bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and characterization of microsatellite markers in Prunus sibirica (Rosaceae)
Authors: Liu Hua‐Bo , Liu Jun , Wang Zhe , Ma Li‐Ying , Wang Si‐Qi , Lin Xing‐Gu , Wu Rong‐Ling , Pang Xiao‐Ming 
Published: March 2013

• Premise of the study: Microsatellite loci were developed for Prunus sibirica to investigate genetic diversity, population genetic structure, and marker‐assisted selection of late‐blooming cultivars in the breeding of P. sibirica.• Methods and Results: Using a magnetic bead enrichment strategy, 19 primer pairs were developed and characterized across 40 individuals from three P. sibirica wild populations and six individuals of P. armeniaca. The number of alleles per locus varied from three to 11 and the observed and expected heterozygosities ranged from 0.063 to 0.917 and 0.295 to 0.876, respectively, in the three P. sibirica wild populations. All primer pairs could be successfully amplified in six individuals of P. armeniaca.• Conclusions: These microsatellite primer pairs should be useful for population genetics, germplasm identification, and marker‐assisted selection in the breeding of P. sibirica and related species.
Isolation and characterization of microsatellite markers for Canavalia cathartica and C. lineata (Fabaceae)
Authors: Yamashiro Asuka , Yamashiro Tadashi , Tateishi Yoichi 
Published: March 2013

• Premise of the study: Microsatellite markers were developed for the sea‐dispersed legume Canavalia cathartica to investigate its genetic diversity and population structure. We also applied these microsatellite markers to the closely related species C. lineata.• Methods and Results: Ten primer sets were developed for C. cathartica, and all of the primers were amplified in C. lineata. The number of alleles per locus ranged from two to 13 and one to 10 for C. cathartica and C. lineata, respectively. The expected heterozygosity ranged from 0.375 to 0.870 and from 0.071 to 0.877 for C. cathartica and C. lineata, respectively.• Conclusions: The 10 microsatellite markers developed in this study can be used to analyze the population genetic structure of C. cathartica and other related taxa.
Annotation and re‐sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae)
Authors: Roschanski Anna M. , Fady Bruno , Ziegenhagen Birgit , Liepelt Sascha 
Published: March 2013

• Premise of the study: We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba.• Methods and Results: A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well‐known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA.• Conclusions: The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single‐nucleotide polymorphism detection in adaptively relevant genes in A. alba.
Isolation and characterization of microsatellite loci for a bioenergy grass, Miscanthus sacchariflorus (Poaceae)
Authors: Zhou Hai‐Fei , Li Shan‐Shan , Ge Song 
Published: March 2013

• Premise of the study: Microsatellite loci were developed for the biomass C4 grass, Miscanthus sacchariflorus, and proved to be suitable markers for population genetic studies and germplasm management of this species.• Methods and Results: Twenty‐three polymorphic microsatellite loci were identified from an enriched genomic library of M. sacchariflorus. The polymorphism was assessed in 50 individuals from two populations in China. The number of alleles per locus varied from two to 18, with a mean of 8.13. The observed and expected heterozygosities ranged from 0.2 to 1.0 and from 0.198 to 0.898, respectively.• Conclusions: These new markers will be useful for further investigation of genetic diversity and population genetic structure as well as molecular breeding of Miscanthus species.
First identification of polymorphic microsatellite markers in the Burgundy truffle, Tuber aestivum (Tuberaceae)
Authors: Molinier Virginie , Murat Claude , Morin Emmanuelle , Gollotte Armelle , Wipf Daniel , Martin Francis 
Published: March 2013

• Premise of the study: Tuber aestivum, the most common truffle in Europe, plays an important role in the commercial truffle market. For the first time, microsatellite primers were developed to investigate polymorphism within this species.• Methods and Results: Using direct shotgun pyrosequencing, 15 polymorphic microsatellites were identified out of the 7784 perfect microsatellites present in the 534620 reads obtained. Tested on 75 samples, these microsatellites were highly polymorphic. The number of alleles varied from four to 15, and the expected heterozygosity ranged from 0.266 to 0.620. A multilocus analysis allowed the identification of 63 genotypes over the 75 samples analyzed.• Conclusions: Direct shotgun pyrosequencing is a fast and relatively low‐cost technique allowing identification of microsatellites in nonmodel species. The microsatellites developed in this study will be useful in population genetic studies to infer the evolutionary history of this species.
Characterization of microsatellite loci in the lichen fungus Lobaria pulmonaria (Lobariaceae)
Authors: Werth Silke , Cornejo Carolina , Scheidegger Christoph 
Published: March 2013

