bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of zooplankton abundance, distribution patterns and patchiness in a large humic lake using an Optical Plankton Counter
Authors: Rahkola-Sorsa Minna , Avinsky Valentin , Can Petra , Rasmus Kai , Waissi Greta , Viljanen Markku 
Published: June 2010

Zooplankton usually behaves in complex and dynamic ways on various temporal and spatial scales and its spatial distribution is usually highly aggregated, as it possesses a large-scale spatial variability similar to that observed in the physical environment in general. We assess here the suitability of the Optical Plankton Counter for estimating zooplankton abundance, as well as the day-to-day temporal and spatial patterns in its distribution during the open water season. The influence of certain environmental variables on zooplankton abundances is also examined.
Abundances of mesozooplankton-sized particles were measured with the Optical Plankton Counter monthly at five stations in a large mesohumic lake from May to September 2005 and agreed rather well with zooplankton abundances counted using a microscope. The poorest agreement was in autumn, when the Counter overestimated the zooplankton abundance, and for some samples in July, when it underestimated the abundance. Fluorescence and chlorophyll a had a significant effect on the Counter readings. Both the intercept and the slope of chlorophyll a varied randomly between depths, because the chlorophyll a decreased much more markedly in deeper waters than did the Counter particle counts. This emphasized the stratified nature of sampling.
In addition to seasonal variations, there were also marked short-interval variations (day-to-day) in zooplankton abundances in all the sampling periods. These patterns are highly dynamic and can on some occasions change rapidly in response to fluctuations in the weather. There were no clear differences in zooplankton abundance between the sampling stations. The horizontal heterogeneity was less pronounced than the seasonal and short-interval heterogeneity, possibly because there were no trophic gradients in the basin.
While the Optical Plankton Counter provided a rapid assessment of temporal and spatial patterns of zooplankton abundances, it does have limitations. At times it either overestimated abundances due to a large contribution from non-zooplankton particles, or underestimated abundances due to coincidence.
Testing multiple gene interactions by the ordered combinatorial partitioning method in case–control studies
Authors: Hua Xing , Zhang Han , Zhang Hong , Yang Yaning , Kuk Anthony Y.C. 
Published: June 2010

AbstractMotivation: The multifactor-dimensionality reduction (MDR) method has been widely used in multi-locus interaction analysis. It reduces dimensionality by partitioning the multi-locus genotypes into a high-risk group and a low-risk group according to whether the genotype-specific risk ratio exceeds a fixed threshold or not. Alternatively, one can maximize the χ2 value exhaustively over all possible ways of partitioning the multi-locus genotypes into two groups, and we aim to show that this is computationally feasible.Methods: We advocate finding the optimal MDR (OMDR) that would have resulted from an exhaustive search over all possible ways of partitioning the multi-locus genotypes into two groups. It is shown that this optimal MDR can be obtained efficiently using an ordered combinatorial partitioning (OCP) method, which differs from the existing MDR method in the use of a data-driven rather than fixed threshold. The generalized extreme value distribution (GEVD) theory is applied to find the optimal order of gene combination and assess statistical significance of interactions.Results: The computational complexity of OCP strategy is linear in the number of multi-locus genotypes in contrast with an exponential order for the naive exhaustive search strategy. Simulation studies show that OMDR can be more powerful than MDR with substantial power gain possible when the partitioning of OMDR is different from that of MDR. The analysis results of a breast cancer dataset show that the use of GEVD accelerates the determination of interaction order and reduces the time cost for P-value calculation by more than 10-fold.Availability: C++ program is available at http://home.ustc.edu.cn/∼zhanghan/ocp/ocp.htmlContact: zhanghan@mail.ustc.edu.cnSupplementary Information: Supplementary data are available at Bioinformatics online.
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
Authors: Zhou Fengfeng , Xu Ying 
Published: June 2010

