bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
Authors: Ishimaru Daniella , Plant Ewan P. , Sims Amy C. , Yount Boyd L. , Roth Braden M. , Eldho Nadukkudy V. , Pérez-Alvarado Gabriela C. , Armbruster David W. , Baric Ralph S. , Dinman Jonathan D. , Taylor Deborah R. , Hennig Mirko 
Published: December 2012

Abstract
Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.
A Step toward Nonrobotic Total Endoscopic Coronary Bypass Grafting: 40 Coronary Anastomoses in a Biomechanical Beating Heart Model
Authors: Gorki Hagen , Patel Nirav C. , Liewald Christian , Wildhirt Stephen , Subramanian Valavanur A. , Liebold Andreas 
Published: December 2012

Objective Nonrobotic total endoscopic coronary bypass grafting is commonly considered as technically too difficult. After endoscopic practicing in a simple box model, we questioned this statement in a more sophisticated training model. Methods In a handmade chest model containing a mechanically actuated porcine heart, anastomoses between homologous vein and shunted anterior coronary artery were performed using Prolene 7–0 sutures or U-clips in 20 anastomoses each. Commercially available endoscopic instruments and exclusive two-dimensional endoscopic vision were used. As quality control, the procedures were recorded, flow was measured, indocyanine green dye angiograms were performed, vinylpolysiloxane endocasts were produced, and finally the anastomoses were assessed from the endothelial side. Three-dimensional computed tomographic reconstruction was explored for cast measuring. Results All anastomoses were completed successfully in a time of 51 ± 14 minutes (Prolene) and 48 ± 10 minutes (U-clips). Despite suboptimal equipment, a reproducible sequence of the procedure was established and documented. Improving surgical performance was reflected in a reduction in anastomotic leakage and time requirement. The quality assessment protocol showed a learning curve and problems itself, which are briefly discussed. Conclusions A beating heart model is an adamant requirement of training for the technically demanding procedure of nonrobotic total endoscopic coronary bypass grafting. Refinement of the model and quality assessment as well as expansion of training to other regions of the heart should prepare for a cost-effective, broad-based clinical application of nonrobotic endoscopic techniques in coronary surgery. Available high-definition three-dimensional vision systems and the development of appropriate (articulating) instruments will make the procedure safer and quicker and will cut the learning curve.
Does Body Mass Index Affect Outcomes in Robotic-Assisted Coronary Artery Bypass Procedures?
Authors: Hemli Jonathan M. , Darla Lincoln S. , Panetta Christopher R. , Jennings Joan , Subramanian Valavanur A. , Patel Nirav C. 
Published: December 2012

Objective Obese patients pose unique technical challenges for minimal-access cardiac surgery. We sought to examine the effect of body mass index on short-term outcomes in robotic-assisted coronary surgery. Methods From January 2010 to November 2011, a total of 110 consecutive patients underwent robotic-assisted coronary surgery at our institution. All patients had robotic-assisted mobilization of the left internal mammary artery. Some patients then underwent direct coronary anastomosis to the left anterior descending coronary artery via a left mini thoracotomy, whereas others had a complete robotic endoscopic procedure within the closed chest. The short-term outcomes of obese patients (n = 39), defined as body mass index greater than 30 kg/m2, were compared with those of nonobese patients (n = 71). Results Mean left internal mammary artery harvest time was longer in obese patients than in nonobese patients (51.03 vs 39.94 minutes; P = 0.007), as was overall operative time (218.15 vs 186.72 minutes; P = 0.034). There were no significant differences in mortality or major morbidity between obese and nonobese patients. Conclusions Obesity does not adversely affect short-term outcomes in robotic-assisted coronary surgery, although operative times are somewhat longer for these patients. Robotic-assisted coronary techniques can be safely pursued in obese patients.
Management of Pleural Empyema with Single-Port Video-Assisted Thoracoscopy
Authors: Marra Alessandro , Huenermann Christoph , Ross Bernd , Hillejan Ludger 
Published: December 2012

