bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
Authors: Dugas Diana V , Monaco Marcela K , Olson Andrew , Klein Robert R , Kumari Sunita , Ware Doreen , Klein Patricia E 
Published: November 2011

Abstract

Background
Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.

Results
RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.

Conclusions
The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.
Novel metabolic biomarkers related to sulfur-dependent detoxification pathways in autistic patients of Saudi Arabia
Authors: Al-Yafee Yusra A , Al- Ayadhi Laila Y , Haq Samina H , El-Ansary Afaf K 
Published: November 2011

Abstract

Background
Xenobiotics are neurotoxins that dramatically alter the health of the child. In addition, an inefficient detoxification system leads to oxidative stress, gut dysbiosis, and immune dysfunction. The consensus among physicians who treat autism with a biomedical approach is that those on the spectrum are burdened with oxidative stress and immune problems. In a trial to understand the role of detoxification in the etiology of autism, selected parameters related to sulfur-dependent detoxification mechanisms in plasma of autistic children from Saudi Arabia will be investigated compared to control subjects.

Methods
20 males autistic children aged 3-15 years and 20 age and gender matching healthy children as control group were included in this study. Levels of reduced glutathione (GSH), total (GSH+GSSG), glutathione status (GSH/GSSG), glutathione reductase (GR), glutathione- s-transferase (GST), thioredoxin (Trx), thioredoxin reductase (TrxR) and peroxidoxins (Prxs I and III) were determined.

Results
Reduced glutathione, total glutathione, GSH/GSSG and activity levels of GST were significantly lower, GR shows non-significant differences, while, Trx, TrxR and both Prx I and III recorded a remarkably higher values in autistics compared to control subjects.

Conclusion
The impaired glutathione status together with the elevated Trx and TrxR and the remarkable over expression of both Prx I and Prx III, could be used as diagnostic biomarkers of autism.
Changes in cholesterol homeostasis modify the response of F1B hamsters to dietary very long chain n-3 and n-6 polyunsaturated fatty acids
Authors: Lecker Jaime L , Matthan Nirupa R , Billheimer Jeffrey T , Rader Daniel J , Lichtenstein Alice H 
Published: November 2011

Abstract

Background
The plasma lipoprotein response of F1B Golden-Syrian hamsters fed diets high in very long chain (VLC) n-3 polyunsaturated fatty acids (PUFA) is paradoxical to that observed in humans. This anomaly is attributed, in part, to low lipoprotein lipase activity and is dependent on cholesterol status. To further elucidate the mechanism(s) for these responses, hamsters were fed diets containing supplemental fish oil (VLC n-3 PUFA) or safflower oil (n-6 PUFA) (both 10% [w/w]) and either cholesterol-supplemented (0.1% cholesterol [w/w]) or cholesterol-depleted (0.01% cholesterol [w/w] and 10 days prior to killing fed 0.15% lovastatin+2% cholestyramine [w/w]).

Results
Cholesterol-supplemented hamsters fed fish oil, relative to safflower oil, had higher non-high density lipoprotein (HDL) cholesterol and triglyceride concentrations (P < 0.001) which were associated with lower hepatic low density lipoprotein (LDL) receptor, sterol regulatory element binding protein (SREBP)-1c and acyl-CoA: cholesterol acyl transferase-2 (ACAT) mRNA and protein (p < 0.05), and higher hepatic apolipoprotein (apo) B-100 and apo E protein levels. In contrast, cholesterol-depleted hamsters fed fish oil, relative to safflower oil, had lower non-HDL cholesterol and triglyceride concentrations (P < 0.001) which were associated with lower hepatic SREBP-1c (p < 0.05) but not apo B-100, apo E or ACAT-2 mRNA or protein levels. Independent of cholesterol status, fish oil fed hamsters had lower HDL cholesterol concentrations (p < 0.001), which were associated with lower hepatic apoA-I protein levels (p < 0.05).

