bluuebunny/crossref_metadata_2025_split huggingface dataset:
Division of labour within cooperatively breeding groups
Authors: Arnold Kathryn E. , Owens Ian P.F. , Goldizen Anne W. 
Published: November 2005

AbstractWithin cooperative societies, group members share in caring for offspring. Although division of labour among group members has been relatively well studied in insects, less is known about vertebrates. Most studies of avian helping focus solely on the extent to which helpers provision the offspring, however, helpers can participate in everything from nest building to predator defence. Bad provisioners may, for example, not be as 'uncooperative' as they appear, if they are good defenders. Thus, the distribution of helping tasks between group members should have important implications for our interpretation of group dynamics. Here, we compare two distinct forms of helping behaviour in the cooperatively breeding noisy miner (Manorina melanocephala): chick provisioning and mobbing nest predators. We show that the way in which individual helpers invest in these two helping behaviours varies enormously across individuals and among social groups. Good provisioners often contributed relatively little to mobbing and vice versa. Indeed, (18%) of helpers only mobbed, 22% just provisioned, whereas 60% of helpers performed both forms of helping. Across nests, provisioning was significantly negatively correlated with mobbing effort. We suggest that small differences in the costs or benefits of different aspects of helping (due to differences in age, relatedness or social status) have a big impact on the division of labour within a group. Consequently, social groups can be made up from individuals who often specialise in one helping behaviour, and/or helpers who perform a number of behaviours to differing degrees. Division of labour within social groups will, therefore, have important consequences for the maintenance of cooperatively breeding in vertebrates.
The Articulation of Religious Identities and their Boundaries in Ethiopia: Labelling Difference and Processes of Contextualization in Islam
Authors: Desplat Patrick 
Published: November 2005

AbstractProcesses of contextualization in Islam are constantly raising questions about self-perception and the 'other', thus challenging the concept of an 'authentic' identity and its boundaries. Innovations and their appropriation or rejection currently play a significant role in Harar, an urban community in Eastern Ethiopia where local saints constitute a key element of everyday religious life. Islamic reform movements have been able to enter Ethiopia since the downfall of the socialist regime in 1991 and have been provoking disputes concerning the 'true' Islam, focusing on saints and related 'un-Islamic' practices. The majority of the Harar community has rejected this essentializing tendency, partly because of the influence of a Harari scholar who presides over the Lebanese organization Hasbashiyya. However, the contemporary role of religious networks and the quest for authenticity must be embedded in both the historical and contemporary socio-political context.
Translating the Qur'ān in Sub-Saharan Africa: Dynamics and Disputes
Authors: Loimeier Roman 
Published: November 2005

AbstractIn the last decades, African Muslim societies have experienced multiple processes of modernization, as, for instance, in the sphere of education. As a consequence, the number of African Muslims literate in African languages has grown tremendously and so has the number of texts, including religious texts, published in these languages. At the same time, the Qur'ān has been translated into many African languages, and these translations of the Qur'ān have triggered disputes among religious scholars on the translatability of the Qur'ān as well as the interpretative orientation of these translations. The disputes over the translation and interpretation of the Qur'ān into African languages might contribute to the emergence, in sub-Saharan Africa, of a tradition of scholarly debates that would stress contextualized interpretations of the text.
Roaming About For God's Sake: The Upsurge of the Tablīgh Jamā'at in the Gambia
Authors: Janson Marloes 
Published: November 2005

AbstractThe proliferation of the Tablīgh Jamā'at, an Islamic missionary movement that strictly observes the fundamentals of the faith, is a manifestation of the recent Islamic resurgence in West Africa. The movement originated in South Asia, but has expanded to Africa. Despite the Jamā'at's great influence on the lives of many West African Muslims, sub-Saharan Africa is a region that has been ignored almost completely in studies of the movement. This article focuses on The Gambia, which appears to be a booming centre of Tablīgh activities in West Africa. On the basis of the conversion stories of a male and a female Tablīgh activist, the central themes in the Gambian branch of the Tablīgh Jamā'at will be explored. These themes result from local factors such as the socio-economic crisis and gender relations. Nevertheless, they also bear similarities with recurrent subjects in other 'fundamentalist' movements throughout the world.
Two Published Hausa Translations of the Qur'ān and their Doctrinal Background
Authors: Brigaglia Andrea 
Published: November 2005

