bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hippocampus, amygdala and global brain changes 10 years after childhood traumatic brain injury
Authors: Beauchamp M.H. , Ditchfield M. , Maller J.J. , Catroppa C. , Godfrey C. , Rosenfeld J.V. , Kean M.J. , Anderson V.A. 
Published: December 2010

AbstractTraumatic brain injury (TBI) in children results in damage to the developing brain, particularly in severely injured individuals. Little is known, however, of the long‐term structural aspects of the brain following childhood TBI. This study investigated the integrity of the brain 10 years post‐TBI using magnetic resonance imaging volumetrics in a sample of 49 participants with mild, moderate and severe TBI, evaluated against a normative sample of 20 individuals from a pediatric database with comparable age and gender distribution. Structural integrity was investigated in gray and white matter, and by manually segmenting two regions of interest (hippocampus, amygdala), potentially vulnerable to the effects of childhood TBI. The results indicate that more severe injuries caused a reduction in gray and white brain matter, while all TBI severity levels resulted in increased volumes of cerebrospinal fluid and smaller hippocampal volumes. In addition, enlarged amygdala volumes were detected in severely injured patients compared to their mild and moderate counterparts, suggesting that childhood TBI may disrupt the development of certain brain regions through diffuse pathological changes. The findings highlight the lasting impact of childhood TBI on the brain and the importance of monitoring brain structure in the long‐term after early injury.
Reduction of first-year survival threatens the viability of the Mariana CrowCorvus kubaryipopulation on Rota, CNMI
Authors: HA JAMES C. , BUTLER ALYSSA , ROBINETTE HA RENEE 
Published: December 2010

SummaryThe Mariana CrowCorvus kubaryiis a species of forest crow originally found only on the adjacent islands of Guam and Rota in the Mariana Islands of the western Pacific Ocean. Rapid and continuing declines led to it being listed by IUCN as "Critically Endangered" in 2008. Using 97 birds marked and resighted over the course of a 21 year period, we showed there was a rapid decline in first-year (fledgling to one year old) survival from 0.7 to 0.4 between 1990 and 2010, representing a doubling in mortality, and a smaller reduction in adult survival from 0.86 to 0.82 over the same period. A population model based on Leslie matrices incorporated the effects of catastrophic events, such as typhoons and human nest removal for captive breeding. All simulations predicted a precipitous decline in future populations and the inclusion of nest removals only shortened the life of the wild population by a few years. Identifying the underlying processes behind the decline in survival is the key research priority and, given the inevitable likelihood of a continuing rapid decline, conservation action should focus on securing the future of the species through captive breeding or captive rearing of wild-born chicks and ensuring that an adaptive management conservation programme is focused on countering the factors (e.g. predation) that are currently thought to impact first-year survival and productivity. Future research may identify other causes behind the Mariana Crow's decline and the conservation programme should be flexible enough to adapt to changing needs.
Where is the ‘Jennifer Aniston neuron’?
Authors: Aur Dorian 
Published: December 2010

AbstractIt is generally believed that spike timing features (firing rate, ISI) are the main characteristics that can be related to neural code. Contrary to this common belief, spike directivity, a new measure that quantifies transient charge density dynamics within action potentials (APs) provides better results in discriminating different categories of visual object recognition. Specifically, intracranial recordings from medial temporal lobe (MTL) of epileptic patients have been analyzed using firing rate, interspike intervals and spike directivity. A comparative statistical analysis of the same spikes from four selected neurons shows that electrical micro-mapped features in neurons display higher separability to input images compared to spike timing features. If the observation vector include data from all 4 neurons then the comparative analysis shows a highly significant separation between categories for spike directivity (p=0.0023) and does not display separability for ISI (p=0.3768) and firing rate (p=0.5492). The presence of electrical micro-maps within APs suggests the existence of an intrinsic “neural code" where information regarding input images is electrically written/coded and read/decoded during AP propagation in the neuron. The occurrence of electrical micro-maps within APs reflects information communication and computation in analyzed neuron within a millisecond-level time domain of AP occurrence. This existence of a “lower level” of coding where information is processed within neurons raises questions regarding the richness and reliability of models that constrain neural code to spike timing features. Additionally, this phenomenon that occurs within APs may provide a step forward in understanding the fundamental gap between molecular description, information processing and neuronal function. Importantly, this paper confirms a new paradigm regarding neural code where information processing, computation and memory formation in the brain can be explained in terms of dynamics and interaction of electric charges.
Argudas: arguing with gene expression information
Authors: McLeod Kenneth 
Published: December 2010