Abstract
Summary: Huge amount of metagenomic sequence data have been produced as a result of the rapidly increasing efforts worldwide in studying microbial communities as a whole. Most, if not all, sequenced metagenomes are complex mixtures of chromosomal and plasmid sequence fragments from multiple organisms, possibly from different kingdoms. Computational methods for prediction of genomic elements such as genes are significantly different for chromosomes and plasmids, hence raising the need for separation of chromosomal from plasmid sequences in a metagenome. We present a program for classification of a metagenome set into chromosomal and plasmid sequences, based on their distinguishing pentamer frequencies. On a large training set consisting of all the sequenced prokaryotic chromosomes and plasmids, the program achieves ∼92% in classification accuracy. On a large set of simulated metagenomes with sequence lengths ranging from 300 bp to 100 kbp, the program has classification accuracy from 64.45% to 88.75%. On a large independent test set, the program achieves 88.29% classification accuracy.
Availability: The program has been implemented as a standalone prediction program, cBar, which is available at http://csbl.bmb.uga.edu/∼ffzhou/cBar
Contact: xyn@bmb.uga.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Large-scale benchmark of Endeavour using MetaCore maps
Authors: Schuierer Sven , Tranchevent Léon-Charles , Dengler Uwe , Moreau Yves 
Published: June 2010

Abstract
Summary: Endeavour is a tool that detects the most promising genes within large lists of candidates with respect to a biological process of interest and by combining several genomic data sources. We have benchmarked Endeavour using 450 pathway maps and 826 disease marker sets from MetaCoreTM of GeneGo, Inc. containing a total of 9911 and 12 432 genes, respectively. We obtained an area under the receiver operating characteristic curves of 0.97 for pathway and of 0.91 for disease gene sets. These results indicate that Endeavour can be used to efficiently prioritize candidate genes for pathways and diseases.
Availability: Endeavour is available at http://www.esat.kuleuven.be/endeavour
Contact: sven.schuierer@novartis.com; leon-charles.tranchevent@esat.kuleuven.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Epidemiology of Uninvestigated Gastrointestinal Symptoms in Adolescents: A Population‐based Study Applying the Rome II Questionnaire
Authors: Sohrabi Sahand , Nouraie Mehdi , Khademi Hooman , Baghizadeh Somayyeh , Nasseri‐Moghaddam Siavosh , Malekzadeh Reza 
Published: June 2010

ABSTRACTObjectives:Gastrointestinal (GI) disorders in early life contribute to a lower quality of life and more persistent GI symptoms during the rest of life. Epidemiologic data on adolescence GI disorders are scarce. We aimed to perform a population‐based study to assess the prevalence of GI symptoms in adolescents and their relation to sex, age, and socioeconomic status.Materials and Methods:A multistage random sample of Tehran middle and high school students (ages 14–19 years) was selected. A validated Persian version of the Rome II questionnaire was used to measure the frequency of different GI disorders as well as demographic socioeconomic variables.Results:A total of 1436 participants were enrolled in the study, 736 (51.3%) of whom were men. Mean (SD) age was 16.9 (1.8) years. The frequency of at least 1 GI symptom was 32.4%. The 4 most prevalent GI symptoms were bloating (16.9%), heartburn (4.9%), incontinence (4.3%), and irritable bowel syndrome (4.1%). Bloating, irritable bowel syndrome, and proctalgia fugax were significantly more common in girls (P < 0.05). Incontinence was significantly more prevalent in lower socioeconomic status levels (P = 0.01). In logistic regression, age was a risk factor for abdominal bloating and dysphagea and a protective factor for incontinence.Conclusions:Our study indicates that GI symptoms are common among adolescents. Girls are more prone to these disorders. Special psychological and medical interventions are necessary for high‐risk groups.
Evidence that CD8 T‐cell homeostasis and function remain intact during murine pregnancy
Authors: Norton Michelle T. , Fortner Karen A. , Oppenheimer Karen H. , Bonney Elizabeth A. 
Published: June 2010

SummaryEvolving models of immune tolerance have challenged the view that the response of the maternal immune system to environmental or fetal antigens must be suppressed or deviated. CD8 T cells play a central role in the immune response to viruses and intracellular pathogens so the maintenance of both the number and function of these cells is critical to protect both the mother and fetus. We show that the numbers of maternal CD8 T cells in both the spleen and the uterine draining lymph nodes are transiently increased at mid‐gestation and this correlates with enhanced CD8 T‐cell proliferation and an increased relative expression of both pro‐survival and pro‐apoptotic molecules. In transgenic mice bearing T‐cell antigen receptors specific for the male HY or allo‐antigens, the transgenic CD8 T cells retain the ability to proliferate and function during pregnancy. Moreover, anti‐HY T‐cell receptor transgenic mice have normal numbers of male pups despite the presence of CD8 T cells at the maternal–fetal interface. These data suggest that pregnancy is a dynamic state in which CD8 T‐cell turnover is increased while the function and ending size of the CD8 T‐cell compartment are maintained.
Weed seedbank responses to 12 years of applications of composts, animal slurries or mineral fertilisers
Authors: DE CAUWER B , VAN DEN BERGE K , COUGNON M , BULCKE R , REHEUL D 
Published: June 2010