Objective The aim of this study was to evaluate the safety and efficacy of an original technique of single-port video-assisted thoracoscopy (S-VATS) for the minimally invasive treatment of pleural empyema in fibrinopurulent stage. Methods Single-port video-assisted thoracoscopy was performed under general anesthesia and single-lung ventilation using a 2-cm incision after ultrasound localization of the projected midpoint of the pleural effusion. Through the single access, a video scope and standard thoracoscopy instruments were simultaneously introduced to perform debridement and lavage of the pleural cavity. Postoperatively, patients underwent continuous or intermittent pleural irrigation through the chest tube until microbiological confirmation of sterility of the pleural fluid. Results Between November 2004 and December 2009, a total of 61 patients underwent S-VATS for pleural empyema in stage I(7%) or II (93%). Median age was 63.5 years (range, 22–94 years). Male-to-female ratio was 4.2. Surgery was performed 3 to 60 days after the onset of symptoms. Macroscopically complete debridement of the pleural cavity was achieved in most (98%) cases. Median operation time was 53 minutes (range, 29–90 minutes). No intraoperative complications occurred. In-hospital mortality and morbidity rates were 3% and 16%, respectively. Deaths were caused by diffuse metastatic colon cancer in one case and severe apoplectic insult in the other. Chest tube was removed after a median time of 12 days (range, 4–64 days). Four (6.5%) patients experienced a relapse of empyema; this was caused by complicated residual pleural space (two cases), persistent pleuropulmonary fistula (one case), or both (one case). Conclusions It seems that S-VATS is a safe and effective procedure for the treatment of pleural empyema in fibrinopurulent stage.
Serum 25‐Hydroxyvitamin D Levels in Preschool‐Age Children in Northern Sweden Are Inadequate After Summer and Diminish Further During Winter
Authors: Öhlund Inger , Silfverdal Sven‐Arne , Hernell Olle , Lind Torbjörn 
Published: December 2012

ABSTRACTBackground and Objective:Despite studies indicating that vitamin D intake among Swedish children does not meet the recommendation, little is known of their vitamin D status. The aim of the present study was to examine vitamin D status in preschool‐age children in relation to vitamin D intake, season, body mass index, and skin color.Methods:Preschool‐age children (n = 90; mean age 54 ± 7.1 months), all living in northern Sweden (latitude 63° north), half of them with fair skin, half with darker complexion, were recruited from well‐baby clinics. The study group was examined first in August–September (late summer) and then the following January–February (winter). Skin type, vitamin D intake, anthropometrics, serum 25‐hydroxyvitamin D (S‐25[OH] D), and serum parathyroid hormone were assessed.Results:Mean ± SD S‐25(OH) D in summer and winter were 60 ± 15 nmol/L and 55 ± 16 nmol/L, respectively (P < 0.001). Fifteen percent and 10% had S‐25(OH) D ≥75 nmol/L, and 25% and 40% had S‐25(OH) D <50 nmol/L, respectively. The mean vitamin D intake was higher in dark‐skinned compared with fair‐skinned children. In spite of this, S‐25(OH) D in dark‐skinned children was lower compared with fair‐skinned children during both seasons. The dietary intake of vitamin D was positively associated with S‐25(OH) D levels.Conclusions:Vitamin D status is inadequate in preschool‐age children living in northern Sweden, especially in dark‐skinned children and during the winter despite vitamin D intakes meeting the recommendations, prompting strategies to improve intake of vitamin D in this population.
Metabolic Effects of Roux‐en‐Y Gastric Bypass in Obese Adolescents and Young Adults
Authors: Sinha Manasi , Stanley Takara L. , Webb Jessica , Scirica Christina , Corey Kathleen , Pratt Janey , Boepple Paul A. , Hoppin Alison , Misra Madhusmita 
Published: December 2012