AbstractThis article presents an analysis of two written Hausa translations of the Qur'ān. Though emphasizing that these endeavours were strictly linked to their authors' previous careers as oral exegetes, the article argues also that a certain shift may take place in the significance of tafsīr through the importance assumed by written translation. These translations were published when a broad dogmatic conflict was taking place in Nigeria, and they feature a strong concern to de-legitimize or defend certain contended issues. The recurring object of debate in the two translations is usually Sufism, but, on a closer look, other related issues emerge as being at stake: the soundness of the local exegetical tradition, and the role of Aš'arism as a set of theological doctrines providing the conventional framework for traditional exegetes to speak about God and His attributes. Issues of language and style are also briefly explored.
Monitoring Selective Logging in Tropical Evergreen Forests Using Landsat: Multitemporal Regional Analyses in Mato Grosso, Brazil
Authors: Matricardi Eraldo A. T. , Skole David L. , Cochrane Mark A. , Qi Jiaguo , Chomentowski Walter 
Published: November 2005

Abstract
Selective logging degrades tropical forests. Logging operations vary in timing, location, and intensity. Evidence of this land use is rapidly obscured by forest regeneration and ongoing deforestation. A detailed study of selective logging operations was conducted near Sinop, State of Mato Grosso, Brazil, one of the key Amazonian logging centers. An 11-yr series of annual Lansdat images (1992–2002) was used to detect and track logged forests across the landscape. A semiautomated method was applied and compared to both visual interpretation and field data. Although visual detection provided precise delineation of some logged areas, it missed many areas. The semiautomated technique provided the best estimates of logging extent that are largely independent of potential user bias. Multitemporal analyses allowed the authors to analyze the annual variations in logging and deforestation, as well as the interaction between them. It is shown that, because of both rapid regrowth and deforestation, evidence of logging activities often disappeared within 1–3 yr. During the 1992–2002 interval, a total of 11 449 km2 of forest was selectively logged. Around 17% of these logged forests had been deforested by 2002. An intra-annual analysis was also conducted using four images spread over a single year. Nearly 3% of logged forests were rapidly deforested during the year in which logging occurred, indicating that even annual monitoring will underestimate logging extent. Great care will need to be taken when inferring logging rates from observations greater than a year apart because of the partial detection of previous years of logging activity.
Tolerance induction by lentiviral gene therapy with a nonmyeloablative regimen
Authors: Mitsuhashi Noboru , Fischer-Lougheed Jacqueline , Shulkin Irina , Kleihauer Annette , Kohn Donald B. , Weinberg Kenneth I. , Starnes Vaughn A. , Kearns-Jonker Mary 
Published: November 2005

AbstractAntibodies (Abs) directed at the Galα1,3Galβ1,4GlcNAc-R (αGal) carbohydrate epitope initiate xenograft rejection. Previously, we have shown that bone marrow transplantation (BMT) with lentivirus-mediated gene transfer of porcine α1,3 galactosyltransferase (GalT) is able to induce tolerance to αGal-expressing heart grafts following a lethal dose of irradiation. Here we show the first demonstration of permanent survival of αGal+ hearts following transplantation with autologous, lentivirus-transduced BM using a nonmyeloablative regimen. Autologous BM from GalT knockout (GalT–/–) mice was transduced with a lentiviral vector expressing porcine GalT and transplanted into sublethally irradiated (3 Gy) GalT–/– mice. Chimerism in the peripheral blood cells (PBCs) remained low but was higher in the BM, especially within the stromal cell population. Mice reconstituted with GalT did not produce anti-αGal Abs over time. We immunized these mice with αGal-expressing cells and assessed humoral immune responses. Anti-αGal xenoantibodies were not produced in mice reconstituted with GalT, but normal Ab responses to other xenoantigens were detected. Mice reconstituted with GalT accepted αGal+ heart grafts over 100 days. Transduction with lentiviral vectors results in chimerism at levels sufficient to induce long-term tolerance under nonmyeloablative conditions.
Lactate dehydrogenase as a biomarker of hemolysis-associated nitric oxide resistance, priapism, leg ulceration, pulmonary hypertension, and death in patients with sickle cell disease
Authors: Kato Gregory J. , McGowan Vicki , Machado Roberto F. , Little Jane A. , Taylor James , Morris Claudia R. , Nichols James S. , Wang Xunde , Poljakovic Mirjana , Morris Sidney M. , Gladwin Mark T. 
Published: November 2005

