bluuebunny/crossref_metadata_2025 huggingface dataset:
qDTY12.1: a locus with a consistent effect on grain yield under drought in rice
Authors: Mishra Krishna Kumar , Vikram Prashant , Yadaw Ram Baran , Swamy BP Mallikarjuna , Dixit Shalabh , Cruz Ma Teresa Sta , Maturan Paul , Marker Shailesh , Kumar Arvind
Published: February 2013

Background

Selection for grain yield under drought is an efficient criterion for improving the drought tolerance of rice. Recently, some drought-tolerant rice varieties have been developed using this selection criterion and successfully released for cultivation in drought-prone target environments. The process can be made more efficient and rapid through marker-assisted breeding, a well-known fast-track approach in crop improvement. QTLs have been identified for grain yield under drought with large effects against drought-susceptible varieties. Most of the identified QTLs show large QTL × environment or QTL × genetic background interactions. The development of mapping populations in the background of popular high-yielding varieties, screening across environments, including the target environments, and the identification of QTLs with a consistent effect across environments can be a suitable alternative marker-assisted breeding strategy. An IR74371-46-1-1 × Sabitri backcross inbred line population was screened for reproductive-stage drought stress at the International Rice Research Institute, Philippines, and Regional Agricultural Research Station, Nepalgunj, Nepal, in the dry and wet seasons of 2011, respectively. A bulk segregant analysis approach was used to identify markers associated with high grain yield under drought.

Results

A QTL, qDTY

12.1
, significantly associated with grain yield under reproductive-stage drought stress was identified on chromosome 12 with a consistent effect in two environments: IRRI, Philippines, and RARS, Nepalgunj, Nepal. This QTL explained phenotypic variance of 23.8% and contributed an additive effect of 45.3% for grain yield under drought. The positive QTL allele for qDTY

12.1
was contributed by tolerant parent IR74371-46-1-1.

Conclusions

In this study, qDTY

12.1
showed a consistent effect across environments for high grain yield under lowland reproductive-stage drought stress in the background of popular high-yielding but drought-susceptible recipient variety Sabitri. qDTY

12.1
was also reported previously [Crop Sci 47:507–516, 2007] to increase grain yield under upland reproductive-stage drought stress situations. qDTY

12.1
is the only QTL reported so far in rice to have shown a large effect against multiple recipient genetic backgrounds as well as under highly diverse upland and lowland rice ecosystems. qDTY

12.1
can be successfully introgressed to improve grain yield under drought of popular high-yielding but drought-susceptible lowland as well as upland adapted varieties following marker-assisted breeding.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation
Authors: Nilsen Gro , Liestøl Knut , Van Loo Peter , Moen Vollan Hans Kristian , Eide Marianne B , Rueda Oscar M , Chin Suet-Feung , Russell Roslin , Baumbusch Lars O , Caldas Carlos , Børresen-Dale Anne-Lise , Lingjærde Ole Christian
Published: February 2013

Background

Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number.

Results

A comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of breakpoints, the estimates are optimal in the least squares sense. A novel and computationally highly efficient algorithm is proposed that utilizes vector-based operations in R. Three case studies are presented.

Conclusions

The R package is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.
Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation
Authors: Levison Scott E , Fisher Paul , Hankinson Jenny , Zeef Leo , Eyre Steve , Ollier William E , McLaughlin John T , Brass Andy , Grencis Richard K , Pennock Joanne L
Published: February 2013

Background

Genetic susceptibility to colonic inflammation is poorly defined at the gene level. Although Genome Wide Association studies (GWAS) have identified loci in the human genome which confer susceptibility to Inflammatory Bowel Disease (Crohn’s and Ulcerative Colitis), it is not clear if precise loci exist which confer susceptibility to inflammation at specific locations within the gut e.g. small versus large intestine. Susceptibility loci for colitis in particular have been defined in the mouse, although specific candidate genes have not been identified to date. We have previously shown that infection withTrichuris muris(T. muris) induces chronic colitis in susceptible mouse strains with clinical, histological, and immunological homology to human colonic Crohn’s disease. We performed an integrative analysis of colitis susceptibility, using an F2 inter-cross of resistant (BALB/c) and susceptible (AKR) mice followingT. murisinfection. Quantitative Trait Loci (QTL), polymorphic and expression data were analysed alongsidein silicoworkflow analyses to discover novel candidate genes central to the development and biology of chronic colitis.

Results

7 autosomal QTL regions were associated with the establishment of chronic colitis following infection. 144 QTL genes had parental strain SNPs and significant gene expression changes in chronic colitis (expression fold-change ≥ +/-1.4). TheT. murisQTL on chromosome 3 (Tm3) mapped to published QTL in 3 unrelated experimental models of colitis and contained 33 significantly transcribed polymorphic genes. Phenotypic pathway analysis, text mining and time-course qPCR replication highlighted several potentialcis-QTL candidate genes in colitis susceptibility, includingFcgR1,Ptpn22,RORc,andVav3.