• Premise of the study: Microsatellite loci were developed for the threatened haploid lichen fungus Lobaria pulmonaria to increase the resolution to identify clonal individuals, and to study its population subdivision.• Methods and Results: We developed 14 microsatellite markers from 454 DNA sequencing data of L. pulmonaria and tested for cross‐amplification with L. immixta and L. macaronesica. The number of alleles per locus ranged from two to 23. Nei's unbiased gene diversity, averaged over loci, ranged from 0.434 to 0.517 in the three studied populations.• Conclusions: The new markers will increase the genetic resolution in studies that aim at disentangling clones in L. pulmonaria and may be useful for closely related species within Lobaria sect. Lobaria.
Microsatellite primers in the lichen symbiotic alga Trebouxia decolorans (Trebouxiophyceae)
Authors: Dal Grande Francesco , Beck Andreas , Singh Garima , Schmitt Imke 
Published: March 2013

• Premise of the study: Polymorphic microsatellite markers were developed for the symbiotic green alga Trebouxia decolorans to study fine‐scale population structure and clonal diversity.• Methods and Results: Using Illumina pyrosequencing, 20 microsatellite primer sets were developed for T. decolorans. The primer sets were tested on 43 individuals sampled from four subpopulations in Germany. The primers amplified di‐, tri‐, and tetranucleotide repeats with three to 15 alleles per locus, and the unbiased haploid diversity per locus ranged from 0.636 to 0.821.• Conclusions: The identified microsatellite markers will be useful to study the genetic diversity, dispersal, and reproductive mode of this common lichen photobiont.
Tuberculosis with malaria or HIV co-infection in a large hospital in Luanda, Angola
Authors: Valadas Emília , Gomes Augusto , Sutre Ana , Brilha Sara , Wete Afonso , Hänscheid Thomas , Antunes Francisco 
Published: March 2013

Introduction: Three major public health problems, tuberculosis, malaria and HIV/AIDS, are widespread in Angola, often as co-infections in the same individual. In 2009, it was assumed that 44,151 new cases of TB occurred in Angola. Interestingly, interventions such as treatment/prevention of malaria appear to reduce mortality in HIV-infected and possibly TB co-infected patients. However, despite the seriousness of the situation, current data on TB and co-infection rates are scarce. This study aimed to characterize all TB cases seen at the Hospital Sanatório de Luanda, and to determine the co-infection rate with HIV and/or malaria. Methodology: This retrospective study collected demographic, diagnostic and clinical data from all patients admitted during 2007. Results: A total of 4,666 patients were admitted, of whom 1,906 (40.8%) were diagnosed with TB. Overall, 1,111 patients (58.3%) were male and most patients (n=1302, 68.3%) were adults (≥14 years). The rate of HIV co-infection was 37.4% (n=712). Malaria was diagnosed during admission and hospital stay in 714 patients (37.5%), with Plasmodium falciparum the predominant species. Overall mortality was 15.2% (n=290). Conclusions: Because Luanda does not have the infrastructure to perform culture-based diagnosis of TB, confirmation of TB is problematic. The HIV-co-infection rate is high, with 37.4% of patients requiring integrated approaches to address this problem. With more than 1/3 of the TB patients co-infected with malaria, even during the hospital stay, the prevention of malaria in TB patients appears to be an effective way to reduce overall mortality.
Exploiting the mycobacterial cell wall to design improved vaccines against tuberculosis
Authors: Morandi Matteo , Sali Michela , Manganelli Riccardo , Delogu Giovanni 
Published: March 2013

The only vaccine available against tuberculosis (TB), the Bacille Calmette-Guerin (BCG), does not provide effective protection against the most common forms of adult TB and in recent years efforts have been made to develop a new and improved vaccine. Among the strategies implemented, the generation of a new live attenuated mycobacterial strain is seen as one of the most promising and feasible, for scientific, ethical and practical reasons. The new understanding of the biology of the tubercle bacilli and of host-pathogen interaction processes, coupled with the possibility to engineer BCG or M. tuberculosis, opened new avenues to design “intelligent” vaccines, capable of eliciting the immune response associated with protection while avoiding the induction of the host immune response associated with immunopathology. The complex and highly immunogenic mycobacterial cell wall can shape the general and antigen specific immune response elicited following immunization, and the possibility to exploit this knowledge may lead to the development of new vaccines that could help conquer this ancient human disease.
L'archéologie virtuelle
Authors: Chanteau Julien 
Published: March 2013