Conclusion
These data suggest disturbing cholesterol homeostasis in F1B hamsters alters their response to dietary fatty acids, which is reflected in altered plasma lipoprotein patterns and regulation of genes associated with their metabolism.
Mitral annular calcification predicts immediate results of percutaneous transvenous mitral commissurotomy
Authors: Salarifar Mojtaba , Rezvanfard Mehrnaz , Sadeghian Hakimeh , Safir-mardanloo Azam , Shafii Nahid 
Published: November 2011

AbstractBackgroundMany previous studies have evaluated the impact of mitral valve (MV) deformity scores on the percutaneous transvenous mitral commissurotomy (PTMC) outcome in patients with mitral stenosis; however, the relationship between mitral annulus calcification (MAC) and the PTMC result has not yet been established. The current study aimed to investigate whether MAC could independently influence the immediate result of PTMC.MethodsOf all patients undergoing PTMC in our institution between April 2005 and November 2009, we included 87 patients (28.7%male, mean ± SD age = 42.8 ± 12.6 years) with rheumatic mitral stenosis who had additional data on the echocardiographic evaluation of MAC along with MV leaflets morphology. Echocardiographic assessments were repeated up to six weeks after PTMC to evaluate the immediate PTMC outcome. The frequency of the optimal PTMC result (secondary MV area > = 1.5 cm2with > = 25% increase and without final mitral regurgitation grade > 2) was compared between two groups of patients with MAC (n = 17) and those without MAC (n = 70).ResultsThe optimal result was obtained in 55 (63.2%) patients, whereas the result was suboptimal in 32 (36.8%) patients due to insufficient MV area increase in 31(96.9%) subjects and post-procedure mitral regurgitation grade > 2 in 1(3.1%). The rate of optimal PTMC results was less in patients with MAC in comparison to those without MAC (29.4% vs.71.4%). After adjustments for possible confounders such as age and leaflets morphological subcomponents (thickening, mobility, calcification, and subvalvular thickening), MAC remained a significant negative predictor of a suboptimal PTMC result (odds ratio = 0.154; 95%CI = 0.038-0.626, p value = 0.009) together with leaflet thickening (odds ratio = 0.214; 95%CI = 0.060-0.770, p value = 0.018).ConclusionsMAC appeared to independently influence the immediate result of PTMC; therefore, mitral annulus evaluation may be considered in the echocardiographic assessment of the mitral apparatus prior to PTMC.
Rapid typing of foot-and-mouth disease serotype Asia 1 by reverse transcription loop-mediated isothermal amplification
Authors: Chen Hao-tai , Zhang Jie , Liu Yong-sheng , Liu Xiang-tao 
Published: November 2011

Abstract
A reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay was rapidly used to detect serotype Asia 1 of foot-and-mouth disease virus (FMDV) within 45 min at 61°C. All FMDV serotype Asia 1 reference strains were positive by RT-LAMP, while other viruses such as FMDV serotypes O, C, A and classical swine fever virus, swine vesicular disease virus, porcine reproductive and respiratory syndrome virus and Japanese encephalitis virus remained negative. Furthermore, FMDV sreotype Asia 1 positive samples were able to detect by RT-LAMP assay. This RT-LAMP assay may be suitable particularly for diagnosis of FMDV serotype Asia 1 infection in field stations.
Which dressing do donor site wounds need?: study protocol for a randomized controlled trial
Authors: Eskes Anne M , Brölmann Fleur E , Gerbens Louise AA , Ubbink Dirk T , Vermeulen Hester ,   The REMBRANDT study group (REMBRANDT)
Published: November 2011

Abstract

Background
Donor site wounds after split-skin grafting are rather 'standard' wounds. At present, lots of dressings and topical agents for donor site wounds are commercially available. This causes large variation in the local care of these wounds, while the optimum 'standard' dressing for local wound care is unclear. This protocol describes a trial in which we investigate the effectiveness of various treatment options for these donor site wounds.