Conclusion

Genetic susceptibility to induced colonic mucosal inflammation in the mouse is conserved atTm3and overlaysCdcs1.1. Genes central to the maintenance of intestinal homeostasis reside within this locus, implicating several candidates in susceptibility to colonic inflammation. Combined methodology incorporating genetic, transcriptional and pathway data allowed identification of biologically relevant candidate genes, withVav3newly implicated as a colitis susceptibility gene of functional relevance.
Effect of emergency major abdominal surgery on CD4 cell count among HIV positive patients in a sub Saharan Africa tertiary hospital - a prospective study
Authors: Okumu Gabriel , Makobore Patson , Kaggwa Sam , Kambugu Andrew , Galukande Moses
Published: February 2013

Background

Surgery plays a key role in HIV palliative care, specifically in the diagnosis and treatment of HIV related and non-related conditions. Yet major surgery depresses the immune system. Whereas the surgical consequences of HIV infection are well described, there is a paucity of published data, in resource-limited settings, on the effects of major surgery on the immune system. The purpose of this study was to determine the effect of major abdominal surgery on CD4 count in HIV positive and HIV negative patients after emergency major surgery.

Methods

A prospective cohort study was done for patients who underwent emergency major abdominal surgery. Their peri-operative CD4 counts were done for both HIV- and HIV + patients. Median CD4s were used in analysis.

Mann Whitney test of significance was used for continuous data and Fisher’ exact test used for categorical data. IRB approval was obtained.

Results

A total of 101 patients were recruited, 25 HIV positive and 76 HIV negative. The median CD4 cell reduction was higher in the HIV negative group (−68 cells) than HIV positive group (−29 cells) (p = 0.480).

There was a general increase in the median CD4 change by 72 cells for the HIV positives and 95 cells for the HIV negatives (p = 0.44). CD4 change rose in both the HIV positive and negative groups by 27 cells for the HIV positives and 28 cells for the HIV negatives (p = 0.94). Relative Risk was 0.96, {CI 0.60 – 1.53}.

Conclusion

Major emergency abdominal surgery had no significant effect on CD4 cell count among HIV positive patients.
Keratinocyte cytoskeletal roles in cell sheet engineering
Authors: Wei Qi , Reidler Daniel , Shen Min Ye , Huang Hayden
Published: February 2013

Background

There is an increasing need to understand cell-cell interactions for cell and tissue engineering purposes, such as optimizing cell sheet constructs, as well as for examining adhesion defect diseases. For cell-sheet engineering, one major obstacle to sheet function is that cell sheets in suspension are fragile and, over time, will contract. While the role of the cytoskeleton in maintaining the structure and adhesion of cells cultured on a rigid substrate is well-characterized, a systematic examination of the role played by different components of the cytoskeleton in regulating cell sheet contraction and cohesion in the absence of a substrate has been lacking.

Results

In this study, keratinocytes were cultured until confluent and cell sheets were generated using dispase to remove the influence of the substrate. The effects of disrupting actin, microtubules or intermediate filaments on cell-cell interactions were assessed by measuring cell sheet cohesion and contraction. Keratin intermediate filament disruption caused comparable effects on cell sheet cohesion and contraction, when compared to actin or microtubule disruption. Interfering with actomyosin contraction demonstrated that interfering with cell contraction can also diminish cell cohesion.

Conclusions

All components of the cytoskeleton are involved in maintaining cell sheet cohesion and contraction, although not to the same extent. These findings demonstrate that substrate-free cell sheet biomechanical properties are dependent on the integrity of the cytoskeleton network.
Heparanase induced by advanced glycation end products (AGEs) promotes macrophage migration involving RAGE and PI3K/AKT pathway
Authors: Qin Qiaojing , Niu Jianying , Wang Zhaoxia , Xu Wangjie , Qiao Zhongdong , Gu Yong
Published: February 2013

Background

Advanced glycation end products (AGEs), inflammatory-associated macrophage migration and accumulation are crucial for initiation and progression of diabetic vascular complication. Enzymatic activity of heparanase (HPA) is implicated strongly in dissemination of metastatic tumor cells and cells of the immune system. In addition, HPA enhances the phosphorylation of selected signaling molecules including AKT pathway independent of enzymatic activity. However, virtually nothing is presently known the role of HPA during macrophage migration exposed to AGEs involving signal pathway.

Methods

These studies were carried out in Ana-1 macrophages. Macrophage viability was measured by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays. HPA and AKT protein expression in macrophages are analysed by Western blotting and HPA mRNA expression by real time quantitative RT-PCR. Release of HPA was determined by ELISA. Macrophage migration was assessed by Transwell assays.

Results

HPA protein and mRNA were found to be increased significantly in AGEs-treated macrophages. Pretreatment with anti-HPA antibody which recognizes the nonenzymatic terminal of HPA prevented AGEs-induced AKT phosphorylation and macrophage migration. LY294002 (PI3k/AKT inhibitor) inhibited AGEs-induced macrophage migration. Furthermore, pretreatment with anti-receptor for advanced glycation end products (RAGE) antibody attenuated AGEs-induced HPA expression, AKT phosphorylation and macrophage migration.

Conclusions

These data indicate that AGEs-induced macrophage migration is dependent on HPA involving RAGE-HPA-PI3K/AKT pathway. The nonenzymatic activity of HPA may play a key role in AGEs-induced macrophage migration associated with inflammation in diabetic vascular complication.
Establishment and characterization of clear cell renal cell carcinoma cell lines with different metastatic potential from Chinese patients
Authors: Tan Xiaojie , He Songqin , Han Yifang , Yu Yongwei , Xiao Jianru , Xu Danfeng , Wang Guoping , Du Yan , Chang Wenjun , Yin Jianhua , Su Tong , Hou Jianguo , Cao Guangwen
Published: February 2013

Abstracts

Background

Clear cell renal cell carcinoma (ccRCC) cell lines with distinct metastatic potential are essential to study the mechanism of ccRCC metastasis. However, none of them originated from Chinese.