ABSTRACTWeight loss surgery is an increasingly common treatment option for obese adolescents, but data are limited regarding the metabolic effects of surgical weight loss procedures. We performed a retrospective review of the electronic medical record to determine metabolic outcomes for 24 adolescents and young adults ages 15 to 22 years undergoing Roux‐en‐Y gastric bypass from 2009 to 2011 as well as 24 age‐, sex‐, and BMI‐matched controls. During a median follow‐up of 6 months after Roux‐en‐Y gastric bypass, fasting glucose, hemoglobin A1c, low‐density lipoprotein, triglyceride, and high‐sensitivity C‐reactive protein decreased significantly. Changes in these measures were not significantly associated with age or extent of weight loss.
Stability of Essential Oils: A Review
Authors: Turek Claudia , Stintzing Florian C. 
Published: January 2013

AbstractIn recent years, consumers have developed an ever‐increasing interest in natural products as alternatives for artificial additives or pharmacologically relevant agents. Among them, essential oils have gained great popularity in the food, cosmetic, as well as the pharmaceutical industries. Constituting an array of many lipophilic and highly volatile components derived from a great range of different chemical classes, essential oils are known to be susceptible to conversion and degradation reactions. Oxidative and polymerization processes may result in a loss of quality and pharmacological properties. Despite their relevance for consumers, there is a paucity of information available addressing this issue. Therefore, the present review provides a comprehensive summary on possible changes in essential oils and factors affecting their stability. Focusing on individual essential oils, the various paths of degradation upon exposure to extrinsic parameters are outlined. Especially temperature, light, and oxygen availability are recognized to have a crucial impact on essential oil integrity. Finally, analytical methods to assess both genuine as well as altered essential oil profiles are evaluated with respect to their suitability to track chemical alterations. It is believed that only a careful inspection of essential oils by a set of convenient methods allows profound quality assessment that is relevant to producers and consumers alike.
Glioblastoma with Oligodendroglioma Component (GBM‐O): Molecular Genetic and Clinical Characteristics
Authors: Appin Christina L. , Gao Jingjing , Chisolm Candace , Torian Mike , Alexis Dianne , Vincentelli Cristina , Schniederjan Matthew J. , Hadjipanayis Costas , Olson Jeffrey J. , Hunter Stephen , Hao Chunhai , Brat Daniel J. 
Published: January 2013

AbstractGlioblastoma (GBM) is an aggressive primary brain tumor with an average survival of approximately 1 year. A recently recognized subtype, glioblastoma with oligodendroglioma component (GBM‐O), was designated by the World Health Organization (WHO) in 2007. We investigated GBM‐Os for their clinical and molecular characteristics as compared to other forms of GBM. Tissue samples were used to determine EGFR, PTEN, and 1p and 19q status by fluorescence in situ hybridization (FISH); p53 and mutant IDH1 protein expression by immunohistochemistry (IHC); and MGMT promoter status by methylation‐specific polymerase chain reaction (PCR). GBM‐Os accounted for 11.9% of all GBMs. GBM‐Os arose in younger patients compared to other forms of GBMs (50.7 years vs. 58.7 years, respectively), were more frequently secondary neoplasms, had a higher frequency of IDH1 mutations and had a lower frequency of PTEN deletions. Survival was longer in patients with GBM‐Os compared to those with other GBMs, with median survivals of 16.2 and 8.1 months, respectively. Most of the survival advantage for GBM‐O appeared to be associated with a younger age at presentation. Among patients with GBM‐O, younger age at presentation and 1p deletion were most significant in conferring prolonged survival. Thus, GBM‐O represents a subset of GBMs with distinctive morphologic, clinical and molecular characteristics.
Identification of novel caspase/autophagy‐related gene switch to cell fate decisions in breast cancers
Authors: Fu L.‐L. , Yang Y. , Xu H.‐L. , Cheng Y. , Wen X. , Ouyang L. , Bao J.‐K. , Wei Y.‐Q. , Liu B. 
Published: January 2013

