bluuebunny/crossref_metadata_2025_split huggingface dataset:
Looking for prognosticators in ovine anaplasmosis: discriminant analysis of clinical and haematological parameters in lambs belonging to differently susceptible breeds experimentally infected with Anaplasma ovis
Authors: Ciani Elena , Alloggio Ingrid , Petazzi Ferruccio , Pieragostini Elisa 
Published: September 2013

Abstract

Background
A study was carried out to evaluate the response of different native sheep breeds to experimental infection with Anaplasma ovis, the most prevalent sheep tick-borne pathogen in Apulia (Southern Italy). Thirty-four lambs belonging to a Northern European breed (Suffolk) and two Southern Italian breeds (Comisana and Altamurana) were infected. Eleven clinical as well as haematological parameters were monitored at different temporal resolutions on the same subjects before and after the infection, resulting in a data set of 435 observations. The present work, aiming to further the research, presents the results of a multivariate analysis carried out to identify which parameters out of the eleven considered are the most reliable parameters to be considered as markers of the disease phenotype as well as prognosticators of practical clinical importance.

Results
Data were analysed by discriminant analysis. Out of the eleven considered variables (red blood cells, packed cell volume, mean corpuscular volume, mean corpuscular haemoglobin, mean corpuscular haemoglobin content, haemoglobin concentration, white blood cells, neutrophils, leukocytes, platelets, rectal temperature), only seven were included in the step-wise model since significantly increasing the Mahlanobis distance between the two closest groups. Both discriminant functions resulted to be highly significant (P < 0.0001) and the percentage of variation accounted for by the first discriminant function was 63.6% of the variance in the grouping variable.

Conclusions
Taken together, the observed results stress the marked differentiation among the three breeds in terms of physio-pathological phenotypes indicating packed cell volume and red blood cell count as the most informative parameters in the routine clinical practice for A. ovis infection in sheep.
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis
Authors: Srivastava Prashant K , Hull Richard P , Behmoaras Jacques , Petretto Enrico , Aitman Timothy J 
Published: September 2013

Abstract

Background
Function and efficiency of a transcription factor (TF) are often modulated by interactions with other proteins or TFs to achieve finely tuned regulation of target genes. However, complex TF interactions are often not taken into account to identify functionally active TF-targets and characterize their regulatory network. Here, we have developed a computational framework for integrated analysis of genome-wide ChIP-seq and gene expression data to identify the functional interacting partners of a TF and characterize the TF-driven regulatory network. We have applied this methodology in a rat model of macrophage dependent crescentic glomerulonephritis (Crgn) where we have previously identified JunD as a TF gene responsible for enhanced macrophage activation associated with susceptibility to Crgn in the Wistar-Kyoto (WKY) strain.

Results
To evaluate the regulatory effects of JunD on its target genes, we analysed data from two rat strains (WKY and WKY.LCrgn2) that show 20-fold difference in their JunD expression in macrophages. We identified 36 TFs interacting with JunD/Jun and JunD/ATF complexes (i.e., AP1 complex), which resulted in strain-dependent gene expression regulation of 1,274 target genes in macrophages. After lipopolysaccharide (LPS) stimulation we found that 2.4 fold more JunD/ATF-target genes were up-regulated as compared with JunD/Jun-target genes. The enriched 314 genes up-regulated by AP1 complex during LPS stimulation were most significantly enriched for immune response (P = 6.9 × 10-4) and antigen processing and presentation functions (P = 2.4 × 10-5), suggesting a role for these genes in macrophage LPS-stimulated activation driven by JunD interaction with Jun/ATF.