AbstractPulmonary hypertension is prevalent in adult patients with sickle cell disease and is strongly associated with early mortality and markers of hemolysis, in particular, serum lactate dehydrogenase (LDH). Intravascular hemolysis leads to impaired bioavailability of nitric oxide (NO), mediated by NO scavenging by plasma oxyhemoglobin and by arginine degradation by plasma arginase. We hypothesized that serum LDH may represent a convenient biomarker of intravascular hemolysis and NO bioavailability, characterizing a clinical subphenotype of hemolysis-associated vasculopathy. In a cohort of 213 patients with sickle cell disease, we found statistically significant associations of steady-state LDH with low levels of hemoglobin and haptoglobin and high levels of reticulocytes, bilirubin, plasma hemoglobin, aspartate aminotransferase, arginase, and soluble adhesion molecules. LDH isoenzyme fractionation confirmed predominance of LD1 and LD2, the principal isoforms within erythrocytes. In a subgroup, LDH levels closely correlated with plasma cell-free hemoglobin, accelerated NO consumption by plasma, and impaired vasodilatory responses to an NO donor. Remarkably, this simple biomarker was associated with a clinical subphenotype of pulmonary hypertension, leg ulceration, priapism, and risk of death in patients with sickle cell disease. We propose that LDH elevation identifies patients with a syndrome of hemolysis-associated NO resistance, endothelial dysfunction, and end-organ vasculopathy.
The hematopoietic stem compartment consists of a limited number of discrete stem cell subsets
Authors: Sieburg Hans B. , Cho Rebecca H. , Dykstra Brad , Uchida Naoyuki , Eaves Connie J. , Muller-Sieburg Christa E. 
Published: November 2005

AbstractHematopoietic stem cells (HSCs) display extensive heterogeneity in their behavior even when isolated as phenotypically homogeneous populations. It is not clear whether this heterogeneity reflects inherently diverse subsets of HSCs or a homogeneous population of HSCs diversified by their response to different external stimuli. To address this, we analyzed 97 individual HSCs in long-term transplantation assays. HSC clones were obtained from unseparated bone marrow (BM) through limiting dilution approaches. Following transplantation into individual hosts, donor-type cells in blood were measured bimonthly and the resulting repopulation kinetics were grouped according to overall shape. Only 16 types of repopulation kinetics were found among the HSC clones even though combinatorially 54 groups were possible. All HSC clones, regardless of their origin, could be assigned to this subset of groups, and the probability of finding new patterns is negligible. Thus, the full repertoire of repopulating HSCs was covered. These data indicate that the HSC compartment consists of a limited number of distinct HSC subsets, each with predictable behavior. Enrichment of HSCs (Lin–Rho–SP) changes the representation of HSC types by selecting for distinct subsets of HSCs. These data from the steady-state HSC repertoire could provide a basis for the diagnosis of perturbed patterns of HSCs potentially caused by disease or aging.
Role of melanotransferrin in iron metabolism: studies using targeted gene disruption in vivo
Authors: Sekyere Eric O. , Dunn Louise L. , Rahmanto Yohan Suryo , Richardson Des R. 
Published: November 2005

AbstractMelanotransferrin (MTf) or tumor antigen p97 is a transferrin homolog that binds one iron (Fe) atom and has been suggested to play roles in a variety of processes, including Fe metabolism, eosinophil differentiation, and plasminogen activation. Considering the vital role of Fe in many metabolic pathways, such as DNA and heme synthesis, it is important to understand the function of MTf. To define this, a MTf knockout (MTf–/–) mouse was generated through targeted disruption of the MTf gene. The MTf–/– mice were viable and fertile and developed normally, with no morphologic or histologic abnormalities. Assessment of Fe indices, tissue Fe levels, hematology, and serum chemistry parameters demonstrated no differences between MTf–/– and wild-type (MTf+/+) mice, suggesting MTf was not essential for Fe metabolism.
Coiled-coil protein composition of 22 proteomes – differences and common themes in subcellular infrastructure and traffic control
Authors: Rose Annkatrin , Schraegle Shannon J , Stahlberg Eric A , Meier Iris 
Published: November 2005

Abstract

Background
Long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems and tissues, motors, levers, rotating arms, and possibly springs. Mutations in long coiled-coil proteins have been implemented in a growing number of human diseases. Using the coiled-coil prediction program MultiCoil, we have previously identified all long coiled-coil proteins from the model plant Arabidopsis thaliana and have established a searchable Arabidopsis coiled-coil protein database.

Results
Here, we have identified all proteins with long coiled-coil domains from 21 additional fully sequenced genomes. Because regions predicted to form coiled-coils interfere with sequence homology determination, we have developed a sequence comparison and clustering strategy based on masking predicted coiled-coil domains. Comparing and grouping all long coiled-coil proteins from 22 genomes, the kingdom-specificity of coiled-coil protein families was determined. At the same time, a number of proteins with unknown function could be grouped with already characterized proteins from other organisms.

