bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound Imaging of Infant Sucking Dynamics during the Establishment of Lactation
Authors: Sakalidis Vanessa S. , Williams Tracey M. , Garbin Catherine P. , Hepworth Anna R. , Hartmann Peter E. , Paech Michael J. , Geddes Donna T. 
Published: September 2012

Background: Infant sucking problems are frequently implicated in early weaning during breastfeeding, yet our understanding of early sucking dynamics is limited. Objective: This study aimed to describe infant sucking patterns during breastfeeding at secretory activation and determine whether they changed by the time of established lactation. Methods: Sucking patterns and milk intake of 15 breastfeeding infants were assessed on day 3.2 ± 0.8 and later at follow-up, 16.0 (11.3-22.8) days postpartum. Nipple diameters, tongue movement, nipple position, and suck rate during nutritive sucking (NS) and non-nutritive sucking (NNS) were measured from ultrasound scans of the intra-oral cavity during breastfeeding. Milk intake and LATCH scores were also recorded. Results: As the tongue lowered during a suck cycle, the nipple increased in size ( P < .001), milk flowed into the intra-oral space and the nipple moved closer to the hard-soft palate junction ( P < .001). During NS, nipple diameters and the mid-tongue movement were greater than during NNS ( P < .001). As the infant aged, the mid-tongue lowered further ( P = .002), suck rates became faster ( P < .001) and milk intake increased ( P = .004), however, no differences were seen for LATCH scores ( P = .34). Conclusion: Differences in tongue movement between NS and NNS suggest that there is an altered sucking action when milk flow is absent. Similar sucking patterns at day 3 and during established lactation imply that infants have a mature sucking pattern in the early postpartum period.
Promoting Sleep for Hospitalized Patients With Advanced Cancer With Relaxation Therapy
Authors: Ducloux Dominique , Guisado Huguette , Pautex Sophie 
Published: September 2012

Aims and Objectives: Sleep disorders are frequent in patients with advanced cancer receiving palliative care. The objective of this study was to demonstrate whether relaxation therapy can improve their satisfaction with sleep. Background: Few studies have investigated the effectiveness of relaxation in patients hospitalized with an advanced chronic disease. Design: Prospective randomized study with an immediate intervention group (IIG; relaxation days 3-6) and a delayed intervention group (DIG; relaxation days 6-9). Methods: The main measure was the overall satisfaction of sleep measured on a Numerical Rating Scale of Satisfaction of Sleep (NRSSS) between 0 and 10. Results: Totally 18 (IIG: 9; DIG: 9) patients were included in this study (mean age 66 ± 10.7). The NRSSS improved in both the groups (almost statistically significant) between the day of inclusion and day 2. Because of the dropout of the patients during the last days of the study, we analyzed the improvement in sleep satisfaction only between day 2 and 5. The NRSSS D5 for the immediate and delayed groups were 4.0 ± 23 and 3.8 ± 2.3, respectively. There was no significant improvement in both the groups. Conclusion: The results demonstrated the difficulty to include patients with advanced cancer in a randomized study with a DIG. We were not able to demonstrate the effectiveness of relaxation therapy on sleep satisfaction. Relevance to Clinical Practice: Techniques that can be easily used to improve sleep in patients with an advanced cancer should be developed and used already early in the disease.
Bridging the Digital Divide in HIV Care
Authors: Luque Amneris E. , Corales Roberto , Fowler Richard J. , DiMarco Jamie , van Keken Adjuah , Winters Paul , Keefer Michael C. , Fiscella Kevin 
Published: September 2012

Background: Persons living with HIV (PLWH) need practical tools to self-manage their condition. Methods: We conducted a proof-of-concept study among PLWH to assess whether patients could learn to use a personal health record (PHR) on a hand-held device (iPod Touch) to manage their condition. We began individual trainings and later adapted this to group training. We assessed usability, acceptability and also effects on self-efficacy for treatment adherence using the HIV Treatment Adherence Self-Efficacy Scale (HIV-ASES). Results: Nine PLWH participated in the individual training and 29 participated in the group sessions. The participants were largely middle aged, low-income and of racial/ethnic minorities. The sessions were well attended and participants fully engaged in tasks and shared learning. Most participants stated they intended to use the PHR and reported improved self-efficacy in treatment adherence ( P = .05) particularly on the integration of treatment adherence into one's routine ( P < .02). Conclusions: Training PLWH in use of a handheld PHR shows promise.
An Incidental Finding of an Intraosseous Metallic Object Within the Os Calcis
Authors: Chaudhary Osman Khan , Trompeter Alex , Ramesh Palanisamy 
Published: September 2012

