bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility and effectiveness of supplementation with locally available foods in prevention of child malnutrition in Kenya
Authors: Tomedi Angelo , Rohan-Minjares Felisha , McCalmont Kate , Ashton Rebecca , Opiyo Rose , Mwanthi Mutuku 
Published: September 2011

AbstractObjectiveTo establish the operational feasibility and effectiveness of using locally available foods to prevent malnutrition and improve child growth in Kenyan children.DesignQuasi-experimental design with an intervention group of children in all villages in one region and a non-intervention group of children in all villages in an adjacent region. The intervention was the distribution of a monthly food ration for the index child, a separate family ration, and group education on appropriate complementary feeding and hygiene.SettingRural villages in the arid lands of eastern Kenya with a high prevalence of child malnutrition.SubjectsAll children in the target villages aged 6–20 months with weight-for-length Z-score (WHZ) greater than −2 at baseline.ResultsChildren in the intervention and non-intervention groups had similar baseline anthropometric measures. The caregivers in the intervention group confirmed that the intended amounts of food supplements were received and child nutrient intake improved. During the 7-month intervention period there were significant group differences in pre–post Z-score changes between the intervention and non-intervention groups for weight-for-age (0·82, P < 0·001) and weight-for-height (1·19, P < 0·001), but not for height-for-age (−0·20, P = 0·09), after adjusting for multiple covariates. Compared with the non-intervention group, the intervention group had a lower prevalence of wasting (0 % v. 8·9 %, P = 0·0002) and underweight (6·3 % v. 23·0 %, P < 0·0001). Infectious morbidity was similar in both groups.ConclusionsThe findings suggest that the distribution of locally available foods is operationally feasible and improves child weight gain and decreases acute malnutrition in Kenyan children.
An Examination of Kernite (Na2B4O6(OH)2·3H2O) Using X-Ray and Electron Spectroscopies: Quantitative Microanalysis of a Hydrated Low-Z Mineral
Authors: Meier Douglas C. , Davis Jeffrey M. , Vicenzi Edward P. 
Published: September 2011

AbstractMineral borates, the primary industrial source of boron, are found in a large variety of compositions. One such source, kernite (Na2B4O6(OH)2·3H2O), offers an array of challenges for traditional electron-probe microanalysis (EPMA)—it is hygroscopic, an electrical insulator, composed entirely of light elements, and sensitive to both low pressures and the electron beam. However, the approximate stoichiometric composition of kernite can be analyzed with careful preparation, proper selection of reference materials, and attention to the details of quantification procedures, including correction for the time dependency of the sodium X-ray signal. Moreover, a reasonable estimation of the mineral's water content can also be made by comparing the measured oxygen to the calculated stoichiometric oxygen content. X-ray diffraction, variable-pressure electron imaging, and visual inspection elucidate the structural consequences of high vacuum treatment of kernite, while Auger electron spectroscopy and X-ray photoelectron spectroscopy confirm electron beam-driven migration of sodium and oxygen out of the near-surface region (sampling depth ≈ 2 nm). These surface effects are insufficiently large to significantly affect the EPMA results (sampling depth ≈ 400 nm at 5 keV).
Neurodegeneration: Potential Causes, Prevention, and Future Treatment Options
Authors: Zhang Zhongtao 
Published: September 2011

AbstractHere I advance a hypothesis that neurodegeneration is a natural process associated with aging due to the loss of genetic redundancy following a mathematical model R(t) = R0(1-αe(βC+γI+δEt)t), where the calorie intake (C) and immune response (I) play critical roles. The early onset of neurodegenerative diseases such as Alzheimer’s disease is due to metabolic imbalance or chronic immune reactions to various infections. Therefore, the potential treatment options for neurodegenerative diseases are to modulate metabolism and immune response.
Kinetic Simulation Algorithm Ontology
Authors: Zhukova Anna , Waltemath Dagmar , Juty Nick , Laibe Camille , Le Novère Nicolas 
Published: September 2011