AbstractIn situ hybridization gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information are often both incomplete and inconsistent. This presentation examines a system, Argudas, designed to help tackle these issues. Argudas is an evolution of an existing system, and so that system is reviewed as a means of both explaining and justifying the behavior of Argudas. Throughout the discussion of Argudas a number of issues will be raised including the appropriateness of argumentation in biology and the challenges faced when integrating apparently similar online biological databases.
Rapid landscape transformation in South Island, New Zealand, following initial Polynesian settlement
Authors: McWethy David B. , Whitlock Cathy , Wilmshurst Janet M. , McGlone Matt S. , Fromont Mairie , Li Xun , Dieffenbacher-Krall Ann , Hobbs William O. , Fritz Sherilyn C. , Cook Edward R. 
Published: December 2010

Humans have altered natural patterns of fire for millennia, but the impact of human-set fires is thought to have been slight in wet closed-canopy forests. In the South Island of New Zealand, Polynesians (Māori), who arrived 700–800 calibrated years (cal y) ago, and then Europeans, who settled ∼150 cal y ago, used fire as a tool for forest clearance, but the structure and environmental consequences of these fires are poorly understood. High-resolution charcoal and pollen records from 16 lakes were analyzed to reconstruct the fire and vegetation history of the last 1,000 y. Diatom, chironomid, and element concentration data were examined to identify disturbance-related limnobiotic and biogeochemical changes within burned watersheds. At most sites, several high-severity fire events occurred within the first two centuries of Māori arrival and were often accompanied by a transformation in vegetation, slope stability, and lake chemistry. Proxies of past climate suggest that human activity alone, rather than unusually dry or warm conditions, was responsible for this increased fire activity. The transformation of scrub to grassland by Europeans in the mid-19th century triggered further, sometimes severe, watershed change, through additional fires, erosion, and the introduction of nonnative plant species. Alteration of natural disturbance regimes had lasting impacts, primarily because native forests had little or no previous history of fire and little resilience to the severity of burning. Anthropogenic burning in New Zealand highlights the vulnerability of closed-canopy forests to novel disturbance regimes and suggests that similar settings may be less resilient to climate-induced changes in the future.
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
Authors: Gidskehaug Lars , Kent Matthew , Hayes Ben J. , Lien Sigbjørn 
Published: December 2010

Abstract
Motivation: Due to a genome duplication event in the recent history of salmonids, modern Atlantic salmon (Salmo salar) have a mosaic genome with roughly one-third being tetraploid. This is a complicating factor in genotyping and genetic mapping since polymorphisms within duplicated regions (multisite variants; MSVs) are challenging to call and to assign to the correct paralogue. Standard genotyping software offered by Illumina has not been written to interpret MSVs and will either fail or miscall these polymorphisms. For the purpose of mapping, linkage or association studies in non-diploid species, there is a pressing need for software that includes analysis of MSVs in addition to regular single nucleotide polymorphism (SNP) markers.
Results: A software package is presented for the analysis of partially tetraploid genomes genotyped using Illumina Infinium BeadArrays (Illumina Inc.) that includes pre-processing, clustering, plotting and validation routines. More than 3000 salmon from an aquacultural strain in Norway, distributed among 266 full-sib families, were genotyped on a 15K BeadArray including both SNP- and MSV-markers. A total of 4268 SNPs and 1471 MSVs were identified, with average call accuracies of 0.97 and 0.86, respectively. A total of 150 MSVs polymorphic in both paralogs were dissected and mapped to their respective chromosomes, yielding insights about the salmon genome reversion to diploidy and improving marker genome coverage. Several retained homologies were found and are reported.
Availability and implementation: R-package beadarrayMSV freely available on the web at http://cran.r-project.org/
Contact: lg@camo.no
Supplementary information: Supplementary data are available at Bioinformatics online.
A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays
Authors: Feng Feng , Sales Ana Paula , Kepler Thomas B. 
Published: December 2010

