bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator
Authors: Liu Ake , Wang Yong , Dang Chunwang , Zhang Debao , Song Huifang , Yao Qin , Chen Keping 
Published: September 2012

Abstract

Background
The basic helix-loop-helix (bHLH) transcription factors and their homologs form a superfamily that plays essential roles in transcriptional networks of multiple developmental processes. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, human and mouse.

Result
In this study, we conducted a genome-wide survey for bHLH sequences, and identified 57 bHLH sequences encoded in complete genome sequence of the ponerine ant, Harpegnathos saltator. Phylogenetic analysis of the bHLH domain sequences classified these genes into 38 bHLH families with 23, 14, 10, 1, 8 and 1 members in group A, B, C, D, E and F, respectively. The number of PabHLHs (ponerine ant bHLHs) with introns is higher than many other insect species, and they are found to have introns with average lengths only inferior to those of pea aphid. In addition, two H. saltator bHLHs named PaCrp1 and PaSide locate on two separate contigs in the genome.

Conclusions
A putative full set of PabHLH genes is comparable with other insect species and genes encoding Oligo, MyoRb and Figα were not found in genomes of all insect species of which bHLH family members have been identified. Moreover, in-family phylogenetic analyses indicate that the PabHLH genes are more closely related with Apis mellifera than others. The present study will serve as a solid foundation for further investigations into the structure and function of bHLH proteins in the regulation of H. saltator development.
Polyphyletic origin of the genus Physarum(Physarales, Myxomycetes) revealed by nuclear rDNA mini-chromosome analysis and group I intron synapomorphy
Authors: Nandipati Satish CR , Haugli Kari , Coucheron Dag H , Haskins Edward F , Johansen Steinar D 
Published: September 2012

AbstractBackgroundPhysarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). Physarales is of particular interest since the two best-studied myxomycete species,Physarum polycephalumandDidymium iridis, belong to this order and are currently subjected to whole genome and transcriptome analyses. Here we report molecular phylogeny based on ribosomal DNA (rDNA) sequences that includes 57 Physarales isolates.ResultsThe Physarales nuclear rDNA sequences were found to be loaded with 222 autocatalytic group I introns, which may complicate correct alignments and subsequent phylogenetic tree constructions. Phylogenetic analysis of rDNA sequences depleted of introns confirmed monophyly of the Physarales families Didymiaceae and Physaraceae. Whereas good correlation was noted between phylogeny and taxonomy among the Didymiaceae isolates, significant deviations were seen in Physaraceae. The largest genus,Physarum, was found to be polyphyletic consisting of at least three well supported clades. A synapomorphy, located at the highly conserved G-binding site of L2449 group I intron ribozymes further supported thePhysarumclades.ConclusionsOur results provide molecular relationship of Physarales genera, species, and isolates. This information is important in further interpretations of comparative genomics nd transcriptomics. In addition, the result supports a polyphyletic origin of the genusPhysarumand calls for a reevaluation of current taxonomy.
Transcriptomic and metabolomic profiling of chicken adipose tissue in response to insulin neutralization and fasting
Authors: Ji Bo , Ernest Ben , Gooding Jessica R , Das Suchita , Saxton Arnold M , Simon Jean , Dupont Joelle , Métayer-Coustard Sonia , Campagna Shawn R , Voy Brynn H 
Published: September 2012

AbstractBackgroundDomestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chicken adipose tissue is considered as poorly sensitive to insulin and lipolysis is under glucagon control. Excessive fat accumulation is also an economic and environmental concern for the broiler industry due to the loss of feed efficiency and excessive nitrogen wasting, as well as a negative trait for consumers who are increasingly conscious of dietary fat intake. Understanding the control of avian adipose tissue metabolism would both enhance the utility of chicken as a model organism for human obesity and insulin resistance and highlight new approaches to reduce fat deposition in commercial chickens.ResultsWe combined transcriptomics and metabolomics to characterize the response of chicken adipose tissue to two energy manipulations, fasting and insulin deprivation in the fed state. Sixteen to 17 day-old commercial broiler chickens (ISA915) were fedad libitum, fasted for five hours, or fed but deprived of insulin by injections of anti-insulin serum. Pair-wise contrasts of expression data identified a total of 2016 genes that were differentially expressed after correction for multiple testing, with the vast majority of differences due to fasting (1780 genes). Gene Ontology and KEGG pathway analyses indicated that a short term fast impacted expression of genes in a broad selection of pathways related to metabolism, signaling and adipogenesis. The effects of insulin neutralization largely overlapped with the response to fasting, but with more modest effects on adipose tissue metabolism. Tissue metabolomics indicated unique effects of insulin on amino acid metabolism.ConclusionsCollectively, these data provide a foundation for further study into the molecular basis for adipose expansion in commercial poultry and identify potential pathways through which fat accretion may be attenuated in the future through genetic selection or management practices. They also highlight chicken as a useful model organism in which to study the dynamic relationship between food intake, metabolism, and adipose tissue biology.
Effect of statin therapy on the progression of coronary atherosclerosis
Authors: Tian Jinwei , Gu Xia , Sun Yanli , Ban Xiang , Xiao Yun , Hu Sining , Yu Bo 
Published: September 2012

Abstract

Background
An increasing number of authors employing intravascular ultrasound (IVUS) and virtual histology (VH-IVUS) have investigated the effect of statin use on plaque volume (PV) and plaque composition. However, inconsistent results have been reported. Therefore, we conducted a meta-analysis to determine the appropriate regimen of statins to effectively stabilize vulnerable coronary plaques.

Methods
Online electronic databases were carefully searched for all relevant studies. We compared mean values of PV and plaque composition between baseline and follow-up in patients receiving statin therapy. We pooled treatment effects and calculated mean differences (MD) with the 95% confidence interval (CI) using a random-effects model. By stratified analyses, we explored the influence of clinical presentation, dose and duration of statin treatment, and low-density lipoprotein-cholesterol (LDL-C) levels on the effects of statins.

Results
Seventeen studies involving 2,171 patients were analyzed. Statin therapy significantly decreased PV (−5.3 mm3; 95% CI: –3.3 mm3 to −7.2 mm3; P < 0.001), without heterogeneity. When considering the dose and duration of statins used, only subgroups employing a high dose and long duration demonstrated a significant reduction in PV (p < 0.001). A significant decrease in PV was noted if achieved LDL-C levels were <100 mg/dL (p < 0.001). Statin treatment could induce a twofold decrease in PV in patients with acute coronary syndrome (ACS) compared with that observed in patients with stable angina pectoris (SAP). A regressive trend was seen for necrotic core volume (MD: –2.1 mm3; 95% CI: –4.7 mm3 to 0.5 mm3, P = 0.11). However, statin use did not induce a significant change for fibrotic, fibro-fatty, or dense calcium compositions.

Conclusions
Our meta-analysis demonstrated that statin therapy (especially that involving a high dose and long duration and achieving <100 mg/dL LDL-C levels) can significantly decrease PV in patients with SAP or ACS. These data suggested that statins can be used to reduce the atheroma burden for secondary prevention by appropriately selecting the statin regimen. No significant change in plaque composition was seen after statin therapy.
The contribution of the ABCG2 C421A polymorphism to cancer susceptibility: a meta-analysis of the current literature
Authors: Chen Pin , Zhao Lin , Zou Peng , Xu Haitao , Lu Ailin , Zhao Peng 
Published: September 2012

Abstract

Background
ABCG2, also known as BCRP, is a half ATP-binding cassette (ABC) transporter that localizes to plasma membranes. Recently, a number of studies have investigated the relationship between the C421A polymorphism in ABCG2 and cancer risk in multiple populations and various types of cancers; however, this relationship remains unclear. Therefore, we performed a meta-analysis to further explore this association.

Methods
The meta-analysis incorporated 10 studies involving a total of 3593 cases and 5875 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated based on the date extracted from the studies to evaluate the strength of association. We also analyzed the heterogeneity and sensitivity of each report and the publication bias of the studies.

