bluuebunny/crossref_metadata_2025_split huggingface dataset:
ncRNAppi—a tool for identifying disease-related miRNA and siRNA targeting pathways
Authors: Ng Ka-Lok , Liu Hsueh-Chuan , Lee Shan-Chih 
Published: October 2009

Abstract
Summary: Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein–protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both. The same approach is also applied to siRNA data. This database provides two types of searches: (i) tissue- and (ii) disease-specific miRNA (or siRNA) targeting pathways. The search allows one to identify tissue- or disease-specific miRNA (or siRNA) target gene's PPI partners two levels beyond.
Availability: The release version 1.0 is a freely accessible database available at http://ncrnappi.cs.nthu.edu.tw and http://ncRNAppi.bioinfo.asia.edu.tw/
Contact: ppiddi@gmail.com; o2snow@gmail.com
HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R
Authors: Dvinge Heidi , Bertone Paul 
Published: October 2009

Abstract
Motivation: Quantitative real-time polymerase chain reaction (qPCR) is routinely used for RNA expression profiling, validation of microarray hybridization data and clinical diagnostic assays. Although numerous statistical tools are available in the public domain for the analysis of microarray experiments, this is not the case for qPCR. Proprietary software is typically provided by instrument manufacturers, but these solutions are not amenable to the tandem analysis of multiple assays. This is problematic when an experiment involves more than a simple comparison between a control and treatment sample, or when many qPCR datasets are to be analyzed in a high-throughput facility.
Results: We have developed HTqPCR, a package for the R statistical computing environment, to enable the processing and analysis of qPCR data across multiple conditions and replicates.
Availability: HTqPCR and user documentation can be obtained through Bioconductor or at http://www.ebi.ac.uk/bertone/software.
Contact: bertone@ebi.ac.uk
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
Authors: Degner Jacob F. , Marioni John C. , Pai Athma A. , Pickrell Joseph K. , Nkadori Everlyne , Gilad Yoav , Pritchard Jonathan K. 
Published: October 2009

Abstract
Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).
Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data.
Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156.
Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of Prosopis species invasion in Kenya using geographical information system techniques
Authors: Muturi Gabriel M. , Mohren Godefridus M. J. , Kimani Jacob N. 
Published: October 2009

AbstractTree species from Prosopis genus were widely planted for rehabilitation of degraded drylands of Kenya. However, they have invaded riverine ecosystems where they cause negative socio‐economic and ecological impacts. GIS was used to estimate the reverine area threatened by Prosopis invasion in Kenya. Landsat satellite images, field surveys and past studies were also used to assess the resulting potential ecological impacts in the Turkwel ecosystem in Kenya. The study revealed that 3.0 to 27.7 million hectares are threatened by invasion, based on documented riverine forests width of 0.5–3 km. Image analysis showed that 34% of the sites under positive change were invaded, with most invasions occurring in natural forests and abandoned farms. Prosopis had overall occurrence of 39% in all the sampled sites in 2007, in contrast to 0% in 1990 that was reported in an earlier study. In these areas, Acacia tortilis occurrence dropped from 81% in 1990 to 43% in 2007, suggesting that Prosopis could be displacing it. Utilization of Prosopis for fodder, fuel wood and pods for animal feeds is recommended as a management tool to reverse the trend. The methods used in this study are also recommended for invasion prediction and management in other similar ecosystems.
Indications of higher diversity and abundance of small rodents in human‐influenced Sudanian savannah than in the Niokolo Koba National Park (Senegal)
Authors: Konečný Adam , Koubek Petr , Bryja Josef 
Published: October 2009

AbstractExpansion of human activities in the Sudanian savannah is changing natural habitats together with their animal communities. The abundance and diversity of small mammal communities were investigated in human‐influenced savannahs in close proximity to Niokolo Koba National Park (NKNP) in south‐eastern Senegal and compared with those from NKNP. Two localities were sampled in natural and two in human‐influenced areas during two dry and two rainy seasons. Total sampling effort was 5400 trap‐nights. Ninety‐eight individuals of eleven species were captured outside NKNP, while only 28 individuals of five rodent species were caught inside the park (all of which were found also outside NKNP). The most abundant species outside NKNP was Mastomys erythroleucus, while inside NKNP it was Praomys daltoni. Both relative abundance and diversity were significantly higher in human‐influenced landscape than in natural savannahs of NKNP. The difference in species richness may be linked with lower population densities of certain species in NKNP and the effect of traditional agriculture, which may support the presence of species typical for deforested landscape. Furthermore, food availability, and predator abundances are discussed as possible reasons for the higher rodent abundances outside NKNP.
Range expansion of the globally Vulnerable Karamoja apalis Apalis karamojae in the Serengeti ecosystem
Authors: Shaw Philip , Sinclair A.R.E. , Metzger Kristine , Nkwabi Ally , Mduma Simon A.R. , Baker Neil 
Published: October 2009