Abstract
Motivation: Immunoassays are primary diagnostic and research tools throughout the medical and life sciences. The common approach to the processing of immunoassay data involves estimation of the calibration curve followed by inversion of the calibration function to read off the concentration estimates. This approach, however, does not lend itself easily to acceptable estimation of confidence limits on the estimated concentrations. Such estimates must account for uncertainty in the calibration curve as well as uncertainty in the target measurement. Even point estimates can be problematic: because of the non-linearity of calibration curves and error heteroscedasticity, the neglect of components of measurement error can produce significant bias.
Methods: We have developed a Bayesian approach for the estimation of concentrations from immunoassay data that treats the propagation of measurement error appropriately. The method uses Markov Chain Monte Carlo (MCMC) to approximate the posterior distribution of the target concentrations and numerically compute the relevant summary statistics. Software implementing the method is freely available for public use.
Results: The new method was tested on both simulated and experimental datasets with different measurement error models. The method outperformed the common inverse method on samples with large measurement errors. Even in cases with extreme measurements where the common inverse method failed, our approach always generated reasonable estimates for the target concentrations.
Availability: Project name: Baecs; Project home page: www.computationalimmunology.org/utilities/; Operating systems: Linux, MacOS X and Windows; Programming language: C++; License: Free for Academic Use.
Contact: feng.feng@duke.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Serial changes in high‐sensitive troponin I predict outcome in patients with decompensated heart failure
Authors: Xue Yang , Clopton Paul , Peacock William F. , Maisel Alan S. 
Published: December 2010

AimsThe aim of this study was to evaluate the prognostic utility of small troponin I (TnI) elevations, serial TnI measurements, and the combination of TnI and brain natriuretic peptide (BNP) in patients with decompensated heart failure (HF).Methods and resultsOne hundred and forty‐four patients with acute HF were followed from admission to 90 days post‐discharge. Primary endpoints were all cause mortality and HF‐related readmission. Troponin I and BNP levels were checked on admission, discharge, and up to four consecutive days during hospitalization. A discharge TnI cut‐off of 23.25 ng/L and discharge BNP cut‐off of 360 ng/L were determined by receiver operator characteristic (ROC). Troponin I above 23.25 ng/L is associated with increased risk for mortality and readmission (P = 0.003). Comparing with TnI quartile 1, TnI quartiles 2–4 had increased mortality and readmission, P = 0.019, P = 0.007, P = 0.014, respectively. Compared with patients with low TnI+low BNP, increased mortality and readmission were seen in patients with high TnI+high BNP (P = 0.007), high TnI+low BNP (P = 0.015), and low TnI+high BNP (P = 0.042). Patients with increasing TnI during treatment had increased mortality compared with patients with stable or decreasing TnI (P = 0.047). In multivariate analysis, TnI reached statistical significance (P = 0.009), while BNP did not.ConclusionThis study demonstrates that very small TnI elevations and BNP elevations are associated with increased 90‐day mortality and readmission. When compared by ROC and multivariate analysis, TnI is as good a predictor of mortality and readmission as BNP if not slightly better. Patients with increasing TnI during hospitalization for acute HF had increased risk for 90‐day mortality.
First Report of False Rust Caused by Synchytrium minutum on Kudzu in Korea
Authors: Yun H. Y. , Kim Y. H. , James T. Y. 
Published: December 2010