Conclusions
In summary, our integrated analyses revealed a large network of TFs interacting with JunD and their regulated targets. Our data also suggest a previously unappreciated contribution of the ATF complex to JunD-mediated mechanisms of macrophage activation in a rat model of crescentic glomerulonephritis.
Omani propolis: chemical profiling, antibacterial activity and new propolis plant sources
Authors: Popova Milena , Dimitrova Rosa , Al-Lawati Hassan Talib , Tsvetkova Iva , Najdenski Hristo , Bankova Vassya 
Published: September 2013

Abstract

Background
Propolis (bee glue) is a resinous honeybee product having a long history of application in many countries as a traditional remedy for treating wounds, burns, soar throat, stomach disorders, etc. It has been proved to possess beneficial biological effects, including antimicrobial, antioxidant, anti-inflammatory, cytotoxic, antiulcer, and many others. Bees gather propolis from diverse resinous plant parts and in different phytogeographic regions its chemical composition might vary significantly. In this article we report the results of the first study on the chemical profiles of propolis from Oman, its plant origin and antibacterial activity.

Results
The chemical profiles of Omani propolis extracts were obtained by GC-MS analysis after silylation. Over 50 individual compounds were identified in the samples, belonging to different compound types: sugars, polyols, hydroxy acids, fatty acids, cardanols and cardols, anacardic acids, flavan derivatives, triterpenes, prenylated flavanones and chalcones. The profiles were dissimilar from other known propolis types. They demonstrate that although Oman is not a large country, the plant sources of propolis vary significantly, even in the same apiary and the same season. Based on chemical profiles, and isolation and identification of major marker compounds (new propolis constituents), new plant sources of propolis were found: Azadiracta indica (neem tree) and Acacia spp. (most probably A. nilotica). The ethanol extracts of the studied propolis samples demonstrated activity against S. aureus (MIC < 100 μg. mL-1) and E. coli (MIC < 380 μg. mL-1).

Conclusion
Omani propolis is different form the known propolis types and demonstrates significant chemical diversity. Its most important plant source is the resin of Azadirachta indica, and as a result its typical components are С5-prenyl flavanones. Other plant sources have been identified, too, playing some role in resin collection by bees in Oman: Acacia spp. (most probably A. nilotica) and Mangifera indica. The results demonstrate also the potential of Omani propolis as antimicrobial.
Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052: genome-wide transcriptional analysis with RNA-Seq
Authors: Wang Yi , Li Xiangzhen , Blaschek Hans P 
Published: September 2013

Abstract

Background
Butanol (n-butanol) has high values as a promising fuel source and chemical feedstock. Biobutanol is usually produced by the solventogenic clostridia through a typical biphasic (acidogenesis and solventogenesis phases) acetone-butanol-ethanol (ABE) fermentation process. It is well known that the acids produced in the acidogenic phase are significant and play important roles in the switch to solventogenesis. However, the mechanism that triggers the metabolic switch is still not clear.

Results
Sodium butyrate (40 mM) was supplemented into the medium for the ABE fermentation with Clostridium beijerinckii NCIMB 8052. With butyrate addition (reactor R1), solvent production was triggered early in the mid-exponential phase and completed quickly in < 50 h, while in the control (reactor R2), solventogenesis was initiated during the late exponential phase and took > 90 h to complete. Butyrate supplementation led to 31% improvement in final butanol titer, 58% improvement in sugar-based yield, and 133% improvement in butanol productivity, respectively. The butanol/acetone ratio was 2.4 versus 1.8 in the control, indicating a metabolic shift towards butanol production due to butyrate addition. Genome-wide transcriptional dynamics was investigated with RNA-Seq analysis. In reactor R1, gene expression related to solventogenesis was induced about 10 hours earlier when compared to that in reactor R2. Although the early sporulation genes were induced after the onset of solventogenesis in reactor R1 (mid-exponential phase), the sporulation events were delayed and uncoupled from the solventogenesis. In contrast, in reactor R2, sporulation genes were induced at the onset of solventogenesis, and highly expressed through the solventogenesis phase. The motility genes were generally down-regulated to lower levels prior to stationary phase in both reactors. However, in reactor R2 this took much longer and gene expression was maintained at comparatively higher levels after entering stationary phase.