AbstractObjectivesCaspases, a family of cysteine proteases with unique substrate specificities, contribute to apoptosis, whereas autophagy‐related genes (ATGs) regulate cytoprotective autophagy or autophagic cell death in cancer. Accumulating evidence has recently revealed underlying mechanisms of apoptosis and autophagy; however, their intricate relationships still remain to be clarified. Identification of caspase/ATG switches between apoptosis and autophagy may address this problem.Materials and methodsIdentification of caspase/ATG switches was carried out using a series of elegant systems biology & bioinformatics approaches, such as network construction, hub protein identification, microarray analyses, targeted microRNA prediction and molecular docking.ResultsWe computationally constructed the global human network from several online databases and further modified it into the basic caspase/ATG network. On the basis of apoptotic or autophagic gene differential expressions, we identified three molecular switches [including androgen receptor, serine/threonine‐protein kinase PAK‐1 (PAK‐1) and mitogen‐activated protein kinase‐3 (MAPK‐3)] between certain caspases and ATGs in human breast carcinoma MCF‐7 cells. Subsequently, we identified microRNAs (miRNAs) able to target androgen receptor, PAK‐1 and MAPK‐3, respectively. Ultimately, we screened a range of small molecule compounds from DrugBank, able to target the three above‐mentioned molecular switches in breast cancer cells.ConclusionsWe have systematically identified novel caspase/ATG switches involved in miRNA regulation, and predicted targeted anti‐cancer drugs. These findings may uncover intricate relationships between apoptosis and autophagy and thus provide further new clues towards possible cancer drug discovery.
Evidence of differential selection for the −α3.7 and −α4.2 single‐α‐globin gene deletions within the same population
Authors: Yap Zhi Min , Sun Kar Mun , Teo Clara R.L. , Tan Arnold S.C. , Chong Samuel S. 
Published: January 2013

AbstractSince the 1950s, a strong correlation between high carrier rates for β‐thalassemia mutations and selective survival advantage in tropical and subtropical ‘malarial belt’ regions has been established. Due to the relatively more complex genetics of α‐thalassemia, a similar relationship was demonstrated for α‐globin gene mutations only from the 1980s, with both single‐ and double‐α‐globin gene deletions prevalent in the malarial belt. Mechanistically, the single‐α‐globin gene deletions arise from non‐allelic recombination between the homologous α1 (HBA1) and α2 (HBA2) globin genes. Compared to the −α3.7 and αααanti3.7 rightward crossover alleles, much less is known about the −α4.2 and αααanti4.2 leftward crossover alleles. We performed a survey of 1,285 unselected cord blood samples from the 3 major ethnic groups in Singapore. Overall, the frequency of the −α3.7 deletion was significantly higher than its reciprocal αααanti3.7 triplication, consistent with positive selection for the −α3.7 single‐gene deletion. In marked contrast, there was no significant difference in frequency between the −α4.2 and reciprocal αααanti4.2 alleles, suggesting the absence of positive selection for the −α4.2 single‐gene deletion. The similar αααanti3.7 and αααanti4.2 allele frequencies also suggested that the crossover rates at X and Z homology boxes are similar. Taken together, these observations suggest a differential positive selection for the −α3.7 and −α4.2 alleles within the same population. Further population and biological studies may be required to explain these current observations.
Structural and functional aspects of PR‐10 proteins
Authors: Fernandes Humberto , Michalska Karolina , Sikorski Michal , Jaskolski Mariusz 
Published: January 2013