Methods

Primary cell cultures were performed using a primary tumor of a 49-year-old male ccRCC patient and a metastatic tumor of a 62-year-old male patient who had received nephrectomy to excise primary ccRCC 10 years ago. Cell growth, microstructure, cytogenetics, cytometry, expression of metastasis-associated molecules, tumorigenesis and metastasis were subsequently characterized.

Results

Two successive cell lines named NRCC from the primary ccRCC and MRCC from the metastatic ccRCC were established, respectively. Compared to NRCC, MRCC exhibited stronger anchorage-independent growth and invasion potentials and contained more glycogen granules in the cytoplasm. Gains of chromosomes and some translocations were the major chromosomal aberrations in both cell strains. CD24 expression was more frequent in MRCC than in NRCC and the same was true for CD56. The transcriptional levels of TNF α, IL-6, VEGF, HIF2 α, MMP2, and RhoC were significantly higher in MRCC than in NRCC. Cytosolic IκBα protein was more degraded in MRCC than in NRCC following TNFα treatment. Both cell lines had strong tumorigenicity in athymic nude mice. However, MRCC had strong potential in generating metastasis to lung and hemorrhagic ascites than NRCC following orthotopic transplantations.

Conclusions

Cancer cells isolated from metastatic ccRCC have more malignant and metastatic potential than those from the primary tumor from the patients who shared the similar race background. Establishment of MRCC and NRCC may provide suitable models with which to investigate molecular mechanisms of ccRCC metastasis.
Stagnation-point flow over a permeable stretching/shrinking sheet in a copper-water nanofluid
Authors: Bachok Norfifah , Ishak Anuar , Nazar Roslinda , Senu Norazak
Published: February 2013

An analysis is carried out to study the heat transfer characteristics of steady two-dimensional stagnation-point flow of a copper (Cu)-water nanofluid over a permeable stretching/shrinking sheet. The stretching/shrinking velocity and the ambient fluid velocity are assumed to vary linearly with the distance from the stagnation-point. Results for the skin friction coefficient, local Nusselt number, velocity as well as the temperature profiles are presented for different values of the governing parameters. It is found that dual solutions exist for the shrinking case, while for the stretching case, the solution is unique. The results indicate that the inclusion of nanoparticles into the base fluid produces an increase in the skin friction coefficient and the heat transfer rate at the surface. Moreover, suction increases the surface shear stress and in consequence increases the heat transfer rate at the fluid-solid interface.

MSC: 34B15, 76D10.
A hierarchical graph model for object cosegmentation
Authors: Li Yanli , Zhou Zhong , Wu Wei
Published: February 2013

Given a set of images containing similar objects, cosegmentation is a task of jointly segmenting the objects from the set of images, which has received increasing interests recently. To solve this problem, we present a novel method based on a hierarchical graph. The vertices of the hierarchical graph involve pixels, superpixels and heat sources, and cosegmentation is performed as iterative object refinement in the three levels. With the inter-image connection in the heat source level and the intra-image connection in the superpixel level, we progressively update the object likelihoods by transferring message across images via belief propagation, diffusing heat energy within individual image via random walks, and refining the foreground objects in the pixel level via guided filtering. Besides, a histogram based saliency detection scheme is employed for initialization. We demonstrate experimental evaluations with state-of-the-art methods over several public datasets. The results verify that our method achieves better segmentation quality as well as higher efficiency.
Evidence for IFNα-induced, SAMHD1-independent inhibitors of early HIV-1 infection
Authors: Goujon Caroline , Schaller Torsten , Galão Rui Pedro , Amie Sarah M , Kim Baek , Olivieri Kevin , Neil Stuart JD , Malim Michael H
Published: February 2013

Background

Type I interferon (IFN) treatment of some cells, including dendritic cells, macrophages and monocytic THP-1 cells, restricts HIV-1 infection and prevents viral cDNA accumulation. Sterile alpha motif and HD domain protein 1 (SAMHD1), a dGTP-regulated deoxynucleotide triphosphohydrolase, reduces HIV-1 infectivity in myeloid cells, likely by limiting dNTPs available for reverse transcription, and has been described as IFNα-inducible. Myeloid cell infection by HIV-1 is enhanced by HIV-2/SIVSM Vpx, which promotes SAMHD1 degradation, or by exogenous deoxyribonucleoside (dN) addition.

Findings

SAMHD1 expression was not substantially influenced by IFNα treatment of monocyte-derived macrophages or THP-1 cells. The contributions of SAMHD1 to the inhibition of HIV-1 infectivity by IFNα were assessed through the provision of Vpx, exogenous dN addition, or via RNAi-mediated SAMHD1 knock-down. Both Vpx and dN efficiently restored infection in IFNα-treated macrophages, albeit not to the levels seen with these treatments in the absence of IFNα. Similarly using differentiated THP-1 cells, the addition of Vpx or dNs, or SAMHD1 knock-down, also stimulated infection, but failing to match the levels observed without IFNα. Neither Vpx addition nor SAMHD1 knock-down reversed the IFNα-induced blocks to HIV-1 infection seen in dividing U87-MG or THP-1 cells. Therefore, altered SAMHD1 expression or function cannot account for the IFNα-induced restriction to HIV-1 infection seen in many cells and cell lines.