L’image d’Épinal de l’archéologue couvert de poussière nettoyant méticuleusement au pinceau les bords d’une jarre millénaire constitue toujours un topos fort de notre imaginaire collectif. Dans le même temps, l’usage de la 3D pour la restitution de sites et de monuments archéologiques, récemment illustré par les modélisations en réalité virtuelle augmentée, créées par la société Dassault Systèmes, du plateau des pyramides de Gizeh et des monuments de la ville de Paris, donne à voir au grand public une archéologie hypermoderne, pouvant même tenir sa place dans les industries du rêve. Faut-il dès lors imaginer que l’archéologue du xxi e siècle travaille avec une truelle dans une main et une tablette numérique dans l’autre ?
TNF-Induced Death Signaling Triggers Alveolar Epithelial Dysfunction in Acute Lung Injury
Authors: Patel Brijesh V. , Wilson Michael R. , O’Dea Kieran P. , Takata Masao 
Published: March 2013

AbstractThe ability of the alveolar epithelium to prevent and resolve pulmonary edema is a crucial determinant of morbidity and mortality in acute lung injury (ALI). TNF has been implicated in ALI pathogenesis, but the precise mechanisms remain undetermined. We evaluated the role of TNF signaling in pulmonary edema formation in a clinically relevant mouse model of ALI induced by acid aspiration and investigated the effects of TNF p55 receptor deletion, caspase-8 inhibition, and alveolar macrophage depletion on alveolar epithelial function. We found that TNF plays a central role in the development of pulmonary edema in ALI through activation of p55-mediated death signaling, rather than through previously well-characterized p55-mediated proinflammatory signaling. Acid aspiration produced pulmonary edema with significant alveolar epithelial dysfunction, as determined by alveolar fluid clearance (AFC) and intra-alveolar levels of the receptor for advanced glycation end-products. The impairment of AFC was strongly correlated with lung caspase-8 activation, which was localized to type 1 alveolar epithelial cells by flow cytometric analysis. p55-deficient mice displayed markedly attenuated injury, with improved AFC and reduced caspase-8 activity but no differences in downstream cytokine/chemokine production and neutrophil recruitment. Caspase-8 inhibition significantly improved AFC and oxygenation, whereas depletion of alveolar macrophages attenuated epithelial dysfunction with reduced TNF production and caspase-8 activity. These results provide in vivo evidence for a novel role for TNF p55 receptor–mediated caspase-8 signaling, without substantial apoptotic cell death, in triggering alveolar epithelial dysfunction and determining the early pathophysiology of ALI. Blockade of TNF-induced death signaling may provide an effective early-phase strategy for ALI.
Conversion of Peripheral Blood NK Cells to a Decidual NK-like Phenotype by a Cocktail of Defined Factors
Authors: Cerdeira Ana Sofia , Rajakumar Augustine , Royle Caroline M. , Lo Agnes , Husain Zaheed , Thadhani Ravi I. , Sukhatme Vikas P. , Karumanchi S. Ananth , Kopcow Hernan D. 
Published: March 2013

Abstract
NK cells that populate the decidua are important regulators of normal placentation. In contrast to peripheral blood NK cells, decidual NK (dNK) cells lack cytotoxicity, secrete proangiogenic factors, and regulate trophoblast invasion. In this study we show that exposure to a combination of hypoxia, TGF-β1, and a demethylating agent results in NK cells that express killer cell Ig-like receptors, the dNK cell markers CD9 and CD49a, and a dNK pattern of chemokine receptors. These cells secrete vascular endothelial growth factor (a potent proangiogenic molecule), display reduced cytotoxicity, and promote invasion of human trophoblast cell lines. These findings have potential therapeutic applications for placental disorders associated with altered NK cell biology.
IL-1β Promotes Antimicrobial Immunity in Macrophages by Regulating TNFR Signaling and Caspase-3 Activation
Authors: Jayaraman Pushpa , Sada-Ovalle Isabel , Nishimura Tomoyasu , Anderson Ana C. , Kuchroo Vijay K. , Remold Heinz G. , Behar Samuel M. 
Published: March 2013