AbstractThe underlying causes of change in geographic range size are less well understood in African birds than in north temperate species. Here, we examine factors associated with range expansion in the Karamoja apalis (Apalis karamojae), a globally Vulnerable warbler confined to north‐east Uganda, north‐central Tanzania and southern Kenya. In Tanzania, it was originally known only from the Wembere Steppe, but since 1993 (and possibly as early as 1983) has extended its range into the Serengeti ecosystem, c. 140 km to the north, reaching southern Kenya by 2004. Changes in the warbler’s range within the Serengeti have broadly reflected a cyclical change in the density of its main habitat, Acacia drepanolobium woodland, which was low in the 1970s, high during the 1980s and 1990s, and declined in the early 2000s. Karamoja apalis records in the Serengeti showed a 5 year time lag behind A. drepanolobium density, which was in turn negatively correlated with the area of grassland burnt 10 years earlier. Previous studies in the Serengeti have also linked Acacia regeneration to changes in grazing pressure, as increasing wildebeest (Connochaetes taurinus) numbers have reduced the volume of combustible material present, and hence the frequency of damaging ‘hot burns’. We conclude that this globally threatened warbler appears to have benefited from changes in ungulate populations in the Serengeti, which have influenced burning intensity and hence tree regeneration. The warbler’s range now appears to be declining, however, following a recent reduction in the density and annual survival of A. drepanolobium in the northern Serengeti.
Density dependence and population dynamics of black rhinos (Diceros bicornis michaeli) in Kenya’s rhino sanctuaries
Authors: Okita‐Ouma Benson , Amin Rajan , Van Langevelde Frank , Leader‐Williams Nigel 
Published: October 2009

AbstractDensity‐dependent feedback mechanisms provide insights into the population dynamics and interactions of large herbivores with their ecosystem. Sex ratio also has particularly important implications for growth rates of many large mammal populations through its influence on reproductive potential. Therefore, the interrelationships between density‐dependent factors, comprising density, sex ratio and underlying growth rates (r) were examined for the Eastern black rhino (Diceros bicornis michaeli) living in three rhino sanctuaries in Kenya using four population models. The exponential and logistic models gave similar results and the former were accepted because they better portrayed the actual situation on the ground. Sex ratios in all sanctuary populations were positively correlated withrbut interpreted with realization of other factors also affectingr. We caution that the results of population models should be interpreted alongside ground‐truthed observations. We recommend that future translocation strategies should take into account sex and age structures of the donor population, while future studies of density dependence should take into account both biotic and abiotic factors.
Habitat selection by blue swallowsHirundo atrocaerulea Sundevall, 1850 breeding in South Africa and its implications for conservation
Authors: Evans Steven W. , Bouwman Henk 
Published: October 2009

AbstractThis study investigated the utilization of mist‐belt grassland habitat by the threatened blue swallow and was conducted over three successive breeding seasons in the Blue Swallow Natural Heritage Site at Kaapsehoop, Mpumalanga, South Africa. Blue swallows significantly preferred wetlands over grasslands for foraging. Sufficient foraging habitat must be within a 1.5 km radius from an active nest site. The minimum size of a pair of blue swallows home range should be 333 ha, consisting at a minimum of grasslands (243 ha or 73%) and wetlands (90 ha or 27%). In order to conserve this threatened species, habitat transformation should not take place within a minimum radius of 1.5 km of any blue swallow nest. Due to the critical dependence of the blue swallow on wetland habitat for foraging, any development outside the 1.5 km radius that would affect hydrology and water quality within this range would need to be considered, and any adverse effect mitigated. Rehabilitation of areas to a grassland/wetland mosaic would rather quickly support foraging, and eventually breeding. Although a better understanding of the dynamics between wetlands and adjacent grasslands regarding blue swallow habitat requirements is needed, action can already be taken, based on our results.
The concordance between serum anti‐Mullerian hormone and testosterone concentrations depends on duration of hCG stimulation in boys undergoing investigation of gonadal function
Authors: Ahmed S. F. , Keir L. , McNeilly J. , Galloway P. , O’Toole S. , Wallace A. M. 
Published: October 2009