Methods
A 14-center, six-armed randomized clinical trial is being carried out in the Netherlands. An a-priori power analysis and an anticipated dropout rate of 15% indicates that 50 patients per group are necessary, totaling 300 patients, to be able to detect a 25% quicker mean time to complete wound healing. Randomization has been computerized to ensure allocation concealment. Adult patients who need a split-skin grafting operation for any reason, leaving a donor site wound of at least 10 cm2 are included and receive one of the following dressings: hydrocolloid, alginate, film, hydrofiber, silicone dressing, or paraffin gauze. No combinations of products from other intervention groups in this trial are allowed. Optimum application and changes of these dressings are pursued according to the protocol as supplied by the dressing manufacturers. Primary outcomes are days to complete wound healing and pain (using a Visual Analogue Scale). Secondary outcomes are adverse effects, scarring, patient satisfaction, and costs. Outcome assessors unaware of the treatment allocation will assess whether or not an outcome has occurred. Results will be analyzed according to the intention to treat principle. The first patient was randomized October 1, 2009.

Discussion
This study will provide comprehensive data on the effectiveness of different treatment options for donor site wounds. The dressing(s) that will prevail in effectiveness, satisfaction and costs will be promoted among clinicians dealing with such patients. Thus, we aim to contribute a well-designed trial, relevant to all clinicians involved in the care for donor site wounds, which will help enhance uniformity and quality of care for these patients.

Trial registration

http://www.trialregister.nl, NTR1849. Date registered: June 9, 2009
A field-study on Leptospira seroprevalence in dairy cows in four geographical areas in Sweden
Authors: Lindahl Elisabeth , Boqvist Sofia , Artursson Karin , Magnusson Ulf 
Published: November 2011

Abstract

Background
Dairy cattle were used as sentinels for the presence of Leptospira infection in Swedish livestock in four regions contrasting in precipitation and temperature during the summer time. The aim of the study was to estimate the prevalence of five serovars of Leptospira of low pathogenicity in dairy cattle in these four regions.

Findings
Around 150 blood samples were collected from five dairy farms from each region, making 610 samples in total, during December 2009. The samples were screened for L. kirschneri sv Grippotyphosa, L. interrogans sv Icterohaemorrhagiae, L. interrogans sv Canicola, L. borgpetersenii sv Sejroe and one domestic strain similar to sv Sejroe, called strain Mouse 2A using the Microscopic Agglutination Test. Six animals (1%) were seropositive for the strain Mouse 2A. Four of the positive samples were from the south-west region which also was the region with highest precipitation. There were no positive samples to any of the other serovars studied.

Conclusions
The present data indicate that there is a low seroprevalence of Leptospira in Swedish dairy cows. These findings can be used as baseline data to investigate the effects of, for instance, climatic change or alterations in wildlife reservoir populations on the seroprevalence of Leptospira in the future.
Effects of alkaline or liquid-ammonia treatment on crystalline cellulose: changes in crystalline structure and effects on enzymatic digestibility
Authors: Mittal Ashutosh , Katahira Rui , Himmel Michael E , Johnson David K 
Published: November 2011

Abstract

Background
In converting biomass to bioethanol, pretreatment is a key step intended to render cellulose more amenable and accessible to cellulase enzymes and thus increase glucose yields. In this study, four cellulose samples with different degrees of polymerization and crystallinity indexes were subjected to aqueous sodium hydroxide and anhydrous liquid ammonia treatments. The effects of the treatments on cellulose crystalline structure were studied, in addition to the effects on the digestibility of the celluloses by a cellulase complex.