AbstractIn vivo control of Mycobacterium tuberculosis reflects the balance between host immunity and bacterial evasion strategies. Effector Th1 cells that mediate protective immunity by depriving the bacterium of its intracellular niche are regulated to prevent overexuberant inflammation. One key immunoregulatory molecule is Tim3. Although Tim3 is generally recognized to downregulate Th1 responses, we recently described that its interaction with Galectin-9 expressed by M. tuberculosis–infected macrophages stimulates IL-1β secretion, which is essential for survival in the mouse model. Why IL-1β is required for host resistance to M. tuberculosis infection is unknown. In this article, we show that IL-1β directly kills M. tuberculosis in murine and human macrophages and does so through the recruitment of other antimicrobial effector molecules. IL-1β directly augments TNF signaling in macrophages through the upregulation of TNF secretion and TNFR1 cell surface expression, and results in activation of caspase-3. Thus, IL-1β and downstream TNF production lead to caspase-dependent restriction of intracellular M. tuberculosis growth.
Cutting Edge: Cell Surface Linker for Activation of T Cells Is Recruited to Microclusters and Is Active in Signaling
Authors: Balagopalan Lakshmi , Barr Valarie A. , Kortum Robert L. , Park Anna K. , Samelson Lawrence E. 
Published: March 2013

Abstract
A controversy has recently emerged regarding the location of the cellular pool of the adapter linker for activation of T cells (LAT) that participates in propagation of signals downstream of the TCR. In one model phosphorylation and direct recruitment of cell surface LAT to activation-induced microclusters is critical for T cell activation, whereas in the other model vesicular, but not surface, LAT participates in these processes. By using a chimeric version of LAT that can be tracked via an extracellular domain, we provide evidence that LAT located at the cell surface can be recruited efficiently to activation-induced microclusters within seconds of TCR engagement. Importantly, we also demonstrate that this pool of LAT at the plasma membrane is rapidly phosphorylated. Our results provide support for the model in which the cell utilizes LAT from the cell surface for rapid responses to TCR stimulation.
Interests among Older People in Relation to Gender, Function and Health-Related Quality of Life
Authors: Källdalen Anette , Marcusson Jan , Wressle Ewa 
Published: March 2013

Introduction: Older people should have opportunities to be active participants in society because aspects such as lifestyle, physical and social environment and physical and mental status have influence on active ageing. The purpose of this study was to explore the interests pursued by 85-year-old people living in ordinary housing in relation to gender, cognition, depression and health-related quality of life (HRQoL). Method: A sample of 240 participants completed a postal questionnaire, including the EuroQoL HRQoL measurement. Additional instruments used during a subsequent home visit were the Canadian Occupational Performance Measure, Mini Mental State Examination and Geriatric Depression Scale. Results: Women experienced poorer health than men, lived alone to a greater extent and used more mobility devices. Compared with men, women had a larger number of interests within household management, but there were no gender differences in the leisure area. A lower number of interests in active recreation was associated with lower cognitive function, poorer HRQoL and a higher risk of depressive symptoms. Conclusion: The main finding is that engaging in active recreation interests is associated with better cognition, less depression and higher HRQoL in these 85-year-old people and is, therefore, a concern of occupational therapists.
Indigenous Psychology
Authors: Hwang Kwang‐Kuo 
Published: March 2013

Abstract

In reaction to the blind implantation of Western mainstream psychology, the emergence of the indigenization movement in psychology can be traced to the early days when Wilhelm Wundt (1832–1920) established his first laboratory at Leipzig in 1879. He conducted experiments on consciousness using scientific methods of the so‐called
physiological psychology
, and recognizing the difficulty of linking science to culture, he studied cultural issues with historical methods in his
Völkerpsychologie
.
Undrawable Architecture: Heritage Buildings and Digital Tectonic
Authors: Dritsas Stylianos , Yeo Kang Shua 
Published: March 2013

AbstractTraditionally architecture in Asia was not graphically represented or formalised, and relied on received knowledge being passed down from generation to generation. Stylianos Dritsas and Kang Shua Yeo describe the Heritage Buildings and Digital Tectonic research project they have been undertaking at Singapore University of Technology and Design (SUTD) , exploring the potential of a start‐to‐end digital design process for historical building conservation.
GECO™: Architectural Design Through Environmental Feedback
Authors: Grabner Thomas , Frick Ursula 
Published: March 2013