The authors present a case of an incidental finding of a metallic foreign body located within the calcaneus of a 17-year-old girl. Although the presence of foreign material is a common occurrence in the foot, intraosseous metallic bodies are rare, especially so when they present as an incidental finding. A literature review of PubMed using keywords metallic, foreign body, and calcaneus revealed only a single case report, which did not present as an incidental finding. The presentation described here is rare and provides a platform for discussion about possible management options. Levels of Evidence: Therapeutic, Level IV: Case study
Super-resolution imaging of remodeled synaptic actin reveals different synergies between NK cell receptors and integrins
Authors: Brown Alice C. N. , Dobbie Ian M. , Alakoskela Juha-Matti , Davis Ilan , Davis Daniel M. 
Published: September 2012

Abstract
Natural killer (NK) cells secrete lytic granules to directly kill virus-infected or transformed cells and secrete cytokines to communicate with other cells. Three-dimensional super-resolved images of F-actin, lytic granules, and IFN-γ in primary human NK cells stimulated through different activating receptors reveal that both IFN-γ and lytic granules accumulated in domains where the periodicity of the cortical actin mesh at the synapse opened up to be penetrable. Ligation of some activating receptors alone (eg, CD16 or NKG2D) was sufficient to increase the periodicity of the actin mesh, but surprisingly, ligation of others (eg, NKp46 or CD2) was not sufficient to induce cortical actin remodeling unless LFA-1 was coligated. Importantly, influenza virus particles that can be recognized by NK cells similarly did not open the actin mesh but could if LFA-1 was coligated. This leads us to propose that immune cells using germline-encoded receptors to directly recognize foreign proteins can use integrin recognition to differentiate between free pathogens and pathogen-infected cells that will both be present in blood. This distinction would not be required for NK cell receptors, such as NKG2D, which recognize host cell–encoded proteins that can only be found on diseased cells and not pathogens.
Human plasmacytoid dendritic cells are equipped with antigen-presenting and tumoricidal capacities
Authors: Tel Jurjen , Smits Evelien L. , Anguille Sébastien , Joshi Rubin N. , Figdor Carl G. , de Vries I. Jolanda M. 
Published: September 2012

AbstractHuman plasmacytoid dendritic cells (pDCs) represent a highly specialized naturally occurring dendritic-cell subset and are the main producers of type I interferons (IFNs) in response to viral infections. We show that human pDCs activated by the preventive vaccine FSME specifically up-regulate CD56 on their surface, a marker that was thought to be specific for NK cells and associated with cytolytic effector functions. We observed that FSME-activated pDCs specifically lysed NK target cells and expressed cytotoxic molecules, such as tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and granzyme B. Elevated levels of these molecules coincided with the expression of CD56, indicative for skewing human pDCs toward an interferon-producing killer DC subset. Detailed phenotypical and functional analysis revealed that pDCs attained a mature phenotype, secreted proinflammatory cytokines, and had the capacity to present antigens and stimulate T cells. Here, we report on the generation of CD56+ human interferon producing killer pDCs with the capacity to present antigens. These findings aid in deciphering the role for pDCs in antitumor immunity and present a promising prospect of developing antitumor therapy using pDCs.
Natural Bagaza virus infection in game birds in southern Spain
Authors: Gamino Virginia , Gutiérrez-Guzmán Ana-Valeria , Fernández-de-Mera Isabel G , Ortíz José-Antonio , Durán-Martín Mauricio , de la Fuente José , Gortázar Christian , Höfle Ursula 
Published: September 2012