AbstractTo enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in conjunction with simulation descriptions, such as SED-ML, will allow simulation software to automatically choose the best algorithm available to perform a simulation. The availability of algorithm parameters, together with their type may permit the automatic generation of user-interfaces to configure simulators. To enable making queries to KiSAO programmaticaly, from simulation experiment description editors and simulation tools, a java library libKiSAO was implemented.
Retinal adaptation to spatial correlations
Authors: Simmons Kristina , Prentice Jason , Homann Jan , Tkacik Gasper , Nelson Philip , Balasubramanian Vijay 
Published: September 2011

AbstractThe classical center-surround retinal ganglion cell receptive field is thought to remove the strong spatial correlations in natural scenes, enabling efficient use of limited bandwidth. While early studies with drifting gratings reported robust surrounds (Enroth-Cugell and Robson, 1966), recent measurements with white noise reveal weak surrounds (Chichilnisky and Kalmar, 2002). This might be evidence for dynamical weakening of the retinal surround in response to decreased spatial correlations, which would be predicted by efficient coding theory. Such adaptation is reported in LGN (Lesica et al., 2007), but whether the retina also adapts to correlations is unknown.We tested for adaptation by recording simultaneously from ~40 ganglion cells on a multi-electrode array while presenting white and exponentially correlated checkerboards and strips. Measuring from ~200 cells responding to 90 minutes each of white and correlated stimuli, we were able to extract precise spatiotemporal receptive fields (STRFs). We found that a difference-of-Gaussians was not a good fit and the surround was generally displaced from the center. Thus, to assess surround strength we found the center and surround regions and the total weight on the pixels in each region. The relative surround strength was then defined as the ratio of surround weight to center weight. Surprisingly, we found that the majority of recorded cells have a stronger surround under white noise than under correlated noise (p<.05), contrary to naive expectation from theory. The conclusion was robust to different methods of extracting STRFs and persisted with checkerboard and strip stimuli.To test, without assuming a model, whether the retina decorrelates stimuli, we also measured the pairwise correlations between spike trains of simultaneously recorded neurons under three conditions: white checkerboard, exponentially correlated noise, and scale-free noise. The typical amount of pairwise correlation increased with extent of input correlation, in line with our STRF measurements.
Systems Biology on Bio-Linux
Authors: Bicak Mesude 
Published: September 2011

AbstractThis presentation introduces the Bio-Linux Operating System which is a popular Computational Biology workstation with 500+ bioinformatics software. It then provides an overview of popular modelling approaches in systems biology, covering top-down, bottom-up and hybrid modelling. Finally it highlights the challenges being faced by systems biology modellers, agent-based modellers in particular, regarding standardisation efforts.
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
Authors: Kamburov Atanas , Cavill Rachel , Ebbels Timothy M. D. , Herwig Ralf , Keun Hector C. 
Published: September 2011

Abstract
Summary:Pathway-level analysis is a powerful approach enabling interpretation of post-genomic data at a higher level than that of individual biomolecules. Yet, it is currently hard to integrate more than one type of omics data in such an approach. Here, we present a web tool ‘IMPaLA’ for the joint pathway analysis of transcriptomics or proteomics and metabolomics data. It performs over-representation or enrichment analysis with user-specified lists of metabolites and genes using over 3000 pre-annotated pathways from 11 databases. As a result, pathways can be identified that may be disregulated on the transcriptional level, the metabolic level or both. Evidence of pathway disregulation is combined, allowing for the identification of additional pathways with changed activity that would not be highlighted when analysis is applied to any of the functional levels alone. The tool has been implemented both as an interactive website and as a web service to allow a programming interface.
Availability:The web interface of IMPaLA is available at http://impala.molgen.mpg.de. A web services programming interface is provided at http://impala.molgen.mpg.de/wsdoc.
Contact: kamburov@molgen.mpg.de; r.cavill@imperial.ac.uk; h.keun@imperial.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
Semi-supervised learning improves gene expression-based prediction of cancer recurrence
Authors: Shi Mingguang , Zhang Bing 
Published: September 2011