Results
Overall, our results showed that there appeared to be a significant association between the ABCG2 C421A polymorphism and decreased cancer susceptibility (heterozygote-AC versus CC: OR = 0.759, 95%CI = 0.620-0.930; dominant effects model-AA/AC versus CC: OR = 0.771, 95%CI = 0.634-0.938; additive effects model-A allele versus C allele: OR = 0.809, 95%CI = 0.687-0.952). Similarly, decreased cancer risk was also found after stratification of the SNP data by cancer type, ethnicity and source of controls in heterozygote model, dominant effects model and additive effects model.

Conclusions
We found that the ABCG2 C421A polymorphism is a protective factor for developing cancer. The same relationship was found when the studies were stratified by cancer type, ethnicity and source of controls.
Recurrent orbital schwannomas: clinical course and histopathologic correlation
Authors: Kron Michelle , Bohnsack Brenda L , Archer Steven M , McHugh Jonathan B , Kahana Alon 
Published: September 2012

Abstract

Background
Schwannomas are slow-growing typically encapsulated tumors composed of differentiated Schwann cells, the primary class of peripheral glial cells. Complete excision is the treatment of choice for orbital schwannomas that cause pain, disfigurement, diplopia, or optic neuropathy. The presence of multiple schwannomas in a single patient suggests possible association with neurofibromatosis type 2 (NF2) or schwannomatosis.

Case presentation
We present 2 patients who experienced recurrent orbital schwannoma without evidence for neurofibromatosis. The recurrence in one patient, a 59-year old man, occurred 6 years after complete excision of the initial tumor. This recurrence consisted of 2 independent tumors in the same orbit. The recurrence in the second patient, a 5 year-old girl, occurred multiple times within days to weeks of partial excisions until eventually a complete excision was performed.

Conclusion
The clinical history, histopathologic features and particularly the intraoperative findings suggest that the 59 year old man suffers from orbital schwannomatosis, while the rapid recurrence in the second patient correlated with the cellular features of her plexiform schwannoma. Hence, the recurrence in each patient is linked to a different etiology, with implications for treatment and patient counseling given the difficulty in treating orbital schwannomatosis. To our knowledge, this is the first description of isolated orbital schwannomatosis.
Determining the use of prophylactic antibiotics in breast cancer surgeries: a survey of practice
Authors: Acuna Sergio A , Angarita Fernando A , Escallon Jaime , Tawil Mauricio , Torregrosa Lilian 
Published: September 2012

AbstractBackgroundProphylactic antibiotics (PAs) are beneficial to breast cancer patients undergoing surgery because they prevent surgical site infection (SSI), but limited information regarding their use has been published. This study aims to determine the use of PAs prior to breast cancer surgery amongst breast surgeons in Colombia.MethodsAn online survey was distributed amongst the breast surgeon members of the Colombian Association of Mastology, the only breast surgery society of Colombia. The scope of the questions included demographics, clinical practice characteristics, PA prescription characteristics, and the use of PAs in common breast surgical procedures.ResultsThe survey was distributed amongst eighty-eight breast surgeons of whom forty-seven responded (response rate: 53.4%). Forty surgeons (85.1%) reported using PAs prior to surgery of which >60% used PAs during mastectomy, axillary lymph node dissection, and/or breast reconstruction. Surgeons reported they targeted the use of PAs in cases in which patients had any of the following SSI risk factors: diabetes mellitus, drainsin situ, obesity, and neoadjuvant therapy. The distribution of the self-reported PA dosing regimens was as follows: single pre-operative fixed-dose (27.7%), single preoperative dose followed by a second dose if the surgery was prolonged (44.7%), single preoperative dose followed by one or more postoperative doses for >24 hours (10.6%), and single preoperative weight-adjusted dose (2.1%).ConclusionAlthough this group of breast surgeons is aware of the importance of PAs in breast cancer surgery there is a discrepancy in how they use it, specifically with regards to prescription and timeliness of drug administration. Our findings call for targeted quality-improvement initiatives, such as standardized national guidelines, which can provide sufficient evidence for all stakeholders and therefore facilitate best practice medicine for breast cancer surgery.
Psychometric properties of the Confidence and Trust in Delivery Questionnaire (CTDQ): a pilot study
Authors: Jeschke Elke , Ostermann Thomas , Dippong Natalie , Brauer Dagmar , Matthes Harald 
Published: September 2012