Kudzu (Pueraria montana var. lobata (Willd.) Maesen & S. Almeida) is a weedy, fabaceous vine that is native to and widely distributed in Asia where it is used for various medicinal purposes such as treating convulsions and fever (2). In the United States, especially the southeastern states, kudzu has become a problematic invasive species that overgrows nearly every substrate on which it occurs. Thus, biological control strategies for controlling this vine are of great interest (4). From October to November 2004, a disease of kudzu was observed in Gwangju and Pyeongtaek in Gyeonggi Province, Korea. The disease appeared on leaves and stems as numerous, discrete, small galls, which enlarged, becoming yellowish orange and eventually erupting into orange, pulverulent sori. Galls were scattered or gregarious, amphigenous, predominately hypophyllous, and sometimes formed along veins as well as on petioles and stems. Sori that formed from galls were solitary but sometimes became confluent, 0.1 to 1 mm in diameter, globose to subglobose, and orange to dark orange; walls were hyaline and thin. Sporangia were copious in sori, typically polyhedral due to compression or globose, 16 to 32 μm in diameter, with smooth, hyaline walls and orange contents. Zoospores were not observed during several failed attempts to germinate sporangia. On the basis of morphological descriptions and keys (3), the fungus was identified as Synchytrium minutum (Pat.) Gäum. (Chytridiomycota), the only species of Synchytrium known to occur on Pueraria (1,3). Comparison with specimens from China and New Guinea (BPI 794733 and BPI 1109528) confirmed this identification. Portions of the nLSU and nSSU rDNA from one of the two Korean specimens deposited as voucher material in the U.S. National Fungus Collections (BPI 880898 and BPI 880899) were sequenced (GenBank Accession Nos. HQ324138 and HQ324139), and a subsequent BLAST search against GenBank confirmed placement in the genus Synchytrium with 95% similarity to S. decipiens. S. minutum is widespread in Asia and Oceania and also has been reported from California (1,3). To our knowledge, this is the first report of S. minutum in Korea (1) and is noteworthy to those interested in biological control of kudzu because S. minutum may have potential in this regard. References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , September, 2010. (2) H. S. Jung. M.S. thesis. Seoul National University, Seoul, Korea, 1997. (3) J. S. Karling. Synchytrium. Academic Press Inc., New York, NY, 1964. (4) M. A. Weaver et al. Biol. Control 50:150, 2009.
Cucurbit yellow stunting disorder virus Detected in Pigweed in Florida
Authors: Webster C. G. , Kousik C. S. , Roberts P. D. , Rosskopf E. N. , Turechek W. W. , Adkins S. 
Published: December 2010

Pigweeds (genus Amaranthus) are problematic weeds in crop production throughout the world and are responsible for significant yield losses in many crops (2). Members of this genus can produce hundreds of thousands of seeds per plant and are also capable of supporting populations of important crop pathogens including viruses, nematodes, fungi, and oomycetes. Thirty-one pigweed samples (tentatively identified as Amaranthus lividus L. based on leaf notch and growth habit) were collected in November and December of 2009 from a watermelon field near Immokalee, FL, previously found to contain watermelon plants infected with three whitefly-transmitted viruses: Cucurbit yellow stunting disorder virus (CYSDV), Cucurbit leaf crumple virus (CuLCrV), and Squash vein yellowing virus (SqVYV). Although no obvious virus symptoms were observed on any of the pigweed plants, whiteflies (Bemisia tabaci), a known vector of CYSDV, CuLCrV, and SqVYV, were observed on leaves. Consequently, replica tissue blots were made from all pigweed samples and tested independently by tissue blot nucleic acid hybridization assay for CYSDV, CuLCrV, or SqVYV (3). Tissue blots indicated CYSDV infection in six pigweed samples. Neither CuLCrV nor SqVYV was detected. Three of the tissue blot-positive pigweed samples were further tested by reverse transcription (RT)-PCR amplification from total RNA (extracted from leaf tissue with TRIzol Reagent [Invitrogen, Carlsbad, CA]) with HSP70 and coat protein (CP) gene primers (1). HSP70 and CP gene RT-PCR products of the expected sizes (175 and 707 nt, respectively) were amplified, sequenced, and found to be 100% identical for all three pigweed samples. The partial HSP70 gene sequence from pigweed shared 98.3 to 100% nucleotide identity with CYSDV isolates from Arizona, California, and Spain (GenBank Accession Nos. FJ492808, EU596530, and NC_004810, respectively). The partial CP gene sequence from pigweed shared 88.8 to 100% nucleotide identity with CYSDV isolates from Arizona, Saudi Arabia, Texas, and Spain (GenBank Accession Nos. EF210558, AF312811, AF312806, and AF312808, respectively). To our knowledge, this is the first report of CYSDV infection of pigweed in Florida. Infection of redroot pigweed (A. retroflexus) was recently reported in California (4). These results collectively indicate that control of noncucurbit weeds may be important for effective management of CYSDV in cucurbit crops. References: (1) S. Adkins et al. Online publication. doi:10.1094/PHP-2009-1118-01-BR. Plant Health Progress, 2009. (2) L. Holm et al. World's Weeds: Natural Histories and Distributions. John Wiley and Sons, Inc. New York, NY, 1997. (3) W. W. Turechek et al. Phytopathology 100:1194, 2010. (4) W. M. Wintermantel et al. Plant Dis. 93:685, 2009.
Function of the usher N‐terminus in catalysing pilus assembly
Authors: Henderson Nadine S. , Ng Tony W. , Talukder Iehab , Thanassi David G. 
Published: December 2010