AbstractIn recent years there has been a disconnect between the early stages of design and the power of evolving analysis tools. Thomas Grabner and Ursula Frick, the founding directors of design research and development consultancy [uto], explain how their plug‐in GECO™ creates essential connections between modelling and analysis software, providing the opportunity to restructure conceptual design.
Firefly: Interactive Prototypes for Architectural Design
Authors: Payne Andrew O , Johnson Jason Kelly 
Published: March 2013

AbstractAndrew O Payne of LIFT architects and Jason Kelly Johnson of Future Cities Lab describe the Firefly plug‐in for Grasshopper® they have developed, which extends geometric control beyond the virtual parametric model to the real world of machines and mechanisms. Firefly also enables communication to flow in the other direction, allowing virtual building models to be informed by, and interact with, data from the real world.
Magnetomechanical Four‐State Memory
Authors: Watson Chad S. , Hollar Courtney , Anderson Kimball , Knowlton William B. , Müllner Peter 
Published: March 2013

AbstractWith current non‐volatile memory technology approaching intrinsic storage density limits, new data storage technologies are under development. Probe‐based storage systems provide alternatives to conventional mass storage technologies. Ni‐Mn‐Ga, a ferromagnetic shape memory alloy (FSMA), is proposed as a medium for multi‐bit storage using scanning probe microscopy (SPM) techniques. Local modifications of the magnetic stray field were achieved using nanoindentation. Magnetic poles collect within the indentation, which is leveraged to control the magnetic stray field for the patterning of magnetic information. Four magnetic‐based memory states are possible due to magnetic field or stress‐induced twin rearrangement along two crystal orientations, each with two possible magnetic orientations.
Xq22.3–q23 deletion including ACSL4 in a patient with intellectual disability
Authors: Gazou Anastasia , Riess Angelika , Grasshoff Ute , Schäferhoff Karin , Bonin Michael , Jauch Anna , Riess Olaf , Tzschach Andreas 
Published: March 2013

AbstractMutations or deletions of ACSL4 (FACL4, OMIM 300157) are a rare cause of non‐syndromic X‐linked intellectual disability. We report on a 10‐year‐old male patient with moderate intellectual disability, sensorineural hearing loss, facial dysmorphism, pyloric stenosis, and intestinal obstruction in whom a de novo Xq22.3–q23 deletion was detected by SNP array analysis. The deleted 1.56 Mb interval harbored ACSL4 and eight neighboring genes (GUCY2F, NXT2, KCNE1L, TMEM164, MIR3978, AMMECR1, SNORD96B, and RGAG1). In contrast to previously reported patients with chromosome aberrations in the region of the AMME complex (Alport syndrome, intellectual disability, midface hypoplasia, and elliptocytosis, OMIM 300194), this deletion did not contain the Alport syndrome gene COL4A5, suggesting that loss of one or several of the other genes in this interval is responsible for the clinical problems. In summary, the patient reported here broadens our knowledge of the phenotypic consequences of deletions of chromosome region Xq22.3–q23 and provides further proof for ACSL4 as an X‐linked intellectual disability gene. © 2013 Wiley Periodicals, Inc.
GPSM2 and Chudley–McCullough Syndrome: A Dutch Founder Variant Brought to North America
Authors: Almomani Rowida , Sun Yu , Aten Emmelien , Hilhorst‐Hofstee Yvonne , Peeters‐Scholte Cacha M.P.C.D. , van Haeringen Arie , Hendriks Yvonne M.C. , den Dunnen Johan T. , Breuning Martijn H. , Kriek Marjolein , Santen Gijs W.E. 
Published: March 2013

AbstractChudley–McCullough syndrome (CMS) is characterized by profound sensorineural hearing loss and brain anomalies. Variants in GPSM2 have recently been reported as a cause of CMS by Doherty et al. In this study we have performed exome sequencing of three CMS patients from two unrelated families from the same Dutch village. We identified one homozygous frameshift GPSM2 variants c.1473delG in all patients. We show that this variant arises from a shared, rare haplotype. Since the c.1473delG variant was found in Mennonite settlers, it likely originated in Europe. To support DNA diagnostics, we established an LOVD database for GPSM2 containing all variants thus far described. © 2013 Wiley Periodicals, Inc.