AbstractBackgroundAssessing expecting mother’s opinions prior to birth draws a comprehensive picture for the caregivers about their emotional state and their expectations. Some questionnaires to cover these aspects do exist. This study aims to present the psychometric properties of a new instrument, the Confidence and Trust in Delivery Questionnaire (CDTQ) a short but reliable a self-report instrument that focuses on confidence and trust as meaningful dimensions for expectant mothers.MethodsA pilot validation study of 221 women 6 weeks before childbirth was conducted in Germany between October 2007 and June 2008. To detect structural relations between the items, factor and reliability analyses were applied to the CTDQ items. Factor analysis was performed by means of principal components analysis and varimax rotation. Internal reliability was assessed by Cronbach’s alpha. External validation was performed using the sense of coherence (SOC) scale.ResultsThe CTDQ comprises of 11 items. We found a 4-factor structure. The internal consistency of the whole item pool (Cronbach’s α = 0.79) and the 4 subscales [confidence in labor (α = 0.82); partner’s support (α = 0.62); trust in medical competency (α = 0.68); being informed (α = 0.60)] can be regarded as sufficient or even excellent. The 4 factors explained 69.6% of total variance. Except for a high intercorrelation (0.70) between “partner’s support” and “trust in medical competence”, the subscales show low intercorrelations, indicating an adequate independence of the respective subscales. Regarding the external validity we found minor respective moderate correlations with the SOC scale.ConclusionsOur data suggest that the CTDQ is a useful instrument to assess confidence and trust in delivery. With 4 clinically relevant dimensions, the CTDQ is now open for further studies in the field of labor.
Anti-proliferative effect of methanolic extract of Gracilaria tenuistipitata on oral cancer cells involves apoptosis, DNA damage, and oxidative stress
Authors: Yeh Chi-Chen , Yang Jing-Iong , Lee Jin-Ching , Tseng Chao-Neng , Chan Ya-Ching , Hseu You-Cheng , Tang Jen-Yang , Chuang Li-Yeh , Huang Hurng-Wern , Chang Fang-Rong , Chang Hsueh-Wei 
Published: September 2012

Abstract

Background
Methanolic extracts of Gracilaria tenuistipitata (MEGT) were obtained from the edible red algae. Previously, we found that water extract of G. tenuistipitata was able to modulate oxidative stress-induced DNA damage and its related cellular responses.

Methods
In this study, the methanol extraction product MEGT was used to evaluate the cell growth inhibition in oral cancer cells and its possible mechanism was investigated.

Results
The cell viability of MEGT treated Ca9-22 oral cancer cell line was significantly decreased in a dose–response manner (p < 0.05). The sub-G1 population and annexin V intensity of MEGT-treated Ca9-22 cancer cells were significantly increased in a dose–response manner (p < 0.0005 and p < 0.001, respectively). The γH2AX intensities of MEGT-treated Ca9-22 cancer cells were significantly increased in a dose–response manner (p < 0.05). The reactive oxygen species (ROS) and glutathione (GSH)-positive intensities of MEGT-treated Ca9-22 oral cancer cells were significantly increased and decreased, respectively, in a dose–response manner (p < 0.05). The DiOC2(3) intensity for mitochondrial membrane potential (MMP) of MEGT-treated Ca9-22 cancer cells was significantly decreased in a dose–response manner (p < 0.05).

