitness and adaptability? A case study of the common frog (Rana temporaria)
Authors: JOHANSSON MARKUS , PRIMMER CRAIG R. , MERILÄ JUHA 
Published: June 2007

AbstractStudies examining the effects of anthropogenic habitat fragmentation on both neutral and adaptive genetic variability are still scarce. We compared tadpole fitness‐related traits (viz. survival probability and body size) among populations of the common frog (Rana temporaria) from fragmented (F) and continuous (C) habitats that differed significantly in population sizes (C > F) and genetic diversity (C > F) in neutral genetic markers. Using data from common garden experiments, we found a significant positive relationship between the mean values of the fitness related traits and the amount of microsatellite variation in a given population. While genetic differentiation in neutral marker loci (FST) tended to be more pronounced in the fragmented than in the continuous habitat, genetic differentiation in quantitative traits (QST) exceeded that in neutral marker traits in the continuous habitat (i.e.QST > FST), but not in the fragmented habitat (i.e.QST ≈ FST). These results suggest that the impact of random genetic drift relative to natural selection was higher in the fragmented landscape where populations were small, and had lower genetic diversity and fitness as compared to populations in the more continuous landscape. The findings highlight the potential importance of habitat fragmentation in impairing future adaptive potential of natural populations.
Effects of treatment latency on response to maintenance treatment in manic‐depressive disorders
Authors: Baldessarini Ross J , Tondo Leonardo , Baethge Christopher J , Lepri Beatrice , Bratti Irene M 
Published: June 2007

Objectives: To further test the hypothesis that past illness episodes and delay of long‐term treatment do not limit maintenance treatment response among patients with manic‐depressive illnesses (MDI).Methods:  In a sample of 764 MDI patients in Cagliari and Berlin, 77% of whom had bipolar disorder (BPD), we: (i) correlated treatment latency or pretreatment episode counts versus hospitalized morbidity during treatment; (ii) correlated treatment duration versus pretreatment morbidity; (iii) correlated treatment latency versus pretreatment or treated morbidity; (iv) modeled factors associated with longer treatment latency; (v) compared treatment latencies at extremes of treatment outcomes, and (vi) compared pretreatment morbidity within 2 years of the longest versus shortest treatment latency quartiles.Results:  Pretreatment morbidity was strongly correlated with shorter treatment latency, but morbidity during treatment was unrelated to treatment latency, pretreatment episode counts, sex, diagnosis, treatment type or treatment duration. In multivariate modeling, treatment latency was longer among patients who had experienced an early onset of illness, mainly in depressive disorders (BPD II and major depression) and among women, but was unrelated to morbidity during treatment. Patients with no illness recurrences during treatment and those who were ill at least 50% of the time had similar treatment latencies. Pretreatment morbidity occurring just prior to the initiation of long‐term treatment was very similar at the highest and lowest treatment latencies.Conclusions:  These findings support the therapeutically favorable conclusion that prior episode counts and treatment delay have little association with morbidity during prophylaxis with mood‐stabilizing agents. Comparisons of morbidity during versus before treatment in episodic disorders are misleading because overall morbidity becomes diluted with longer time‐at‐risk, whereas therapeutic intervention is typically determined by immediately preceding illness.