Results
From X-ray diffractograms and nuclear magnetic resonance spectra, it was revealed that treatment with liquid ammonia produced the cellulose IIII allomorph; however, crystallinity depended on treatment conditions. Treatment at a low temperature (25°C) resulted in a less crystalline product, whereas treatment at elevated temperatures (130°C or 140°C) gave a more crystalline product. Treatment of cellulose I with aqueous sodium hydroxide (16.5 percent by weight) resulted in formation of cellulose II, but also produced a much less crystalline cellulose. The relative digestibilities of the different cellulose allomorphs were tested by exposing the treated and untreated cellulose samples to a commercial enzyme mixture (Genencor-Danisco; GC 220). The digestibility results showed that the starting cellulose I samples were the least digestible (except for corn stover cellulose, which had a high amorphous content). Treatment with sodium hydroxide produced the most digestible cellulose, followed by treatment with liquid ammonia at a low temperature. Factor analysis indicated that initial rates of digestion (up to 24 hours) were most strongly correlated with amorphous content. Correlation of allomorph type with digestibility was weak, but was strongest with cellulose conversion at later times. The cellulose IIII samples produced at higher temperatures had comparable crystallinities to the initial cellulose I samples, but achieved higher levels of cellulose conversion, at longer digestion times.

Conclusions
Earlier studies have focused on determining which cellulose allomorph is the most digestible. In this study we have found that the chemical treatments to produce different allomorphs also changed the crystallinity of the cellulose, and this had a significant effect on the digestibility of the substrate. When determining the relative digestibilities of different cellulose allomorphs it is essential to also consider the relative crystallinities of the celluloses being tested.
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology
Authors: Lin Yu , Xiang Zuoshuang , He Yongqun 
Published: November 2011

Abstract

Background
Caused by intracellular Gram-negative bacteria Brucella spp., brucellosis is the most common bacterial zoonotic disease. Extensive studies in brucellosis have yielded a large number of publications and data covering various topics ranging from basic Brucella genetic study to vaccine clinical trials. To support data interoperability and reasoning, a community-based brucellosis-specific biomedical ontology is needed.

Results
The Brucellosis Ontology (IDOBRU: http://sourceforge.net/projects/idobru), a biomedical ontology in the brucellosis domain, is an extension ontology of the core Infectious Disease Ontology (IDO-core) and follows OBO Foundry principles. Currently IDOBRU contains 1503 ontology terms, which includes 739 Brucella-specific terms, 414 IDO-core terms, and 350 terms imported from 10 existing ontologies. IDOBRU has been used to model different aspects of brucellosis, including host infection, zoonotic disease transmission, symptoms, virulence factors and pathogenesis, diagnosis, intentional release, vaccine prevention, and treatment. Case studies are typically used in our IDOBRU modeling. For example, diurnal temperature variation in Brucella patients, a Brucella-specific PCR method, and a WHO-recommended brucellosis treatment were selected as use cases to model brucellosis symptom, diagnosis, and treatment, respectively. Developed using OWL, IDOBRU supports OWL-based ontological reasoning. For example, by performing a Description Logic (DL) query in the OWL editor Protégé 4 or a SPARQL query in an IDOBRU SPARQL server, a check of Brucella virulence factors showed that eight of them are known protective antigens based on the biological knowledge captured within the ontology.

Conclusions
IDOBRU is the first reported bacterial infectious disease ontology developed to represent different disease aspects in a formal logical format. It serves as a brucellosis knowledgebase and supports brucellosis data integration and automated reasoning.
Menin Missense Mutants Encoded by the MEN1 Gene that Are Targeted to the Proteasome: Restoration of Expression and Activity by CHIP siRNA
Authors: Canaff Lucie , Vanbellinghen Jean-François , Kanazawa Ippei , Kwak Hayeon , Garfield Natasha , Vautour Line , Hendy Geoffrey N. 
Published: November 2011

Context:
In multiple endocrine neoplasia type 1 (MEN1) characterized by tumors of parathyroid, enteropancreas, and anterior pituitary, missense mutations in the MEN1 gene product, menin, occur in a subset of cases. The mutant proteins are degraded by the proteasome. However, whether their expression and activity can be restored is not known.