SummaryBackground  In boys undergoing investigation of gonadal function, the relationship between a single measurement of serum anti‐Mullerian hormone (AMH) and hCG stimulated serum testosterone is unclear.Aim  The aim of the study was to assess concordance between serum AMH and testosterone concentrations following hCG stimulation of two different durations.Methods  Samples from 284 children (M : F, 154 : 130) with a median age of 8 years (10th, 90th centiles, 0·25, 14) were used to establish an AMH reference range. Clinical data were reviewed in boys undergoing investigation of gonadal function and who had an AMH measurement and a hCG stimulated (3‐day or 3‐week) (n = 26) testosterone. Of these 26 boys, 11 had combined genital anomalies, whereas the rest had conditions such as isolated hypospadias, undescended testes or microphallus. Normal testosterone response to hCG stimulation was defined as a level greater than 3·5 nmol at day 4 and 9·5 nmol/l at day 22.Results  In the reference group, the 5th centile AMH for boys below 1 year was 215 pmol/l and between 1 and 8 years 180 pmol/l. The 95th centile for girls for these respective age groups was 30 pmol/l and 25 pmol/l. In those cases where serum testosterone concentrations were available at day 1, day 4 and day 22 of the 3 week‐hCG test, five cases had a normal serum testosterone at day 4 and three cases only showed such a response by day 22. In those where serum AMH was less than 180 pmol/l, a poor testosterone response of less than 3·5 nmol was observed in approximately seven of eight (88%) cases with a 3‐day hCG stimulation test or the 3‐week test. An AMH of greater than 180 pmol/l was associated with a normal testosterone response at day 4 in 10 out of 15 (67%) cases and at day 22 in eight of 11 (73%) cases. However, a low serum testosterone concentration of less than 3·5 nmol after the 3‐day hCG test was only associated with a likelihood of a low AMH in three of eight (37%) cases. With the 3‐week hCG test, a low day 22 testosterone of 9·5 mmol/l or less was associated with a low AMH of 180 pmol/l or less in four of seven (57%) cases.Conclusion  In boys undergoing investigation of gonadal function, the concordance between AMH and testosterone is better at day 22 than day 4. A normal AMH may provide useful information on overall testicular function but does not exclude the need for an hCG stimulation test.
MMP/ TIMP balance is modulated in vitro by 15dPGJ2 in fetuses and placentas from diabetic rats
Authors: Pustovrh M. C. , Capobianco E. , Martínez N. , Higa R. , White V. , Jawerbaum A. 
Published: October 2009

AbstractBackground  Maternal diabetes is associated with morphological placental abnormalities and foeto‐placental impairments. These alterations are linked with a dysregulation of the activity of matrix metalloproteinases (MMPs). We investigated the action of 15deoxyΔ12,14 prostaglandin J2 (15dPGJ2), a natural ligand of the peroxisome proliferator activated receptor (PPAR) γ, on MMP‐2 and MMP‐9 activities and tissue inhibitors of matrix metalloproteinases (TIMP) levels in foetuses and placentas from diabetic rats.Materials and methods  Diabetes was induced in rat neonates by a single streptozotocin administration (90 mg kg−1 s.c.). At 13·5 days of gestation, foetal and placental homogenates were prepared for the determination of PPARγ levels (western blot) and 15dPGJ2 concentration (enzyme‐immunoassay), whereas the in vitro effect of 15dPGJ2 (2 μM) was evaluated on placental and foetal MMPs and TIMP activities (zymography and reverse zymography), nitrate/nitrite concentrations (Griess method) and thiobarbituric acid reactive substances (TBARS).Results  PPARγ was increased while 15dPGJ2 was decreased in placentas and foetuses from diabetic rats. 15dPGJ2 additions were able to reduce the high activities of MMP‐2 and MMP‐9 present in diabetic placental tissues. 15dPGJ2 additions reduced MMP‐2 activity in control and diabetic foetuses. TIMP‐3 levels were decreased in diabetic placentas and 15dPGJ2 was able to enhance them to control values. Nitrates/nitrites and TBARS, metabolites of MMPs activators, were increased in the diabetic placenta and reduced by 15dPGJ2.Conclusions  This study demonstrates that 15dPGJ2 is a potent modulator of the balance between MMP activities and TIMP levels, which is needed in the correct formation and function of the placenta and foetal organs.
High plasma levels of the soluble receptor for advanced glycation endproducts in patients with symptomatic carotid atherosclerosis
Authors: Basta G. , Castagnini M. , Del Turco S. , Epistolato M. C. , Righini P. , Sangiorgi G. M. , De Caterina R. , Tanganelli P. 
Published: October 2009