SummaryThe chaperone/usher (CU) pathway is a conserved bacterial secretion system that assembles adhesive fibres termed pili or fimbriae. Pilus biogenesis by the CU pathway requires a periplasmic chaperone and an outer membrane (OM) assembly platform termed the usher. The usher catalyses formation of subunit–subunit interactions to promote polymerization of the pilus fibre and provides the channel for fibre secretion. The mechanism by which the usher catalyses pilus assembly is not known. Using the P and type 1 pilus systems of uropathogenic Escherichia coli, we show that a conserved N‐terminal disulphide region of the PapC and FimD ushers, as well as residue F4 of FimD, are required for the catalytic activity of the ushers. PapC disulphide loop mutants were able to bind PapDG chaperone–subunit complexes, but did not assemble PapG into pilus fibres. FimD disulphide loop and F4 mutants were able to bind chaperone–subunit complexes and initiate assembly of pilus fibres, but were defective for extending the pilus fibres, as measured using in vivo co‐purification and in vitro pilus polymerization assays. These results suggest that the catalytic activity of PapC is required to initiate pilus biogenesis, whereas the catalytic activity of FimD is required for extension of the pilus fibre.
Influence of irradiation on in vitro red‐blood‐cell (RBC) storage variables of leucoreduced RBCs in additive solution PAGGS‐M
Authors: Hauck B. , Oremek D. , Zimmermann R. , Ruppel R. , Troester B. , Eckstein R. 
Published: December 2010

Background  The effect of gamma irradiation on leucoreduced red‐blood‐cells (RBCs) stored in an additive solution (AS) containing phosphate, adenine, glucose, guanosine, saline and mannitol (PAGGS‐M) has not yet been studied, and there are different recommendations about storage time of leucoreduced RBCs after irradiation.Study Design and Methods  We studied 63 leucoreduced RBC units. All RBCs were stored in AS PAGGS‐M and leucoreduced on the collection day. Twenty‐one components were irradiated on Day +14 with 30 Gy and 22 served as non‐irradiated controls. Samples were drawn and analysed from these 43 units on Day +7, +14, +21, +28, +35, +42 and +49 from the collection day. From 20 units, no samples were taken earlier than on Day +49. Of these, 10 components had been irradiated on Day +14 with 30 Gy and 10 served as non‐irradiated controls.Results  Gamma irradiation induced an enhanced in vitro haemolysis rate in the irradiated components. One of the irradiated units showed a haemolysis rate over the recommended limit of 0·8% on Day +42 and four on Day +49. The leakage of potassium ions from irradiated RBCs started to increase faster than that of unirradiated RBCs from the day of irradiation. Lactate dehydrogenase levels increased faster in irradiated units 3 weeks after irradiation. We showed that taking samples weekly does not affect the final result.Conclusions  Our findings show that the European recommendations should not be changed in regard to the limitation of the storageability after irradiation of leucoreduced RBCs. The damage after irradiation and storage cannot be prevented by using the high‐quality AS PAGGS‐M.