Abstract
Motivation: Gene expression profiling has shown great potential in outcome prediction for different types of cancers. Nevertheless, small sample size remains a bottleneck in obtaining robust and accurate classifiers. Traditional supervised learning techniques can only work with labeled data. Consequently, a large number of microarray data that do not have sufficient follow-up information are disregarded. To fully leverage all of the precious data in public databases, we turned to a semi-supervised learning technique, low density separation (LDS).
Results: Using a clinically important question of predicting recurrence risk in colorectal cancer patients, we demonstrated that (i) semi-supervised classification improved prediction accuracy as compared with the state of the art supervised method SVM, (ii) performance gain increased with the number of unlabeled samples, (iii) unlabeled data from different institutes could be employed after appropriate processing and (iv) the LDS method is robust with regard to the number of input features. To test the general applicability of this semi-supervised method, we further applied LDS on human breast cancer datasets and also observed superior performance. Our results demonstrated great potential of semi-supervised learning in gene expression-based outcome prediction for cancer patients.
Contact: bing.zhang@vanderbilt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Hierarchical Bayesian estimation of the population viability of an epixylic moss
Authors: Ruete Alejandro , Wiklund Karin , Snäll Tord 
Published: September 2011

Summary1. Understanding the variation in population abundances requires accounting for the environmental variability and uncertainty on different scales. We developed and evaluated a Bayesian hierarchical model for the inter‐annual variation in population abundance of the epixylic bryophyte Buxbaumia viridis. The model accounts for spatio‐temporal variability on two spatial scales. We used data on population abundance and on the weather variables at regional level collected between 1996 and 2003, and data on dead wood amount collected between 1996 and 2008. We also provide a Bayesian estimate of the population viability, specifically the population stochastic growth rate (log λS), which accounts for natural variability and uncertainty.2. Previous estimates of population viability did not account for uncertainties in a satisfactory way. First, point estimates of log λS cannot, by definition, express variation. Second, the commonly used approach to estimate log λS and its confidence interval underestimates uncertainties. The approach aims to estimate the mean of log λS, with the confidence interval representing the uncertainty in the estimate of this mean. The interval does not reflect the natural variation and uncertainty.3. We estimated a probability distribution of log λS, where the probability distributions of the year‐specific growth rates (log λy) are accounted for. The species is likely to decline under current environmental conditions. Based on the probability distribution of log λS, we estimated this risk to be 81%.4. We found support for the hypotheses that the population dynamics are driven by autumn frosts, by spring precipitation and temperature (regional variables), and by the preceding year’s population abundance (local variable).5. Synthesis. Statements about the viability of populations should not be based on point estimates of log λS. Instead, the full probability distribution of log λS should be used, which explicitly accounts for the hierarchically structured natural variability and uncertainty. This distribution allows estimating the risk for a population decline, or providing an estimate of the confidence in a statement about a decline. This quantitative information can be weighed against other interests. We expect this Bayesian approach to be especially useful in the viability analysis of natural populations experiencing environmental variability.
Determination of spatial correlation functions of refractive index of living tissue
Authors: GAO WANRONG 
Published: September 2011

SummaryWe present what to our knowledge the first method of determination of spatial correlation functions of refractive index fluctuations of living tissues by Fourier domain optical coherence tomography (FDOCT). Based on the second‐order statistical description of the random characteristic of living tissue, a formula which clearly relates the spectral electrical power from the detector to the Fourier spectrum of the refractive index correlation function is given. The method is characterized by its capability of noninvasive measurements in vivo. It has the potential of allowing quantitative discrimination between different tissue types or the same tissue at different pathological states by determining their Fourier components of spatial correlation functions of refractive index.
Relationship between sleep‐disordered breathing and markers of systemic inflammation in women from the general population
Authors: SVENSSON MALIN , VENGE PER , JANSON CHRISTER , LINDBERG EVA 
Published: September 2011