Conclusion

IFNα establishes an anti-HIV-1 phenotype in many cell types, and appears to accomplish this without potentiating SAMHD1 function. We conclude that additional IFNα-induced suppressors of the early stages of HIV-1 infection await identification.
Australian Diabetes Foot Network: practical guideline on the provision of footwear for people with diabetes
Authors: Bergin Shan M , Nube Vanessa L , Alford Jan B , Allard Bernard P , Gurr Joel M , Holland Emma L , Horsley Mark W , Kamp Maarten C , Lazzarini Peter A , Sinha Ashim K , Warnock Jason T , Wraight Paul R
Published: February 2013

Trauma, in the form of pressure and/or friction from footwear, is a common cause of foot ulceration in people with diabetes. These practical recommendations regarding the provision of footwear for people with diabetes were agreed upon following review of existing position statements and clinical guidelines. The aim of this process was not to re‐invent existing guidelines but to provide practical guidance for health professionals on how they can best deliver these recommendations within the Australian health system. Where information was lacking or inconsistent, a consensus was reached following discussion by all authors. Appropriately prescribed footwear, used alone or in conjunction with custom‐made foot orthoses, can reduce pedal pressures and reduce the risk of foot ulceration. It is important for all health professionals involved in the care of people with diabetes to both assess and make recommendations on the footwear needs of their clients or to refer to health professionals with such skills and knowledge. Individuals with more complex footwear needs (for example those who require custom‐made medical grade footwear and orthoses) should be referred to health professionals with experience in the prescription of these modalities and who are able to provide appropriate and timely follow‐up. Where financial disadvantage is a barrier to individuals acquiring appropriate footwear, health care professionals should be aware of state and territory based equipment funding schemes that can provide financial assistance. Aboriginal and Torres Strait Islanders and people living in rural and remote areas are likely to have limited access to a broad range of footwear. Provision of appropriate footwear to people with diabetes in these communities needs be addressed as part of a comprehensive national strategy to reduce the burden of diabetes and its complications on the health system.
Increased T-bet is associated with senescence of influenza virus-specific CD8 T cells in aged humans
Authors: Dolfi Douglas V , Mansfield Kathleen D , Polley Antonio M , Doyle Susan A , Freeman Gordon J , Pircher Hanspeter , Schmader Kenneth E , Wherry E John
Published: February 2013

Increased T-bet levels and senescence in CD8 T cells from aged individuals as possible mechanisms for decreased influenza-specific functionality.

Aged individuals have increased morbidity and mortality following influenza and other viral infections, despite previous exposure or vaccination. Mouse and human studies suggest increased senescence and/or exhaustion of influenza virus-specific CD8 T cells with advanced age. However, neither the relationship between senescence and exhaustion nor the underlying transcriptional pathways leading to decreased function of influenza virus-specific cellular immunity in elderly humans are well-defined. Here, we demonstrate that increased percentages of CD8 T cells from aged individuals express CD57 and KLRG1, along with PD-1 and other inhibitory receptors, markers of senescence, or exhaustion, respectively. Expression of T-box transcription factors, T-bet and Eomes, were also increased in CD8 T cells from aged subjects and correlated closely with expression of CD57 and KLRG1. Influenza virus-specific CD8 T cells from aged individuals exhibited decreased functionality with corresponding increases in CD57, KLRG1, and T-bet, a molecular regulator of terminal differentiation. However, in contrast to total CD8 T cells, influenza virus-specific CD8 T cells had altered expression of inhibitory receptors, including lower PD-1, in aged compared with young subjects. Thus, our data suggest a prominent role for senescence and/or terminal differentiation for influenza virus-specific CD8 T cells in elderly subjects.
PGC-1α Regulates Hepatic Hepcidin Expression and Iron Homeostasis in Response to inflammation
Authors: Qian Jinchun , Chen Siyu , Huang Yueyue , Shi Xiaoli , Liu Chang
Published: February 2013

Systemic iron homeostasis is finely regulated by the liver through synthesis of the peptide hormone hepcidin (HAMP), which plays an important role in duodenal iron absorption and macrophage iron release. Clinical investigations have shown that chronic and low-grade inflammation leads to the increase of serum HAMP levels and the development of various diseases such as anemia of inflammation. However, gaps remain to fully elucidate the mechanism linking inflammation and iron dysregulation. Here we show that although inflammatory stimuli increase hepatic HAMP expression and cause systemic iron deficiency in mice, they inhibit the expression of peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α), a transcriptional coactivator actively involved in metabolic regulation. Liver-specific overexpression of PGC-1α antagonizes lipopolysaccharide-induced HAMP expression and alleviates various pathophysiological changes similar to anemia of inflammation. Consistently, overexpression of PGC-1α in HepG2 or HuH7 cells also suppresses HAMP expression and reduces iron accumulation. In contrast, knockdown of PGC-1α exaggerates LPS-induced HAMP expression and iron dysregulation. At the molecular level, PGC-1α suppresses HAMP transcription via the interaction with hepatocyte nuclear factor 4α. In addition, PGC-1α is present near hepatocyte nuclear factor 4α-binding site on the proximal HAMP promoter and turns the chromatin structure into an inactive state. Our data suggest a critical role for PGC-1α in the regulation of hepatic HAMP expression and iron homeostasis under inflammatory circumstances.
Dynamic temporal requirement ofWnt1in midbrain dopamine neuron development
Authors: Yang Jasmine , Brown Ashly , Ellisor Debra , Paul Erin , Hagan Nellwyn , Zervas Mark
Published: February 2013