Abstract
In late summer 2010 a mosquito born flavivirus not previously reported in Europe called Bagaza virus (BAGV) caused high mortality in red-legged partridges (Alectoris rufa) and ring-necked pheasants (Phasianus colchicus). We studied clinical findings, lesions and viral antigen distribution in naturally BAGV infected game birds in order to understand the apparently higher impact on red-legged partridges. The disease induced neurologic signs in the two galliform species and, to a lesser extent, in common wood pigeons (Columba palumbus). In red-legged partridges infection by BAGV caused severe haemosiderosis in the liver and spleen that was absent in pheasants and less evident in common wood pigeons. Also, BAGV antigen was present in vascular endothelium in multiple organs in red-legged partridges, and in the spleen in common wood pigeons, while in ring-necked pheasants it was only detected in neurons and glial cells in the brain. These findings indicate tropism of BAGV for endothelial cells and a severe haemolytic process in red-legged partridges in addition to the central nervous lesions that were found in all three species.
Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish
Authors: Mazzuchelli Juliana , Kocher Thomas David , Yang Fengtang , Martins Cesar 
Published: September 2012

Abstract

Background
The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence in situ hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an Oreochromis niloticus library covering the linkage groups (LG) 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of O. niloticus and comparatively analyzed against the genome of other fish species and vertebrates.

Results
The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative in silico analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates.

Conclusions
Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.
A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica
Authors: Krishnan Neeraja M , Pattnaik Swetansu , Jain Prachi , Gaur Prakhar , Choudhary Rakshit , Vaidyanathan Srividya , Deepak Sa , Hariharan Arun K , Krishna PG Bharath , Nair Jayalakshmi , Varghese Linu , Valivarthi Naveen K , Dhas Kunal , Ramaswamy Krishna , Panda Binay 
Published: September 2012

Abstract

Background
The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach.

Results
The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs.

Conclusions
This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.
Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae
Authors: Strobel Tina , Al-Dilaimi Arwa , Blom Jochen , Gessner Arne , Kalinowski Jörn , Luzhetska Marta , Pühler Alfred , Szczepanowski Rafael , Bechthold Andreas , Rückert Christian 
Published: September 2012

Abstract

Background
The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast.

Results
To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified.

Conclusion

S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain’s potential for natural product synthesis.
Tracing genomic variations in two highly virulent Yersinia enterocolitica strains with unequal ability to compete for host colonization
Authors: Garzetti Debora , Bouabe Hicham , Heesemann Juergen , Rakin Alexander 
Published: September 2012

Abstract

Background

Yersinia enterocolitica is a gastrointestinal foodborne pathogen found worldwide and which especially affects infants and young children. While different bioserotypes have been associated with varying pathogenicity, research on Y. enterocolitica is mainly conducted on the highly virulent mouse-lethal strains of biotype 1B and serotype O:8. We demonstrate here that two Y. enterocolitica bioserotype 1B/O:8 strains, 8081 and WA-314, display different virulence and fitness properties in a mouse model. In vivo co-infection experiments revealed that strain WA-314 overcomes strain 8081 in the colonization of spleen and liver. To trace the reasons of this incongruity, we present here the first high-quality sequence of the whole genome of strain WA-314 and compare it to the published genome of strain 8081.

Results
Regions previously accepted as unique to strain 8081, like the YAPI and YGI-3 genomic islands, are absent from strain WA-314, confirming their strain-specificity. On the other hand, some fitness- and bacterial competition-associated features, such as a putative colicin cluster and a xenobiotic-acyltransferase-encoding gene, are unique to strain WA-314. Additional acquisitions of strain WA-314 are seven prophage-like regions. One of these prophages, the 28-kb P4-like prophage YWA-4, encodes a PilV-like protein that may be used for adhesion to and invasion of the intestinal cells. Furthermore, a putative autotransporter and two type 1 fimbrial proteins of strain WA-314 show a sequence similarity <50% with the orthologous proteins in strain 8081. The dissimilar sequences of these proteins indicate possible different functions or interaction modes, reflecting the specific adhesion properties of Y. enterocolitica strains 8081 and WA-314 and thus the different efficiency of host colonization. Further important differences were found in two pYV plasmid-encoded virulence factors, YopM and YscP. The impact of these differences on virulence is discussed.