SummarySleep‐disordered breathing (SDB) is a risk factor for cardiovascular disease (CVD). The underlying pathogenesis is not clear. In patients with obstructive sleep apnoea syndrome (OSAS) elevated levels of inflammatory markers, such as C‐reactive protein (CRP), interleukin‐6 (IL‐6) and tumour necrosis factor α (TNFα) have been found. These markers have also been shown as independent markers of CVD in other populations. The aim of the study was to investigate the association between SDB and systemic inflammation in a population‐based cohort of women. From 6817 women who previously answered a questionnaire concerning snoring habits, 230 habitually snoring women and 170 women regardless of snoring status went through polysomnography, anthropometric measurements and blood sampling. Analyses were made for CRP, TNFα, IL‐6, myeloperoxidase (MPO) and lysozyme. The levels of CRP, IL‐6 and lysozyme were significantly higher in subjects with apnoea–hypopnoea index (AHI) ≥15 compared with women with lower AHI. All inflammatory markers except MPO correlated to AHI and oxygen desaturation measures, and to waist circumference. In multiple linear regressions adjusting for age, waist circumference and smoking, independent correlations between oxygen desaturation indices (ODI) and inflammation were found for IL‐6 (P = 0.03 for % sleep time with saturation <90%) and TNFα (P = 0.03 for ODI 3%). No significant correlations were found between AHI and inflammation. Also, for women from the general population there is an independent correlation between SDB and inflammation, even after adjusting for obesity. The results indicate that intermittent hypoxia, and not the AHI, is related to systemic inflammation seen in OSAS.
Identification and characterization of stationary phase inducible genes in Escherichia coli
Authors: Weichart Dieter , Lange Roland , Henneberg Nicola , Hengge‐Aronis Regine 
Published: September 2011

SummaryDuring transition into stationary phase a large set of proteins is induced in Escherichia coli. Only a minority of the corresponding genes has been identified so far. Using the λplacMu system and a plate screen for carbon starvation‐induced fusion activity, a series of chromosomal lacZ fusions (csi::lacZ) was isolated. In complex medium these fusions were induced either during late exponential phase or during entry into stationary phase. csi::lacZ expression in minimal media in response to starvation for carbon, nitrogen and phosphate sources and the roles of global regulators such as the alternative sigma factor sigma;S (encoded by rpoS), cAMP/CRP and the relA gene product were investigated. The results show that almost every fusion exhibits its own characteristic pattern of expression, suggesting a complex control of stationary phase‐inducible genes that involves various combinations of regulatory mechanisms for different genes. All fusions were mapped to the E. coli chromosome. Using fine mapping by Southern hybridization, cloning, sequencing and/or phenotypic analysis, csi‐5, csi‐17, and csi‐18 could be localized in osmY (encoding a periplasmic protein), glpD (aerobic glycerol‐3‐phosphate dehydrogenase) and glgA (glycogen synthase), respectively. The other fusions seem to specify novel genes now designated csiA through to csiF. csi‐17(glpD)::lacZ was shown to produce its own glucose‐starvation induction, thus illustrating the Intricacies of gene‐fusion technology when applied to the study of gene regulation.
Xcp‐mediated protein secretion in Pseudomonas aeruginosa: identification of two additional genes and evidence for regulation of xcp gene expression
Authors: Akrim Mohammed , Bally Marc , Ball Geneviève , Tommassen Jan , Teerink Henk , Filloux Alain , Lazdunski Andrée 
Published: September 2011