Wnt1-expressing progenitors generate midbrain dopamine (MbDA) and cerebellum (Cb) neurons in distinct temporal windows and from spatially discrete progenitor domains. It has been shown that Wnt1 and Lmx1a participate in a cross-regulatory loop that is utilized during MbDA neuron development. However, Wnt1 expression dynamically changes over time and precedes that of Lmx1a. The spatial and temporal requirements of Wnt1 in development and specifically its requirement for MbDA neurons remain to be determined. To address these issues, we generated a conditional Wnt1 allele and temporally deleted Wnt1 coupled with genetic lineage analysis. Using this approach, we show that patterning of the midbrain (Mb) and Cb by Wnt1 occurs between the one-somite and the six- to eight-somite stages and is solely dependent on Wnt1 function in the Mb, but not in the Cb. Interestingly, an En1-derived domain persists after the early deletion of Wnt1 and mutant cells express OTX2. However, the En1-derived Wnt1-mutant domain does not contain LMX1a-expressing progenitors, and MbDA neurons are depleted. Thus, we demonstrate an early requirement of Wnt1 for all MbDA neurons. Subsequently, we deleted Wnt1 in the ventral Mb and show a continued late requirement for Wnt1 in MbDA neuron development, but not in LMX1a-expressing progenitors. Specifically, Wnt1 deletion disrupts the birthdating of MbDA neurons and causes a depletion of MbDA neurons positioned medially and a concomitant expansion of MbDA neurons positioned laterally during embryogenesis. Collectively, our analyses resolve the spatial and temporal function of Wnt1 in Mb and Cb patterning and in MbDA neuron development in vivo.
Drosophilap53-related protein kinase is required for PI3K/TOR pathway-dependent growth
Authors: Ibar Consuelo , Cataldo Vicente F. , Vásquez-Doorman Constanza , Olguín Patricio , Glavic Álvaro
Published: February 2013

Cell growth and proliferation are pivotal for final organ and body size definition. p53-related protein kinase (Bud32/PRPK) has been identified as a protein involved in proliferation through its effects on transcription in yeast and p53 stabilization in human cell culture. However, the physiological function of Bud32/PRPK in metazoans is not well understood. In this work, we have analyzed the role of PRPK in Drosophila development. Drosophila PRPK is expressed in every tissue analyzed and is required to support proliferation and cell growth. The Prpk knockdown animals show phenotypes similar to those found in mutants for positive regulators of the PI3K/TOR pathway. This pathway has been shown to be fundamental for animal growth, transducing the hormonal and nutritional status into the protein translation machinery. Functional interactions have established that Prpk operates as a transducer of the PI3K/TOR pathway, being essential for TOR kinase activation and for the regulation of its targets (S6K and 4E-BP, autophagy and bulk endocytosis). This suggests that Prpk is crucial for stimulating the basal protein biosynthetic machinery in response to insulin signaling and to changes in nutrient availability.
Gibberellin signaling in plants
Authors: Davière Jean-Michel , Achard Patrick
Published: February 2013

The plant hormone gibberellin (GA) regulates major aspects of plant growth and development. The role of GA in determining plant stature had major impacts on agriculture in the 1960s, and the development of semi-dwarf varieties that show altered GA responses contributed to a huge increase in grain yields during the ‘green revolution’. The past decade has brought great progress in understanding the molecular basis of GA action, with the cloning and characterization of GA signaling components. Here, we review the molecular basis of the GA signaling pathway, from the perception of GA to the regulation of downstream genes.
Epigenetic mechanisms in the development and maintenance of dopaminergic neurons
Authors: van Heesbeen Hendrikus J. , Mesman Simone , Veenvliet Jesse V. , Smidt Marten P.
Published: February 2013

Mesodiencephalic dopaminergic (mdDA) neurons are located in the ventral mesodiencephalon and are involved in psychiatric disorders and severely affected in neurodegenerative diseases such as Parkinson’s disease. mdDA neuronal development has received much attention in the last 15 years and many transcription factors involved in mdDA specification have been discovered. More recently however, the impact of epigenetic regulation has come into focus, and it’s emerging that the processes of histone modification and DNA methylation form the basis of genetic switches that operate during mdDA development. Here, we review the epigenetic control of mdDA development, maturation and maintenance. As we highlight, epigenetic mechanisms play a pivotal role in all of these processes and the knowledge gathered from studying epigenetics in these contexts may aid our understanding of mdDA-related pathologies.
Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture
Authors: Darnell James E.
Published: February 2013