De Cauwer B, Van Den Berge K, Cougnon M, Bulcke R & Reheul D (2010). Weed seedbank responses to 12 years of applications of composts, animal slurries or mineral fertilisers. Weed Research50, 425–435.SummaryFertiliser amendments can impact weed populations in a variety of ways. This study evaluated the effects of 12‐year‐long applications of different fertilisation systems on size and composition of the weed seedbank in a conventionally managed maize monoculture field. Fertilisation systems included all factorial combinations of two dairy cattle slurry rates, three vegetable, fruit and garden waste compost rates, and three synthetic N fertiliser rates. Soil samples were taken in each subplot in May 2008 after sowing and prior to herbicide application. Residues recovered from soil samples were tested for weed seedling emergence to characterise soil seedbanks. Total weed seedbank density was affected by mineral N fertilisation, but not by compost or animal slurry application. Weed seedbank composition was related to compost amendment and mineral N fertilisation. Annual compost amendments reduced seedbank density of some persistent species (e.g., Chenopodium album and Solanum nigrum) irrespective of mineral N fertilisation. Compost is a promising tool for incorporation into integrated weed control strategies aimed at reducing weed seedbank persistence.
Cardioprotective medication use after renal transplantation
Authors: Dawson Kyle L. , Patel Samir J. , Putney David , Suki Wadi N. , Osama Gaber A. 
Published: June 2010

Dawson KL, Patel SJ, Putney D, Suki WN, Gaber AO. Cardioprotective medication use after renal transplantation.  Clin Transplant 2010: 24: E253–E256. © 2010 John Wiley & Sons A/S.Abstract:  Cardiovascular disease is the leading cause of death in renal transplant patients. This study compares the use of cardioprotective medications in adult kidney transplant recipients at a single center with recommendations, which have been validated in the general population. Cardioprotective medication use was retrospectively collected post‐renal transplant. Patients were defined as high risk if they had pre‐transplant coronary heart disease or equivalent risk. “Optimal” treatment was defined as a patient receiving aspirin, statin, angiotensin‐converting enzyme inhibitors/angiotensin receptor blocker, and a beta‐blocker according to cardiovascular risk. The percentage of high‐risk patients optimally treated at one, three, six, and 12 months was 7.7%, 11.5%, 17.6%, and 18.8%, respectively. Although the use of cardioprotective medications was evident in transplant recipients, opportunities exist to increase the use of optimal cardioprotective regimens after renal transplantation.
Caregiver burden and coping strategies for patients with schizophrenia: Comparison between Japan and Korea
Authors: Hanzawa Setsuko , Bae Jeong‐Kyu , Tanaka Hideki , Bae Yong Jun , Tanaka Goro , Inadomi Hiroyuki , Nakane Yoshibumi , Ohta Yasuyuki 
Published: June 2010

Aim:  With the current shift to community‐centered mental health services, considerable research on the family burden of caring for patients with schizophrenia has been conducted in developed countries. However, there has been no investigation of families with Japanese or Korean sociocultural backgrounds. Therefore, the present study compared the caregiver burden and coping strategies of families of patients with schizophrenia in Japan and Korea in order to elucidate similarities and differences in the sociocultural factors that affect the care experience of families in Northeast Asia.Methods:  A total of 99 Japanese (Nagasaki) and 92 Korean (Seoul, Daegu) family members of patients with schizophrenia were surveyed in regards to caregiver burden, coping strategies, and nursing awareness of the caregiver role regarding the patient with schizophrenia.Results:  Analysis revealed the following: (i) although no difference in caregiver burden and coping strategy was observed between the countries, the nursing awareness of families' caregiver role was significantly higher in Japan than in Korea; (ii) caregiver burden was significantly associated with the patient's social functioning and care needs in both countries; and (iii) caregiver burden was significantly associated with reduction of social interests, coercion, avoidance, resignation, and nursing awareness of caregiver role in both countries.Conclusion:  Although the nursing awareness of families' roles in caring for patients with schizophrenia differed between Japan and Korea, similar trends were observed for the causes of caregiver burden. These findings suggest that in order to provide effective support for reducing caregiver burden, the necessity of such support must be emphasized in both countries.
Taste reactivity deficit in anorexia nervosa
Authors: Szalay Csaba , Ábrahám Ildikó , Papp Szilárd , Takács Gábor , Lukáts Balázs , Gáti Ágnes , Karádi Zoltán 
Published: June 2010