SummaryIn Pseudomonas aeruginosa, several exoproteins synthesized with a signal sequence (elastase, lipase, phospholipases, alkaline phosphatase and exotoxin A) are secreted by a two‐step mechanism. They first cross the inner membrane in a signal sequence‐dependent way, and are further translocated across the outer membrane in a second step requiring secretion functions encoded by several xcp genes. Ten xcp genes have already been characterized (Bally et al., 1992a). In this study, two additional xcp genes, xcpP and xcpQ, are described. They are located in the 40 min region of the chromosome where they probably define an operon, divergent from the xcpR–Z operon previously characterized in this region. These two genes encode two proteins, XcpP and XcpQ, similar to PulC and PulD of the pul system of Klebsiella oxytoca. Moreover, the two divergent operons share a common regulation which is growth‐phase dependent.
Split decision: a thaumarchaeon encoding both FtsZ and Cdv cell division proteins chooses Cdv for cytokinesis
Authors: Busiek Kimberly K. , Margolin William 
Published: September 2011

SummaryCytoskeletal proteins play a pivotal role in cytokinesis in prokaryotes and eukaryotes. Most bacteria and a major branch of the archaea called the Euryarchaeota harbour a tubulin homologue, FtsZ, which assembles into a dynamic polymeric ring structure required for cytokinesis. However, Crenarchaeota, another branch of the archaea, lack FtsZ and instead use Cdv proteins, which are homologues of the ESCRT‐III‐like system involved in vesicular sorting and cytokinesis in eukaryotes, for cell division. Recently, a group of Crenarchaeota that grow in non‐extreme environments was found to be sufficiently divergent to warrant its own branch of the archaea called the Thaumarchaeota. Notably, Thaumarchaeota have both Cdv and FtsZ homologues, which begs the question of which system is used for cell division. In this issue of Molecular Microbiology,Pelve et al. (2011) Pelve and colleagues tackle this question. They found that cells of the thaumarchaeon Nitrosopumilus maritimus likely divide using the Cdv system and not FtsZ, based on localization of Cdv proteins but not FtsZ to division sites. The authors also provide evidence that the cell cycle during growth of N. maritimus differs significantly from those of other archaea.
GSK962040: a small molecule motilin receptor agonist which increases gastrointestinal motility in conscious dogs
Authors: Leming S. , Broad J. , Cozens S. J. , Otterson M. , Winchester W. , Lee K. , Dukes G. E. , Sanger G. J. 
Published: September 2011

AbstractBackground  GSK962040, a small molecule motilin receptor agonist, was identified to address the need for a safe, efficacious gastric prokinetic agent. However, as laboratory rodents lack a functional motilin system, studies in vivo have been limited to a single dose, which increased defecation in rabbits. Motilin agonists do not usually increase human colonic motility, so gastric prokinetic activity needs to be demonstrated.Methods  The effect of intravenous GSK962040 on gastro‐duodenal motility was assessed in fasted dogs implanted with strain gauges. Activity was correlated with blood plasma concentrations of GSK962040 (measured by HPLC‐MS/MS) and potency of GSK962040 at the dog recombinant receptor [using a Fluorometric Imaging Plate Reader (Molecular Devices, Wokingham, UK) after expression in HEK293 cells].Key Results  GSK962040 activated the dog motilin receptor (pEC50 5.79; intrinsic activity 0.72, compared with [Nle13]‐motilin). In vivo, GSK962040 induced phasic contractions, the duration of which was dose‐related (48 and 173 min for 3 and 6 mg kg−1), driven by mean plasma concentrations >1.14 μmol L−1. After the effects of GSK962040 faded, migrating motor complex (MMC) activity returned. Migrating motor complex restoration was unaffected by 3 mg kg−1 GSK962040 but at 6 mg kg−1, MMCs returned 253 min after dosing, compared with 101 min after saline (n = 5 each).Conclusions & Inferences  The results are consistent with lower potency for agonists at the dog motilin receptor, compared with humans. They also define the doses of GSK962040 which stimulate gastric motility. Correlation of in vivo and in vitro data in the same species, together with plasma concentrations, guides further studies and translation to other species.