AbstractBackground  Advanced glycation endproducts (AGEs), particularly carboxymethyl(lysine)‐adducts (CML), exert part of their cellular effects by binding to a receptor, named receptor for AGEs (RAGE). The soluble form of this receptor (sRAGE) has been shown to have an athero‐protective role. We hypothesized the existence of a relationship between the AGE–RAGE axis and the occurrence of symptoms related to carotid atherosclerosis in nondiabetic conditions.Materials and methods  We evaluated plasma levels of CML and sRAGE (by ELISA), and tissue levels (tAGEs and tRAGE, semiquantitatively, by immunohistochemistry) in endarterectomy carotid plaque tissue in 29 nondiabetic patients. At the time of surgery, 10 patients were asymptomatic and 19 were symptomatic.Results  Plasma levels of sRAGE were higher in symptomatic patients than in asymptomatic patients [median (interquartile range): 676 (394–858) pg mL−1 vs. 347 (284–479) pg mL−1, P = 0·009]. In symptomatic patients, plasma levels of sRAGE correlated positively with CML (r = 0·60, P < 0·01), C‐reactive protein (CRP) (r = 0·618, P < 0·01) and fibrinogen (r = 0·522, P<0·005), while in asymptomatic patients, no correlation was observed. Although tissue and plasma levels of AGEs and RAGE did not correlate between each other, tAGEs and tRAGE were also positively correlated only in symptomatic patients (χ2 = 8·93, P = 0·003).Conclusions  Plasma levels of sRAGE are higher in symptomatic than asymptomatic carotid atherosclerosis. Higher levels of sRAGE in symptomatic patients may be markers of a higher degree of vascular inflammation in such patients.
Discriminant analysis of biogeochemical indicators of nutrient enrichment in a Florida wetland
Authors: Corstanje R. , Portier K. M. , Reddy K. R. 
Published: October 2009

SummaryEutrophication of wetlands can lead to extensive changes in the ecosystem structures. The water‐borne nutrient inputs change the soil biogeochemistry prior to structural changes in the ecosystem. The objective of this study was to determine the biogeochemical variables that are strongly associated with eutrophication. We postulated that in wetlands the soil chemical properties function as driving factors (primary indicators) to which the indicators of the soil biological processes respond (secondary indicators). The alternative hypothesis is that the soil biology shows a more rapid response to an increase in nutrient availability from the water column, with the soil chemical properties responding more slowly. This study employed an extensive database from three sites covering a nutrient enrichment gradient in the Everglades, Florida (enriched, intermediate and unenriched). This database contained 28 biogeochemical variables, which we divided into two sets: a set of chemical descriptors and a set of microbiological descriptors. We applied a combination of stepwise discrimination and canonical discrimination (“stepwise canonical discrimination”) to determine differences between the sites. For the group of chemical descriptors, the variables selected were total nitrogen (N), total carbon (C), organic C, labile organic phosphorus (P), fulvic‐, humic‐, labile inorganic‐ and residual P, ammonia and aluminium. We then applied the discriminant analysis using the microbiological descriptors. The variables selected were mineralizable P and N, microbial P and phosphatase activity. Discrimination using chemical variables was more successful than that based on the microbiological variables. Subsequent bootstrap cross‐validation indicated that the microbiological variables seemed to have a more integrative function with associated stability and robustness. We suggest that for this system the canonical variates themselves may be viewed as indicator variables of enrichment, and that the constituent variables may be important as indicators in other P‐limited marsh systems at risk of eutrophication.
Silage quality whenMoringa oleiferais ensiled in mixtures with Elephant grass, sugar cane and molasses
Authors: Mendieta‐Araica B. , Spörndly E. , Reyes‐Sánchez N. , Norell L. , Spörndly R. 
Published: October 2009

AbstractFourteen different silages were prepared using mixtures of Moringa (Moringa oleifera), Elephant grass (Pennisetum purpureumcv Taiwan) or sugar cane (Saccharum officinarum). Molasses from sugar cane was used in the amounts of either 10 or 50 g kg−1fresh matter (FM) in treatments without sugar cane. A completely randomized design with three replicates of each treatment was used. The silages were prepared in 1800 mL micro silos and opened after 120 d. The presence of Moringa and Elephant grass in the silage changed the pH by −0·8 and +0·7, respectively (P < 0·001), indicating a favourable effect of Moringa on silage pH. Overall differences were found among treatments for dry matter content, crude protein and acetic acid concentrations, weight loss, CO2production and silage pH after spoilage (P < 0·001). Weight loss was proportionately 0·034 and 0·014 in silages with and without sugar cane respectively (P < 0·001). Overall, differences (P < 0·05) were also found for neutral‐detergent fibre and lactic acid concentrations, lactic acid bacteria counts, clostridial counts and time to spoilage of the silages. Treatments containing Moringa had higher lactic acid concentrations (+16 g kg−1DM;P < 0·01) compared to treatments without but the presence of Moringa decreased time to spoilage by 67 h (P < 0·05). No differences were found in propionic acid concentration or fungal growth of the silages. It is concluded that Moringa can be used as a component of high quality silages which also contain high concentrations of crude protein.