Aim:  Anorexia nervosa is a complex psychiatric disorder posing a rapidly increasing burden on modern societies. Our purpose was to clarify perceptual‐motivational aspects of gustatory disturbances in the disease.Methods:  A taste reactivity test, with the use of all five primary qualities in two concentrations, was performed in restrictive‐type anorexic patients, and their hedonic evaluations were compared to those of age‐matched healthy control subjects.Results:  The patients gave significantly lower pleasantness scores for pleasant taste stimuli compared with controls. The differences were the greatest for the lower concentration sucrose, umami and sodium chloride. Ratings given for the aversive taste stimuli were similar in both experimental groups.Conclusion:  Our findings contribute to a better understanding of complex symptoms of anorexia nervosa, and may also help to develop more effective cognitive‐behavioral therapies.
Production of monoclonal antibodies with a controlledN‐glycosylation pattern in seeds ofArabidopsis thaliana
Authors: Loos Andreas , Van Droogenbroeck Bart , Hillmer Stefan , Grass Josephine , Kunert Renate , Cao Jingyuan , Robinson David G. , Depicker Ann , Steinkellner Herta 
Published: June 2010

SummarySeed‐specific expression is an appealing alternative technology for the production of recombinant proteins in transgenic plants. Whereas attractive yields of recombinant proteins have been achieved by this method, little attention has been paid to the intracellular deposition and the quality of such products. Here, we demonstrate a comparative study of two antiviral monoclonal antibodies (mAbs) (HA78 against Hepatitis A virus; 2G12 against HIV) expressed in seeds of Arabidopsis wild‐type (wt) plants and glycosylation mutants lacking plant specificN‐glycan residues. We demonstrate that 2G12 is produced with complexN‐glycans at great uniformity in the wt as well as in the glycosylation mutant, carrying a single dominant glycosylation species, GnGnXF and GnGn, respectively. HA78 in contrast, contains additionally to complexN‐glycans significant amounts of oligo‐mannosidic structures, which are typical for endoplasmic reticulum (ER)‐retained proteins. A detailed subcellular localization study demonstrated the deposition of both antibodies virtually exclusively in the extracellular space, illustrating their efficient secretion. In addition, although a KDEL‐tagged version of 2G12 exhibited an ER‐typicalN‐glycosylation pattern, it was surprisingly detected in protein storage vacuoles. The different antibody variants showed different levels of degradation with hardly any degradation products detectable for HA78 carrying GnGnXF glycans. Finally, we demonstrate functional integrity of the HA78 and 2G12 glycoforms using viral inhibition assays. Our data therefore demonstrate the usability of transgenic seeds for the generation of mAbs with a controlledN‐glycosylation pattern, thus expanding the possibilities for the production of optimally glycosylated proteins with enhanced biological activities for the use as human therapeutics.
HORIZONTAL MERGERS IN A DIFFERENTIATED COURNOT OLIGOPOLY
Authors: Hsu Judy , Wang X. Henry 
Published: June 2010

ABSTRACTUsing a standard differentiated goods quantity competition setting, we show three facts about horizontal two‐firm mergers that are not true for a homogeneous goods Cournot market. First, merger of two firms is profitable for the merging firms provided that goods are sufficiently distant substitutes. Second, merging of two firms can lead to more two‐firm mergers. Third, an initially non‐profitable two‐firm merger can occur in anticipation of subsequent mergers. These facts imply that mergers are more likely to occur in differentiated goods markets than in homogeneous goods markets.
OUTLOOK ON EUROPE: THE SPATIAL VARIABLE IN THE RECENT CONFIGURATION OF THE VALUE CHAIN IN THE EUROPEAN AUTOMOTIVE INDUSTRY
Authors: BILBAO‐UBILLOS JAVIER 
Published: June 2010

ABSTRACTThis paper takes the framework of the ‘economics of proximity’ to distinguish between territory‐based and agent‐based proximity approaches in dealing with the dynamic interaction between changes in the organisation of production on the one hand and the role of territory on the other. The paper sets out to determine which of these approaches works best to explain the main changes carried out in the most recent configuration of value chain in the European automotive industry.
Playing with the ‘Erbe’: Songs of the 1848 Revolution in the GDR
Authors: Robb David 
Published: June 2010