Conclusions
Supplemented butyrate provided feedback inhibition to butyrate formation and may be re-assimilated through the reversed butyrate formation pathway, thus resulting in an elevated level of intracellular butyryl phosphate, which may act as a phosphate donor to Spo0A and then trigger solventogenesis and sporulation events. High-resolution genome-wide transcriptional analysis with RNA-Seq revealed detailed insights into the biochemical effects of butyrate on solventogenesis related-events at the gene regulation level.
An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer
Authors: Jia Jinping , Parikh Hemang , Xiao Wenming , Hoskins Jason W , Pflicke Holger , Liu Xuelu , Collins Irene , Zhou Weiyin , Wang Zhaoming , Powell John , Thorgeirsson Snorri S , Rudloff Udo , Petersen Gloria M , Amundadottir Laufey T 
Published: September 2013

AbstractBackgroundPancreatic cancer is a highly lethal cancer with limited diagnostic and therapeutic modalities.MethodsTo begin to explore the genomic landscape of pancreatic cancer, we used massively parallel sequencing to catalog and compare transcribed regions and potential regulatory elements in two human cell lines derived from normal and cancerous pancreas.ResultsBy RNA-sequencing, we identified 2,146 differentially expressed genes in these cell lines that were enriched in cancer related pathways and biological processes that include cell adhesion, growth factor and receptor activity, signaling, transcription and differentiation. Our high throughput Chromatin immunoprecipitation (ChIP) sequence analysis furthermore identified over 100,000 regions enriched in epigenetic marks, showing either positive (H3K4me1, H3K4me3, RNA Pol II) or negative (H3K27me3) correlation with gene expression. Notably, an overall enrichment of RNA Pol II binding and depletion of H3K27me3 binding were seen in the cancer derived cell line as compared to the normal derived cell line. By selecting genes for further assessment based on this difference, we confirmed enhanced expression of aldehyde dehydrogenase 1A3 (ALDH1A3) in two larger sets of pancreatic cancer cell lines and in tumor tissues as compared to normal derived tissues.ConclusionsAs aldehyde dehydrogenase (ALDH) activity is a key feature of cancer stem cells, our results indicate that a member of the ALDH superfamily,ALDH1A3, may be upregulated in pancreatic cancer, where it could mark pancreatic cancer stem cells.
Prenatal diagnosis and post-mortem examination in a fetus with thrombocytopenia-absent radius (TAR) syndrome due to compound heterozygosity for a 1q21.1 microdeletion and a RBM8A hypomorphic allele: a case report
Authors: Bottillo Irene , Castori Marco , De Bernardo Carmelilia , Fabbri Romano , Grammatico Barbara , Preziosi Nicoletta , Scassellati Giovanna Sforzolini , Silvestri Evelina , Spagnuolo Antonella , Laino Luigi , Grammatico Paola 
Published: September 2013

Abstract

Background
Thrombocytopenia–absent radius syndrome is a rare autosomal recessive disorder characterized by megakaryocytic thrombocytopenia and longitudinal limb deficiencies mostly affecting the radial ray. Most patients are compound heterozygotes for a 200 kb interstitial microdeletion in 1q21.1 and a hypomorphic allele in RBM8A, mapping in the deleted segment. At the moment, the complete molecular characterization of thrombocytopenia–absent radius syndrome is limited to a handful of patients mostly ascertained in the pediatric age

Case presentation
We report on a fetus with bilateral upper limb deficiency found at standard prenatal ultrasound examination. The fetus had bilateral radial agenesis and humeral hypo/aplasia with intact thumbs, micrognathia and urinary anomalies, indicating thrombocytopenia–absent radius syndrome. Molecular studies demonstrated compound heterozygosity for the 1q21.1 microdeletion and the RBM8A rs139428292 variant at the hemizygous state, inherited from the mother and father, respectively

Conclusion
The molecular information allowed prenatal diagnosis in the following pregnancy resulting in the birth of a healthy carrier female. A review was carried out with the attempt to the trace the fetal ultrasound presentation of thrombocytopenia–absent radius syndrome and discussing opportunities for second-tier molecular studies within a multidisciplinary setting.
Differences in timing of mating swarms in sympatric populations of Anopheles coluzzii and Anopheles gambiae s.s. (formerly An. gambiae M and S molecular forms) in Burkina Faso, West Africa
Authors: Sawadogo Simon P , Costantini Carlo , Pennetier Cédric , Diabaté Abdoulaye , Gibson Gabriella , Dabiré Roch K 
Published: September 2013