Several strong conclusions emerge concerning pre-mRNA processing from both old and newer experiments. The RNAPII complex is involved with pre-mRNA processing through binding of processing proteins to the CTD (carboxyl terminal domain) of the largest RNAPII subunit. These interactions are necessary for efficient processing, but whether factor binding to the CTD and delivery to splicing sites is obligatory or facilitatory is unsettled. Capping, addition of an m7Gppp residue (cap) to the initial transcribed residue of a pre-mRNA, occurs within seconds. Splicing of pre-mRNA by spliceosomes at particular sites is most likely committed during transcription by the binding of initiating processing factors and ∼50% of the time is completed in mammalian cells before completion of the primary transcript. This fact has led to an outpouring in the literature about “cotranscriptional splicing.” However splicing requires several minutes for completion and can take longer. The RNAPII complex moves through very long introns and also through regions dense with alternating exons and introns at an average rate of ∼3 kb per min and is, therefore, not likely detained at each splice site for more than a few seconds, if at all. Cleavage of the primary transcript at the 3′ end and polyadenylation occurs within 30 sec or less at recognized polyA sites, and the majority of newly polyadenylated pre-mRNA molecules are much larger than the average mRNA. Finally, it seems quite likely that the nascent RNA most often remains associated with the chromosomal locus being transcribed until processing is complete, possibly acquiring factors related to the transport of the new mRNA to the cytoplasm.
Centering the Chārbāgh
Authors: Johnson-Roehr Susan N.
Published: February 2013

In Centering the Chārbāgh: The Mughal Garden as Design Module for the Jaipur City Plan, Susan N. Johnson-Roehr argues that the privileging of a Hindu-Vedic worldview has had a significant effect on our understanding of Jaipur City’s history. Current interpretive approaches assume that the city’s patron, Sawai Jai Singh II, relied on the maṇḍala when shaping the city plan in the eighteenth century. The emphasis on the maṇḍala as governing device has encouraged historians to neglect other sources of Jaipur’s city plan. Specifically, scholars have not considered the role of the quadripartite Mughal paradise garden (chahār bāgh, Persian; chārbāgh, Hindi) in the planning of the city. Johnson-Roehr suggests that Jaipur’s spatial organization was defined by the chārbāgh rather than the navagraha or vāstu puruṣa maṇḍala, and demonstrates that the plan was a response to a specific chārbāgh, Jai Niwas Bagh, built by Sawai Jai Singh in 1713. Combining a rereading of eighteenth-century documents with an analysis of the physical characteristics of Jai Niwas Bagh, the author concludes that the chārbāgh was the most important element in the development of the rectilinear boulevards, bazaars, and walls that characterize Jaipur today.
A Case of Double Identity
Authors: Grossman Max
Published: February 2013

The Palazzo Tolomei (1270–75) was not only the private residence of a prominent Sienese family, but was also the first legislative headquarters of the Guelph commune. In A Case of Double Identity: The Public and Private Faces of the Palazzo Tolomei in Siena, Max Grossman argues that the unusual features and ornament of this building may be linked to the original public function of its ground-level hall and to the city’s allegiance to the papacy and the Angevin monarchy after 1270. As a hybrid civic-private edifice, the Palazzo Tolomei defies traditional categorization and calls into question our current understanding of the typology and function of civic palaces. Grossman suggests that as a new architectural type, the building served as the template for the initial versions of the Palazzo Pubblico in Siena and the Palazzo Vecchio in Florence.
Albert Kahn’s Partners in Industrial Architecture
Authors: Meister Chris
Published: February 2013

The narrative of Albert Kahn’s rags-to-riches career, as previously told, suggests that his success was a matter of happenstance, augmented by a remarkable work ethic. The happenstance factor turns out to be a distortion resulting from the architect’s innate humility and a need to downplay his relationship with Joseph Boyer for business reasons. Although Boyer did not hire him in 1900 to design a machine shop as widely believed, the industrialist was nonetheless integral to the careers of Albert and Julius Kahn as the brothers developed their respective niches in industrial work. Having experienced numerous setbacks and few triumphs in his first attempt at an architectural practice, Kahn specialized in industrial work as a determined act of reinvention made possible by Boyer. Chris Meister offers a fresh examination of the architect’s work in the first years of the twentieth century and the role that his business partners played in shaping his career in Albert Kahn’s Partners in Industrial Architecture.
Long-term Right Ventricular Assist Device Support for Congenitally Corrected Transposition of the Great Arteries
Authors: Morgan Jeffrey A. , Paone Gaetano , Brewer Robert J.
Published: February 2013

With congenitally corrected transposition of the great arteries, the right ventricle (RV) supports the systemic circulation. These patients have an increased risk of developing heart failure. Implantation of a ventricular assist device may be the only therapeutic option for patients who are not transplantation candidates. The technical aspects of implanting a mechanical device into the RV have not been well described, however. We describe our experience with one such case and describe our operative strategy in obtaining optimal placement of the inflow cannula.
Results of Additional Pulsatile Pulmonary Blood Flow with Bidirectional Glenn Cavopulmonary Anastomosis: Positive Effect on Main Pulmonary Artery Growth and Less Need for Fontan Conversion
Authors: Demirtürk Orhan Saim , Güvener Murat , Coşkun İsa , Yıldırım Selman Vefa
Published: February 2013