Physical, chemical and biological stress factors, such as microbial infection, upregulate the transcription levels of a number of plant genes, coding for the so‐called pathogenesis‐related (PR) proteins. For PR proteins of class‐10 (PR‐10), the biological function remains unclear, despite two decades of scientific research. PR‐10 proteins have a wide distribution throughout the plant kingdom and the class members share size and secondary structure organization. Throughout the years, we and other groups have determined the structures of a number of PR‐10 proteins, both in the crystalline state by X‐ray diffraction and in solution by NMR spectroscopy. Despite the accumulating structural information, our understanding of PR‐10 function is still limited. PR‐10 proteins are rather small (~ 160 amino acids) with a fold consisting of three α helices and seven antiparallel β strands. These structural elements enclose a large hydrophobic cavity that is most probably the key to their functional relevance. Also, the outer surface of these proteins is of extreme interest, as epitopes from a PR‐10 subclass cause allergic reactions in humans.
Effects of species richness and functional groups on chemical constituents relevant for methane yields from anaerobic digestion: results from a grassland diversity experiment
Authors: Khalsa J. , Fricke T. , Weigelt A. , Wachendorf M. 
Published: December 2012

AbstractChanges in livestock production systems have led to land‐use changes and abandonment, especially of semi‐natural grassland in agriculturally less favoured regions. The generation of energy from biomass of extensive, high‐diversity grasslands can be an alternative to their abandonment, and anaerobic digestion is one possible method for converting grassland biomass into energy. However, little is known about the effects of species richness (SR) and functional groups on chemical constituents relevant for anaerobic digestion and the resulting energy potential. In this study, changes in the herbage chemical constituents that are relevant for forage quality were studied along a well‐defined diversity gradient (one to sixty species) and across different combinations of functional groups (legumes, small herbs, tall herbs and grasses). Substrate‐specific methane yield (CH4 sub) was estimated through the concentrations of forage‐quality parameters such as crude fibre (CF), crude protein (CP), crude lipid, nitrogen‐free extract and their documented digestibility values, as well as the respective methane yields. Results show that with increasing SR, the CF increased and CP decreased, even though these effects could not be fully disentangled from the presence of grasses. These trends led to a negative effect of SR on CH4 sub, while the area‐specific methane yield (CH4 area = CH4 sub × biomass yield) increased due to a strong increase in biomass with increasing SR. The CH4 sub was increased when legumes were present, and it declined with the presence of grasses. Generally, CH4 sub and CH4 area varied between functional‐group monocultures and all functional‐group mixtures.
Isolation and characterization of H3N8 equine influenza A virus associated with the 2011 epizootic in Mongolia
Authors: Yondon Myagmarsukh , Heil Gary L. , Burks John P. , Zayat Batsukh , Waltzek Thomas B. , Jamiyan Bekh‐Ochir , McKenzie Pamela P. , Krueger Whitney S. , Friary John A. , Gray Gregory C. 
Published: January 2013

BackgroundEquine influenza virus (EIV) epizootics affect 2·1 million Mongolian horses approximately every 10 years and critically impact economy and nomadic livelihood of Mongolia.ObjectivesAn active surveillance program was established in 2011 to monitor influenza viruses circulating among Mongolian horses.MethodsNasal swabs were collected from horses in free‐ranging horse herds in Töv, Khentii, and Dundgovi aimags (provinces) from January to September 2011. Real‐time reversetranscriptase–polymerase chain reaction (rRT‐PCR) was used to determine the presence of influenza A virus. Influenza A‐positive specimens were cultured to amplify virus; viral RNA was extracted, and gene segments were amplified and sequenced by Sanger sequencing.ResultsA total of 745 horses were swabbed; most horses were without clinical signs of illness. In July 2011, reports of influenza‐like illnesses emerged among horses in Mongolia's capital, and subsequently, surveillance efforts were adjusted to swab horses associated with the epizootic. Thirty‐four specimens of rRT‐PCR influenza‐positive virus were collected in May, June, August, and September. Three specimens yielded detectable virus. Gene sequence studies suggested that all three isolates were identical H3N8 viruses. Phylogenetic analyses indicated the strain was very similar to other H3N8 EIVs circulating in central Asia between 2007 and 2008.ConclusionsAs large Mongolian equine herds often seem to suffer from EIV epizootics, it seems prudent to continue such routine equine influenza surveillance. Doing so will provide an early warning system, should novel viruses emerge, help in assessing if EIV is crossing over to infect humans and provide data to assess the likely effectiveness of current EIV vaccines.