AbstractBackgroundThe M and S molecular forms ofAnopheles gambiae s.s.Giles appear to have speciated in West Africa and the M form is now formally namedAn. coluzziiCoetzee & Wilkersonsp.n.and the S form retains the nominotypical name (abbreviated here toAn. gambiae). Reproductive isolation is thought to be the main barrier to hybridisation; even though both species are found in the same mating swarms, hybrid fertilisations incopulaehave not been found in the study area. The aim of the study, therefore, was to determine whether differences in circadian and/or environmental control over the timing of swarming in the two species contribute to reproductive isolation.MethodsThe timing of male swarming in these species was recorded four nights per month over four years at five swarming sites in each of two villages. The timing of the start and end of swarming, and the concurrent environmental parameters, temperature, humidity and light intensity, were recorded for n = 20 swarms/month/species. The timing of 'spontaneous’ activity at dusk of individualAn. coluzziiandAn. gambiaemales was video-recorded in an actograph outdoors for 21 nights.ResultsOf the environmental parameters considered, swarming was most strongly correlated with sunset (r2 > 0.946).Anopheles gambiaestarted and stopped swarming earlier thanAn. coluzzii(3:35 ± 0:68 min:sec and 4:51 ± 1:21, respectively), and the mean duration of swarming was 23:37 ± 0:33 forAn. gambiaeand 21:39 ± 0:33 forAn. coluzzii.Accordingly, in principle, whenever both species swarm over the same marker, a mean of 15.3 ± 3.1% ofAn. gambiaeswarming would occur beforeAn. coluzziimales arrived, and 19.5 ± 4.55% ofAn. coluzziiswarming would occurred afterAn. gambiaemales had stopped swarming. These results are consistent with the finding thatAn. gambiaemales became active in the actograph 09:35 ± 00:22 min:sec earlier thanAn. coluzziimales.ConclusionsThe timing of swarming and spontaneous activity at dusk are primarily under circadian control, with the phase linked closely to sunset throughout the year. The mating activity of these two species is temporally segregated for 15-20% of the swarming period, which may contribute to the observed reproductive isolation of these species in local sympatric populations.
Flexible fixation of syndesmotic diastasis using the assembled bolt-tightrope system
Authors: Xu Guohui , Chen Wei , Zhang Qi , Wang Juan , Su Yanling , Zhang Yingze 
Published: September 2013

Abstract

Background
Syndesmotic diastasis is a common injury. Syndesmotic bolt and tightrope are two of the commonly used methods for the fixation of syndesmotic diastasis. Syndesmotic bolt can be used to reduce and maintain the syndesmosis. However, it cannot permit the normal range of motion of distal tibiofibular joint, especially the rotation of the fibula. Tightrope technique can be used to provide flexible fixation of the syndesmosis. However, it lacks the ability of reducing the syndesmotic diastasis. To combine the advantages of both syndemostic bolt and tightrope techniques and simultaneously avoid the potential disadvantages of both techniques, we designed the assembled bolt-tightrope system (ABTS). The purpose of this study was to evaluate the primary effectiveness of ABTS in treating syndesmotic diastasis.

Methods
From October 2010 to June 2011, patients with syndesmotic diastasis met the inclusion criteria were enrolled into this study and treated with ABTS. Patients were followed up at 2, 6 weeks and 6, 12 months after operation. The functional outcomes were assessed according to the American Orthopedic Foot and Ankle Society (AOFAS) scores at 12 months follow-up. Patients’ satisfaction was evaluated based upon short form-12 (SF-12) health survey questionnaire. The anteroposterior radiographs of the injured ankles were taken, and the medial clear space (MCS), tibiofibular overlap (TFOL), and tibiofibular clear space (TFCS) were measured. All hardwares were routinely removed at 12-month postoperatively. Follow-ups continued. The functional and radiographic assessments were done again at the latest follow-up.