Conclusion
MultiCoil predicts proteins with extended coiled-coil domains (more than 250 amino acids) to be largely absent from bacterial genomes, but present in archaea and eukaryotes. The structural maintenance of chromosomes proteins and their relatives are the only long coiled-coil protein family clearly conserved throughout all kingdoms, indicating their ancient nature. Motor proteins, membrane tethering and vesicle transport proteins are the dominant eukaryote-specific long coiled-coil proteins, suggesting that coiled-coil proteins have gained functions in the increasingly complex processes of subcellular infrastructure maintenance and trafficking control of the eukaryotic cell.
Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones
Authors: Chen Kefei , Knorr Christoph , Bornemann-Kolatzki Kirsten , Ren Jun , Huang Lusheng , Rohrer Gary A , Brenig Bertram 
Published: November 2005

Abstract

Background
In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP) as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD) than does a di-allelic marker system [1]. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced.

Results
Seventeen porcine microsatellite markers were isolated from eleven PAC clones by
t
argeted
o
ligonucleotide-
m
ediated
m
icrosatellite
i
dentification (TOMMI), an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT) microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC), average heterozygosity (HT), and effective allele number (NE) for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds). Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles) in this heterogeneous sampling. Most of the publicly available (porcine) microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions.

Conclusion
The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.
Leveraging human genomic information to identify nonhuman primate sequences for expression array development
Authors: Spindel Eliot R , Pauley Mark A , Jia Yibing , Gravett Courtney , Thompson Shaun L , Boyle Nicholas F , Ojeda Sergio R , Norgren Robert B 
Published: November 2005

Abstract

Background
Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene expression profiling. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays.

Results
We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We found the mean length of complete last exons to be approximately 1,400 bp, significantly longer than previous estimates. We designed primers to amplify genomic DNA, which included at least 300 bp of the terminal exon. We cloned and sequenced the PCR products representing over 5,500 Macaca mulatta (rhesus monkey) orthologs of human genes. This sequence information has been used to select probes for rhesus gene expression profiling. We have also tested 10 sets of primers with genomic DNA from Macaca fascicularis (Cynomolgus monkey), Papio hamadryas (Baboon), and Chlorocebus aethiops (African green monkey, vervet). The results indicate that the primers developed for this study will be useful for acquiring sequence from the 3' end of genes for other nonhuman primate species.

Conclusion
This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3' end of NHP orthologs and that this sequence can then be used to generate NHP oligonucleotide microarrays. Affymetrix and Agilent used sequences obtained with this approach in the design of their rhesus macaque oligonucleotide microarrays.
Construction and characterization of a genomic BAC library for the Mus m. musculus mouse subspecies (PWD/Ph inbred strain)
Authors: Jansa Petr , Divina Petr , Forejt Jiří 
Published: November 2005

Abstract

Background
The genome of classical laboratory strains of mice is an artificial mosaic of genomes originated from several mouse subspecies with predominant representation (>90%) of the Mus m. domesticus component. Mice of another subspecies, East European/Asian Mus m. musculus, can interbreed with the classical laboratory strains to generate hybrids with unprecedented phenotypic and genotypic variations. To study these variations in depth we prepared the first genomic large insert BAC library from an inbred strain derived purely from the Mus m. musculus-subspecies. The library will be used to seek and characterize genomic sequences controlling specific monogenic and polygenic complex traits, including modifiers of dominant and recessive mutations.

Results
A representative mouse genomic BAC library was derived from a female mouse of the PWD/Ph inbred strain of Mus m. musculus subspecies. The library consists of 144 768 primary clones from which 97% contain an insert of 120 kb average size. The library represents an equivalent of 6.7 × mouse haploid genome, as estimated from the total number of clones carrying genomic DNA inserts and from the average insert size. The clones were arrayed in duplicates onto eight high-density membranes that were screened with seven single-copy gene probes. The individual probes identified four to eleven positive clones, corresponding to 6.9-fold coverage of the mouse genome. Eighty-seven BAC-ends of PWD/Ph clones were sequenced, edited, and aligned with mouse C57BL/6J (B6) genome. Seventy-three BAC-ends displayed unique hits on B6 genome and their alignment revealed 0.92 single nucleotide polymorphisms (SNPs) per 100 bp. Insertions and deletions represented 0.3% of the BAC end sequences.

Conclusion
Analysis of the novel genomic library for the PWD/Ph inbred strain demonstrated coverage of almost seven mouse genome equivalents and a capability to recover clones for specific regions of PWD/Ph genome. The single nucleotide polymorphism between the strains PWD/Ph and C57BL/6J was 0.92/100 bp, a value significantly higher than between classical laboratory strains. The library will serve as a resource for dissecting the phenotypic and genotypic variations between mice of the Mus m. musculus subspecies and classical laboratory mouse strains.