Conclusions
Our study emphasizes that the virulence of pathogens can be increased, by acquiring new genes and/or improving the function of essential virulence proteins, resulting in permanently hyper-virulent strains. This work also highlights the importance of addressing genetic and phenotypic variations among closely related bacterial strains, even those belonging to the same bioserotype.
Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii
Authors: Qian Chao-Dong , Liu Tian-Zhe , Zhou Shuang-Lin , Ding Rui , Zhao Wen-Peng , Li Ou , Wu Xue-Chang 
Published: September 2012

Abstract

Background
Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway.

Results
A potential pelgipeptin synthetase gene cluster (plp) was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs), with one, seven, and one module(s), respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1) provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis.

Conclusions
In this study, a gene cluster (plp) responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.
Tyrosine-containing peptides are precursors of tyramine produced by Lactobacillus plantarum strain IR BL0076 isolated from wine
Authors: Bonnin-Jusserand Maryse , Grandvalet Cosette , Rieu Aurélie , Weidmann Stéphanie , Alexandre Hervé 
Published: September 2012

Abstract

Background
Biogenic amines are molecules with allergenic properties. They are found in fermented products and are synthesized by lactic acid bacteria through the decarboxylation of amino acids present in the food matrix. The concentration of biogenic amines in fermented foodstuffs is influenced by many environmental factors, and in particular, biogenic amine accumulation depends on the quantity of available precursors. Enological practices which lead to an enrichment in nitrogen compounds therefore favor biogenic amine production in wine. Free amino acids are the only known precursors for the synthesis of biogenic amines, and no direct link has previously been demonstrated between the use of peptides by lactic acid bacteria and biogenic amine synthesis.

Results
Here we demonstrate for the first time that a Lactobacillus plantarum strain isolated from a red wine can produce the biogenic amine tyramine from peptides containing tyrosine. In our conditions, most of the tyramine was produced during the late exponential growth phase, coinciding with the expression of the tyrDC and tyrP genes. The DNA sequences of tyrDC and tyrP in this strain share 98% identity with those in Lactobacillus brevis consistent with horizontal gene transfer from L. brevis to L. plantarum.

Conclusion
Peptides amino acids are precursors of biogenic amines for Lactobacillus plantarum strain IR BL0076.
Increasing extracellular matrix collagen level and MMP activity induces cyst development in polycystic kidney disease
Authors: Liu Bin , Li Chenghai , Liu Zijuan , Dai Zonghan , Tao Yunxia 
Published: September 2012

Abstract

Background
Polycystic Kidney Disease (PKD) kidneys exhibit increased extracellular matrix (ECM) collagen expression and metalloproteinases (MMPs) activity. We investigated the role of these increases on cystic disease progression in PKD kidneys.

Methods
We examined the role of type I collagen (collagen I) and membrane bound type 1 MMP (MT1-MMP) on cyst development using both in vitro 3 dimensional (3D) collagen gel culture and in vivo PCK rat model of PKD.

Results
We found that collagen concentration is critical in controlling the morphogenesis of MDCK cells cultured in 3D gels. MDCK cells did not form 3D structures at collagen I concentrations lower than 1 mg/ml but began forming tubules when the concentration reaches 1 mg/ml. Significantly, these cells began to form cyst when collagen I concentration reached to 1.2 mg/ml, and the ratios of cyst to tubule structures increased as the collagen I concentration increased. These cells exclusively formed cyst structures at a collagen I concentration of 1.8 mg/ml or higher. Overexpression of MT1-MMP in MDCK cells significantly induced cyst growth in 3D collagen gel culture. Conversely, inhibition of MMPs activity with doxycycline, a FDA approved pan-MMPs inhibitor, dramatically slowed cyst growth. More importantly, the treatment of PCK rats with doxycycline significantly decreased renal tubule cell proliferation and markedly inhibited the cystic disease progression.

Conclusions
Our data suggest that increased collagen expression and MMP activity in PKD kidneys may induce cyst formation and expansion. Our findings also suggest that MMPs may serve as a therapeutic target for the treatment of human PKD.