Results
Twelve patients were enrolled into this study, including 8 males and 4 females with a mean age of 39.5 years (range, 26 to 56 years). All patients also sustained ankle fractures. At 12 months follow-up, the mean AOFAS score was 95.4 (range, 85 to 100), and all patients were satisfied with the functional recoveries. The radiographic MCS, TFOL, and TFCS were within the normal range in all patients. After hardware removal, follow-up continued. At the latest follow-up (28 months on average, (range, 25 to 33 months) from internal fixation), the mean AOFAS score was 96.3 (range, 85 to 100), without significant difference with those assessed at 12 months after fixation operations. No syndesmotic diastasis reoccurred based upon the latest radiographic assessment.

Conclusions
ABTS can be used to reduce the syndesmotic diastasis and provide flexible fixation in a minimally invasive fashion. It seems to be an effective alternative technique to treat syndesmotic diastasis.
Prevalence of selected clinical problems in older adults with autism and intellectual disability
Authors: Kats Dmitry , Payne Leslie , Parlier Morgan , Piven Joseph 
Published: September 2013

Abstract

Background
Originally described as a disorder of childhood, evidence now demonstrates the lifelong nature of autism spectrum disorder (ASD). Despite the increase of the population over age 65, older adults with ASD remain a scarcely explored subpopulation. This study set out to investigate the prevalence of clinically relevant behaviors and medical problems in a sample of US adults aged 30 to 59 with ASD and intellectual disability (ID), in comparison to those with ID only.

Methods
A cross-sectional study, with both an exploratory and replication analysis, was conducted using National Core Indicators (NCI) multi-state surveys from 2009 to 2010 and 2010 to 2011. There were 4,989 and 4,261 adults aged 30–59 with ID examined from the 2009 to 2010 and 2010 to 2011 samples, respectively. The two consecutive annual samples consisted of 438 (9%) and 298 (7%) individuals with ASD and ID. Variables were chosen from the NCI data as outcomes, including medication use for behavior problems, severe or aggressive behavior problems and selected medical conditions.

Results
No age-associated disparities were observed between adults with ASD and ID versus adults with ID only in either sample. For the 2009 to 2010 sample, the prevalence of support needed to manage self-injurious, disruptive and destructive behavior in subjects with ASD and ID ranged from 40 to 60%. Similarly, the prevalence estimates of self-injurious, disruptive and destructive behavior were each almost double in adults with ASD and ID relative to those with ID only. These results were replicated in the 2010 to 2011 sample.

Conclusions
The findings of this study highlight the urgent need for research on the nature and treatment of severe behavior problems in the rapidly increasing population of older adults with ASD. They also suggest the importance of developing policies that expand our capacity to care for these individuals.
Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice
Authors: Kakei Yusuke , Ogo Yuko , Itai Reiko N , Kobayashi Takanori , Yamakawa Takashi , Nakanishi Hiromi , Nishizawa Naoko K 
Published: September 2013

Abstract

Background

Cis-acting elements are essential genomic sequences that control gene expression. In higher eukaryotes, a series of cis-elements function cooperatively. However, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. The aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (Fe) deficiency.

Results
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. Based on sequences of Oryza sativa genes upregulated by Fe deficiency, MAMA returned experimentally identified cis-elements responsible for Fe deficiency in O. sativa. When this method was applied to O. sativa subjected to zinc deficiency and Arabidopsis thaliana subjected to salt stress, several novel candidate cis-acting elements that overlap with known cis-acting elements, such as ZDRE, ABRE, and DRE, were identified. After optimization, MAMA accurately simulated more than 87% of gene expression. Predicted motifs strongly co-localized in the upstream regions of regulated genes and sequences around transcription start sites. Furthermore, in many cases, the separation (in bp) between co-localized motifs was conserved, suggesting that predicted motifs and the separation between them were important in the co-regulation of gene expression.

Conclusions
Our results are suggestive of a typical sequence model for Fe deficiency-responsive promoters and some strong candidate cis-elements that function cooperatively with known cis-elements.