Background: Additional antegrade pulsatile pulmonary blood flow obtained by leaving the main pulmonary artery patent during bidirectional cavopulmonary shunt has been shown to give additional benefits to the bidirectional Glenn cavopulmonary anastomosis. We retrospectively evaluated our 20-patient pulsatile Glenn series in order to find out whether these salutary effects were valid or not.
Methods: Between June 2007 and November 2011, 20 patients (11 girls and 9 boys) with single-ventricle physiology underwent bidirectional cavopulmonary anastomosis. The additional source of blood flow was through the unligated main pulmonary artery in all patients. A retrospective review of our surgical experience was performed focusing on the role of additional pulmonary flow. Medical records and perioperational and postoperative follow-up data including clinical outcomes were retrospectively retrieved and analyzed.
Results: Two patients died in the early postoperative period. One patient died in the follow-up period. Mean follow-up time was 23.9 ± 15.7 months. No superior vena cava syndrome and no increase in pulmonary vascular resistance were observed. Improvement of partial oxygen pressure after pulsatile Glenn has been shown in all patients (P = .00). At a mean interval of 22.9 months, main pulmonary artery size continued to increase after pulsatile Glenn cavopulmonary anastomosis (P = .028). Only 1 patient was converted to Fontan type circulation after pulsatile Glenn cavopulmonary anastomosis.
Conclusions: The pulsatile cavopulmonary shunt is a useful procedure in the early and intermediate term management of patients with a functional univentricular heart. It improves partial oxygen pressure and the impact of pulsatility on the main pulmonary artery.
Cardiac Tamponade due to Left Ventricular Pseudoaneurysm After Aortic Valve Replacement
Authors: Baydar Onur , Coşkun Ugur , Balaban Betul , Cetin Gurkan , Firatli Inci , Ersanli Murat Kazim , Kucukoglu Mehmet Serdar
Published: February 2013

Left ventricular outflow tract pseudoaneurysm is a rare but a potentially lethal complication, mainly after aortic root endocarditis or surgery. Usually, it originates from a dehiscence in the mitral-aortic intervalvular fibrosa and arises posteriorly to the aortic root. We report a rare case of a patient with cardiac tamponade due to left ventricular pseudoaneurysm after aortic valve replacement. The subsequent surgical resection was performed successfully.
Associations of Food Stamp Participation With Dietary Quality and Obesity in Children
Authors: Leung Cindy W. , Blumenthal Susan J. , Hoffnagle Elena E. , Jensen Helen H. , Foerster Susan B. , Nestle Marion , Cheung Lilian W.Y. , Mozaffarian Dariush , Willett Walter C.
Published: February 2013

OBJECTIVE:

To determine if obesity and dietary quality in low-income children differed by participation in the Supplemental Nutrition Assistance Program (SNAP), formerly the Food Stamp Program.

METHODS:

The study population included 5193 children aged 4 to 19 with household incomes ≤130% of the federal poverty level from the 1999–2008 NHANES. Diet was measured by using 24-hour recalls.

RESULTS:

Among low-income US children, 28% resided in households currently receiving SNAP benefits. After adjusting for sociodemographic differences, SNAP participation was not associated with a higher rate of childhood obesity (odds ratio = 1.11, 95% confidence interval [CI]: 0.71–1.74). Both SNAP participants and low-income nonparticipants were below national recommendations for whole grains, fruits, vegetables, fish, and potassium, while exceeding recommended limits for processed meat, sugar-sweetened beverages, saturated fat, and sodium. Zero percent of low-income children met at least 7 of 10 dietary recommendations. After multivariate adjustment, compared with nonparticipants, SNAP participants consumed 43% more sugar-sweetened beverages (95% CI: 8%–89%), 47% more high-fat dairy (95% CI: 7%, 101%), and 44% more processed meats (95% CI: 9%–91%), but 19% fewer nuts, seeds, and legumes (95% CI: –35% to 0%). In part due to these differences, intakes of calcium, iron, and folate were significantly higher among SNAP participants. Significant differences by SNAP participation were not evident in total energy, macronutrients, Healthy Eating Index 2005 scores, or Alternate Healthy Eating Index scores.

CONCLUSIONS:

The diets of low-income children are far from meeting national dietary recommendations. Policy changes should be considered to restructure SNAP to improve children’s health.
Facial Dysmorphism Across the Fetal Alcohol Spectrum
Authors: Suttie Michael , Foroud Tatiana , Wetherill Leah , Jacobson Joseph L. , Molteno Christopher D. , Meintjes Ernesta M. , Hoyme H. Eugene , Khaole Nathaniel , Robinson Luther K. , Riley Edward P. , Jacobson Sandra W. , Hammond Peter
Published: February 2013

OBJECTIVE:

Classic facial characteristics of fetal alcohol syndrome (FAS) are shortened palpebral fissures, smooth philtrum, and thin upper vermillion. We aim to help pediatricians detect facial dysmorphism across the fetal alcohol spectrum, especially among nonsyndromal heavily exposed (HE) individuals without classic facial characteristics.

METHODS:

Of 192 Cape Coloured children recruited, 69 were born to women who reported abstaining from alcohol during pregnancy. According to multifaceted criteria, the remainder were allocated clinically to the FAS (n = 22), partial FAS (n = 26) or nonsyndromal HE (n = 75) categories. We used dense surface modeling and signature analyses of 3-dimensional facial photographs to determine agreement between clinical categorization and classifications induced from face shape alone, to visualize facial differences, and to consider predictive links between face shape and neurobehavior.

RESULTS:

Face classification achieved significant agreement with clinical categories for discrimination of nonexposed from FAS alone (face: 0.97–1.00; profile: 0.92) or with the addition of partial FAS (face: 0.90; profile: 0.92). Visualizations of face signatures delineated dysmorphism across the fetal alcohol spectrum and in half of the nonsyndromal HE category face signature graphs detected facial characteristics consistent with prenatal alcohol exposure. This subgroup performed less well on IQ and learning tests than did nonsyndromal subjects without classic facial characteristics.