Objective:
Our objective was to functionally characterize a panel of 16 menin missense mutants, including W423R and S443Y identified in new MEN1 families, with respect to protein stability, targeting to the proteasome and restoration of expression by proteasome inhibitors and expression and function by small interfering RNA technology.

Methods:
Flag-tagged wild-type (WT) and missense menin mutant expression vectors were transiently transfected in human embryonic kidney (HEK293) and/or rat insulinoma (Rin-5F) cells.

Results:
The majority of mutants were short-lived, whereas WT menin was stable. Proteasome inhibitors MG132 and PS-341 and inhibition of the chaperone, heat-shock protein 70 (Hsp70), or the ubiquitin ligase, COOH terminus of Hsp70-interacting protein (CHIP), by specific small interfering RNA, restored the levels of the mutants, whereas that of WT menin was largely unaffected. Inhibition of CHIP restored the ability of mutants to mediate normal functions of menin: TGF-β up-regulation of the promoters of its target genes, the cyclin-dependent kinase inhibitors p15 and p21 as well as TGF-β inhibition of cell numbers.

Conclusion:
When the levels of missense menin mutants that are targeted to the proteasome are normalized they may function similarly to WT menin. Potentially, targeting specific components of the proteasome chaperone pathway could be beneficial in treating a subset of MEN1 cases.
MicroRNA-mediated gene silencing: are we close to a unifying model?
Authors: James Victoria , Wong Sybil C.K. , Sharp Tyson V. 
Published: November 2011

AbstractMicroRNAs (miRNAs) comprise a group of small non-coding RNA –21 nucleotides in length. They act as post-transcriptional regulators of gene expression by forming base pairing interactions with target messenger RNA (mRNA). At least 1000 miRNAs are predicted to be expressed in humans and are encoded for in the genome of almost all organisms. Functional studies indicate that every cellular process studied thus far is regulated at some level by miRNAs. Given this expansive role, it is not surprising that disruption of this crucial pathway underlies the initiation of, or in the least, contributes to the development and progression of numerous human diseases and physiological disorders. This review will focus on the latest developments in uncovering the mechanism(s) of miRNA-mediated silencing with specific reference to the function of terminal effector proteins, how translation of target mRNA is inhibited and whether we are moving towards understanding this fundamental gene silencing paradigm.
Checklist of marine benthic green algae (Chlorophyta) on Hainan, a subtropical island off the coast of China: comparisons between the 1930s and 1990–2009 reveal environmental changes
Authors: Titlyanov Eduard A. , Titlyanova Tamara V. , Xia Bangmei , Bartsch Inka 
Published: November 2011

Abstract
A complete checklist of intertidal to shallow subtidal marine green seaweeds (Chlorophyta) growing on the subtropical island of Hainan (China) is presented here for the first time. It covers data from extensive recent (1990–2009) and historical (1933–1935) collections, and additional published records from various time periods. Data were analyzed by time period. We postulate that environmental changes on Hainan Island documented since the 1980s (e.g., degradation of coral reefs, development of tourism and mariculture farms) are reflected in the green algal species complement and in the dominance or absence of specific algal groups during different time periods. In total, 105 green algal taxa were recorded, including 37 new to Hainan Island, and 18 new records for China. There was a clearly evident change in floristic composition between early and recent collections. In the 1930s, there was a dominance of Caulerpaceae, Codiaceae and Cladophoraceae. By 1990/1992, the numbers of Ulvaceae had increased 1.6-fold and numbers of Cladophoraceae 1.7-fold. Both families contain many opportunistic species that prefer nutrient-enriched or degraded environments. At the same time, species richness of Codiaceae, Caulerpaceae and Udotaceae, families with complex thallus structures, decreased considerably. The floristic differences between the 1990/1992 and 2008/2009 collections were minor.