Conclusions
These results indicated that MEGT had apoptosis-based cytotoxicity against oral cancer cells through the DNA damage, ROS induction, and mitochondrial depolarization. Therefore, MEGT derived from the edible algae may have potential therapeutic effects against oral squamous cell carcinoma (OSCC).
Scale up, optimization and stability analysis of Curcumin C3 complex-loaded nanoparticles for cancer therapy
Authors: Ranjan Amalendu P , Mukerjee Anindita , Helson Lawrence , Vishwanatha Jamboor K 
Published: September 2012

Abstract

Background
Nanoparticle based delivery of anticancer drugs have been widely investigated. However, a very important process for Research & Development in any pharmaceutical industry is scaling nanoparticle formulation techniques so as to produce large batches for preclinical and clinical trials. This process is not only critical but also difficult as it involves various formulation parameters to be modulated all in the same process.

Methods
In our present study, we formulated curcumin loaded poly (lactic acid-co-glycolic acid) nanoparticles (PLGA-CURC). This improved the bioavailability of curcumin, a potent natural anticancer drug, making it suitable for cancer therapy. Post formulation, we optimized our process by Reponse Surface Methodology (RSM) using Central Composite Design (CCD) and scaled up the formulation process in four stages with final scale-up process yielding 5 g of curcumin loaded nanoparticles within the laboratory setup. The nanoparticles formed after scale-up process were characterized for particle size, drug loading and encapsulation efficiency, surface morphology, in vitro release kinetics and pharmacokinetics. Stability analysis and gamma sterilization were also carried out.

Results
Results revealed that that process scale-up is being mastered for elaboration to 5 g level. The mean nanoparticle size of the scaled up batch was found to be 158.5 ± 9.8 nm and the drug loading was determined to be 10.32 ± 1.4%. The in vitro release study illustrated a slow sustained release corresponding to 75% drug over a period of 10 days. The pharmacokinetic profile of PLGA-CURC in rats following i.v. administration showed two compartmental model with the area under the curve (AUC0-∞) being 6.139 mg/L h. Gamma sterilization showed no significant change in the particle size or drug loading of the nanoparticles. Stability analysis revealed long term physiochemical stability of the PLGA-CURC formulation.

Conclusions
A successful effort towards formulating, optimizing and scaling up PLGA-CURC by using Solid-Oil/Water emulsion technique was demonstrated. The process used CCD-RSM for optimization and further scaled up to produce 5 g of PLGA-CURC with almost similar physicochemical characteristics as that of the primary formulated batch.
Insulin-stimulated phosphorylation of protein phosphatase 1 regulatory subunit 12B revealed by HPLC-ESI-MS/MS
Authors: Pham Kimberly , Langlais Paul , Zhang Xiangmin , Chao Alex , Zingsheim Morgan , Yi Zhengping 
Published: September 2012

Abstract

Background
Protein phosphatase 1 (PP1) is one of the major phosphatases responsible for protein dephosphorylation in eukaryotes. Protein phosphatase 1 regulatory subunit 12B (PPP1R12B), one of the regulatory subunits of PP1, can bind to PP1cδ, one of the catalytic subunits of PP1, and modulate the specificity and activity of PP1cδ against its substrates. Phosphorylation of PPP1R12B on threonine 646 by Rho kinase inhibits the activity of the PP1c-PPP1R12B complex. However, it is not currently known whether PPP1R12B phosphorylation at threonine 646 and other sites is regulated by insulin. We set out to identify phosphorylation sites in PPP1R12B and to quantify the effect of insulin on PPP1R12B phosphorylation by using high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry.

Results
14 PPP1R12B phosphorylation sites were identified, 7 of which were previously unreported. Potential kinases were predicted for these sites. Furthermore, relative quantification of PPP1R12B phosphorylation sites for basal and insulin-treated samples was obtained by using peak area-based label-free mass spectrometry of fragment ions. The results indicate that insulin stimulates the phosphorylation of PPP1R12B significantly at serine 29 (3.02 ± 0.94 fold), serine 504 (11.67 ± 3.33 fold), and serine 645/threonine 646 (2.34 ± 0.58 fold).

Conclusion
PPP1R12B was identified as a phosphatase subunit that undergoes insulin-stimulated phosphorylation, suggesting that PPP1R12B might play a role in insulin signaling. This study also identified novel targets for future investigation of the regulation of PPP1R12B not only in insulin signaling in cell models, animal models, and in humans, but also in other signaling pathways.