CONCLUSIONS:

Heat maps and morphing visualizations of face signatures may help clinicians detect facial dysmorphism across the fetal alcohol spectrum. Face signature graphs show potential for identifying nonsyndromal heavily exposed children who lack the classic facial phenotype but have cognitive impairment.
Increased Length of Stay and Costs Associated With Weekend Admissions for Failure to Thrive
Authors: Thompson Rachel T. , Bennett William E. , Finnell S. Maria E. , Downs Stephen M. , Carroll Aaron E.
Published: February 2013

OBJECTIVE:

To evaluate whether admission day of the week affects the length of stay (LOS) and health care costs for failure to thrive (FTT) admissions.

METHODS:

Administrative data were obtained for all children aged <2 years (N = 23 332) with a primary admission diagnosis of FTT from 2003-2011 from 42 freestanding US hospitals. Demographic characteristics, day of admission, LOS, costs per stay, number of discharge diagnoses, primary discharge diagnoses, primary procedure code, number of radiologic and laboratory units billed during admission were obtained for each admission. Linear regression and zero-truncated Poisson regression were used for analysis.

RESULTS:

Weekend admission was significantly correlated with increased LOS and increased average cost (P < .002). This finding was also true for children with both admission and discharge diagnoses of FTT (P < .001). The number of procedures for children admitted on the weekend was not significantly different compared with children admitted on the weekdays (incident rate ratio [IRR]:1.04 [95% confidence interval (CI): 0.99–1.09]). However, weekend admissions did have more radiologic studies (IRR: 1.13 [95% CI: 1.10–1.16]) and laboratory tests (IRR: 1.39 [95% CI: 1.38–1.40]) performed. If one-half of weekend admissions in 2010 with both admission and discharge diagnoses of FTT were converted to Monday admissions, total savings in health care dollars for 2010 would be $534, 145.

CONCLUSIONS:

Scheduled FTT admissions on weekends increased LOS and health care costs compared with weekday admissions of similar levels of complexity. Reduction in planned weekend admissions for FTT could significantly reduce health care costs.
Marriage and the Well-Being of Children
Authors: Garrett Jeremy R. , Lantos John D.
Published: February 2013

Children’s well-being has become the focal consideration in legal and public policy debates regarding same-sex marriage. In this article, we critically examine and rebut the central moral argument made by opponents of same-sex marriage: that the state should not license any domestic arrangement other than “traditional marriage” because doing so would be detrimental to children’s well-being. Although many have challenged the empirical premise that children raised by same-sex couples fare worse than children in other arrangements, we focus primarily on the normative premises for exclusively licensing traditional (that is, monogamous, heterosexual) marriage. We argue that even if the empirical support for its claims was strong, the argument is morally insufficient for denying state recognition to other types of relationships. Importantly, we affirm the state’s vital role in promoting children’s well-being. We question, however, the approach of delegitimizing certain relationships as a means to that end. Instead, we argue, the state should encourage and support individuals who want to care for children, presume that any couple or individual is capable of adequate child-rearing, and ensure that all adults who are raising children (whether married or not) have the material resources and support necessary to be good parents. Such a policy would (1) set a reasonable minimal threshold for state recognition, (2) be vigilant in identifying cases falling below this threshold, and then (3) either assist or disqualify underperforming arrangements. It would also, appropriately, decouple arguments about legitimate and illegitimate types of relationships from arguments about what is best for children.
Community Pediatrics: Navigating the Intersection of Medicine, Public Health, and Social Determinants of Children’s Health
Authors:   COUNCIL ON COMMUNITY PEDIATRICS, Gorski Peter A. , Kuo Alice A. , Granado-Villar Deise C. , Gitterman Benjamin A. , Brown Jeffrey M. , Chilton Lance A. , Cotton William H. , Gambon Thresia B. , Gorski Peter A. , Kraft Colleen A. , Kuo Alice A. , Paz-Soldan Gonzalo J. , Zind Barbara
Published: February 2013

This Policy Statement was reaffirmed October 2016 and December 2023.

This policy statement provides a framework for the pediatrician’s role in promoting the health and well-being of all children in the context of their families and communities. It offers pediatricians a definition of community pediatrics, emphasizes the importance of recognizing social determinants of health, and delineates the need to partner with public health to address population-based child health issues. It also recognizes the importance of pediatric involvement in child advocacy at local, state, and federal levels to ensure all children have access to a high-quality medical home and to eliminate child health disparities. This statement provides a set of specific recommendations that underscore the critical nature of this dimension of pediatric practice, teaching, and research.
Meeting report: BDS conference in Leeds, September 2012
Authors: Butterworth Jonathan D.
Published: February 2013

The 17th biennial conference of the British Dam Society (BDS) took place at the University of Leeds, with tours to several of Yorkshire Water's reservoirs, and the conference banquet in the Royal Armouries Hall.
Technical visit: Pre-conference tour to Butterley reservoir
Authors: Goff Craig
Published: February 2013

The pre-conference tour for the British Dam Society conference in Leeds in September 2012 visited Yorkshire Water's Butterley reservoir and the Canal and River Trust's Stanedge tunnel.