ABSTRACTAfter the twelve‐year rupture caused by the Nazis, in the Soviet zone after 1945 attempts were made to reconnect with the traditions of workers’ songs and critical folk songs that were viewed as the cultural heritage of the communist movement. One of these ‘repertoires’ of song was that of the 1848 Revolution. In the 1950s GDR researchers such as the Germanist Bruno Kaiser, the musicologist Inge Lammel and in particular the folklorist Wolfgang Steinitz made substantial contributions to the collecting and publishing of the 1848 songs. Their work provided an important reference point for the singers of the German folk song revival in the GDR from the late 1970s onwards. As the cases of groups such as Folkländer and Wacholder showed, theirs was a particularly creative appropriation of the revolutionary ‘Erbe’ that involved performing protest songs of the past as if they were criticising the present.Nach dem zwölfjährigen Kulturbruch in Deutschland während des ‘Dritten Reichs’ versuchte man nach 1945 in der sowjetischen Zone, an demokratische Traditionen wie die Lieder der Arbeiterbewegung oder sozialkritische Volkslieder anzuknüpfen. Lieder der 1848er Revolution gehörten auch zu dieser Tradition. In den 1950er Jahren trugen Forscher wie der Germanist Bruno Kaiser, die Musikwissenschaftlerin Inge Lammel und vor allem der Volkskundler Wolfgang Steinitz wesentlich dazu bei, diese 1848er Lieder zu sammeln und zu veröffentlichen. Ihre Arbeiten wurden zwei Jahrzehnte später zu einem wichtigen Anknüpfungspunkt für Sänger und Gruppen des Folksong‐Revivals in der DDR. Dies war – wie beispielhaft die Gruppen Folkländer und Wacholder zeigen – eine recht kreative und spezielle Aneignung des revolutionären Erbes: der Vortrag von Liedern der Vergangenheit wurde hier zu einem Medium, in dem man sich kritisch über die Gegenwart äußern konnte.
‘Ich wollte eine Distel im sozialistischen Rosengarten sein’– Autobiographische Texte von zwei DDR‐Jugendgenerationen
Authors: Warchold Katja 
Published: June 2010

ABSTRACTSince the turn of the century many autobiographical texts have been published by authors born during the sixties and seventies in the GDR. The texts discussed here exemplify in many respects a generation‐specific view of childhood and youth in the GDR and of the ‘Wende’ in 1989. The national education system is just one part of the shared experiences in the socialisation of these writers. They share a good deal more in the way of everyday‐life experiences both culturally and as consumers, but such experiences differ depending on the year in which the authors were born. As a result the texts can be categorised into two ‘youth generation units’, as they have been called. Analysing these generations in terms of sociological constructs we see that for those born during the period between the end of the sixties and the beginning of the seventies there was a break with the political system of the GDR. In contrast, authors born from the middle of the seventies on experienced a feeling of security in the world of real existing socialism, which sometimes led to an idealisation of the former GDR after the ‘Wende’. Therefore, these texts also illustrate the authors’ feelings of being ‘at home’ or ‘homeless’ in Germany following the ‘Wende’.Seit der Jahrhundertwende sind zahlreiche autobiographische Texte von Autoren, die in den 60er und 70er Jahren in der DDR geboren wurden, erschienen. Die exemplarisch ausgewählten Texte zeigen in vieler Hinsicht eine generationsspezifische Sicht auf Kindheit und Jugend in der DDR sowie die Wende 1989. Gemeinsame Sozialisationserfahrungen der Autoren sind nur teilweise auf das staatlich organisierte Erziehungs‐ und Bildungssystem zurückzuführen. Viel mehr teilen die Autoren konsumkulturelle Alltagserfahrungen, die abhängig vom jeweiligen Jahrgang differieren. Deswegen lassen sich die Texte zwei Jugendgenerationseinheiten zuordnen. Die soziologischen Generationskonstrukte zeigen für die Ende der 60er bis Anfang der 70er Jahre Geborenen einen Bruch mit dem politischen System der DDR auf. Die ab Mitte der 70er Jahre Geborenen hingegen erlebten die Welt des real existierenden Sozialismus als eine Geborgenheit bietende Ordnung, was nach der Wende zu einer Idyllisierung der Erinnerungsheimat DDR führen konnte. Somit veranschaulichen die Texte auch das Angekommensein bzw. die Unbehaustheit dieser Autoren im Nachwendedeutschland.