bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of a mentored research competition for authoring pediatric case reports in chiropractic
Authors: Pohlman Katherine A. , Vallone Sharon , Nightingale Lia M. 
Published: January 2013

Objective
A chiropractic pediatric specialist often encounters novel clinical findings not reported currently in the literature. This project matched board certified chiropractic pediatric specialists with a mentor experienced in scientific writing to co-author a research paper to add to the literature base available on chiropractic pediatric practice.

Methods
Clinicians who had received their Diplomate in Clinical Chiropractic Pediatrics and mentors in scientific writing were teamed up. Two surveys were conducted to collect quantitative data, and focus groups were held to gather qualitative data about the overall experience of the mentor and mentee (clinicians) participating in the study. The first survey was sent to the clinicians to gather information about their research idea and their experience in research. The second survey was conducted upon project completion by clinicians and mentors. A project wiki was used as a communication strategy.

Results
Ten reports were submitted by authorship teams. Time spent on this project was an average of 58 hours by clinicians and 36 hours by the mentors. Mentors aided by adding content material, editing manuscripts, and educating the clinicians in the art of writing a paper. Improvements for this project included clearer mentoring guidelines and not using the wiki as a communication venue.

Conclusion
The project ultimately fulfilled the goal of using a mentorship model to facilitate scientific writing education and ease the anxiety of authoring a first publication. The overall experience was “good”; however, there are opportunities for improvement.
SHAPE–Seq: High‐Throughput RNA Structure Analysis
Authors: Mortimer Stefanie A. , Trapnell Cole , Aviran Sharon , Pachter Lior , Lucks Julius B. 
Published: December 2012

AbstractKnowledge of RNA structure is critical to understanding both the important functional roles of RNA in biology and the engineering of RNA to control biological systems. This article contains a protocol for selective 2′‐hydroxyl acylation analyzed by primer extension and sequencing (SHAPE‐Seq) that, through a combination of structure‐dependent chemical probing and next‐generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment. This protocol is applicable in a variety of conditions, and represents an important tool for understanding RNA biology. The protocol includes methods for the design and synthesis of RNA mixtures for study, and the construction and analysis of structure‐dependent sequencing libraries that reveal structural information of the RNAs in the mixtures. The methods are generally applicable to studying RNA structure and interactions in vitro in a variety of conditions, and allows for the rapid characterization of RNA structures in a high‐throughput manner. Curr. Protoc. Chem. Biol. 4:275‐297 © 2012 by John Wiley & Sons, Inc.
Specificity Profiling of Protein‐Binding Domains Using One‐Bead‐One‐Compound Peptide Libraries
Authors: Kunys Andrew R. , Lian Wenlong , Pei Dehua 
Published: December 2012

AbstractOne‐bead‐one‐compound (OBOC) libraries consist of structurally related compounds (e.g., peptides) covalently attached to a solid support, with each resin bead carrying a unique compound. OBOC libraries of high structural diversity can be rapidly synthesized and screened without the need for any special equipment, and therefore can be employed in any chemical or biochemical laboratory. OBOC peptide libraries have been widely used to map the ligand specificity of proteins, to determine the substrate specificity of enzymes, and to develop inhibitors against macromolecular targets. They have proven particularly useful in profiling the binding specificity of protein modular domains (e.g., SH2 domains, BIR domains, and PDZ domains); subsequently, the specificity information can be used to predict the protein targets of these domains. The protocols outlined in this article describe the methodologies for synthesizing and screening OBOC peptide libraries against SH2 and PDZ domains, and the related data analysis. Curr. Protoc. Chem. Biol. 4:331‐355 © 2012 by John Wiley & Sons, Inc.
A Screening Protocol for Identification of Functional Mutants of RNA Editing Adenosine Deaminases
Authors: Eifler Tristan , Chan Dalen , Beal Peter A. 
Published: December 2012

AbstractGenetic screens can be used to evaluate a spectrum of mutations and thereby infer the function of particular residues within a protein. The Adenosine Deaminase Acting on RNA (ADAR) family of RNA‐editing enzymes selectively deaminate adenosines (A) in double‐helical RNA, generating inosine (I). The protocol described here exploits the editing activity of ADAR2 in a yeast‐based screen by inserting an editing substrate sequence with a stop codon incorporated at the editing site upstream from the sequence encoding the reporter α‐galactosidase. A‐to‐I editing changes the stop codon to a tryptophan codon, allowing normal expression of the reporter. This technique is particularly well‐suited for screening ADAR and ADAR substrate mutant libraries for editing activity. Curr. Protoc. Chem. Biol. 4:357‐369 © 2012 by John Wiley & Sons, Inc.
Evaluation of the suchey–brooks method of age estimation in an Australian subpopulation using computed tomography of the pubic symphyseal surface
Authors: Lottering Nicolene , MacGregor Donna M. , Meredith Matthew , Alston Clair L. , Gregory Laura S. 
Published: January 2013

AbstractDespite the prominent use of the Suchey–Brooks (S–B) method of age estimation in forensic anthropological practice, it is subject to intrinsic limitations, with reports of differential interpopulation error rates between geographical locations. This study assessed the accuracy of the S–B method to a contemporary adult population in Queensland, Australia and provides robust age parameters calibrated for our population. Three‐dimensional surface reconstructions were generated from computed tomography scans of the pubic symphysis of male and female Caucasian individuals aged 15–70 years (n = 195) in Amira® and Rapidform®. Error was analyzed on the basis of bias, inaccuracy and percentage correct classification for left and right symphyseal surfaces. Application of transition analysis and Chi‐square statistics demonstrated 63.9 and 69.7% correct age classification associated with the left symphyseal surface of Australian males and females, respectively, using the S–B method. Using Bayesian statistics, probability density distributions for each S–B phase were calculated, providing refined age parameters for our population. Mean inaccuracies of 6.77 (±2.76) and 8.28 (±4.41) years were reported for the left surfaces of males and females, respectively; with positive biases for younger individuals (<55 years) and negative biases in older individuals. Significant sexual dimorphism in the application of the S–B method was observed; and asymmetry in phase classification of the pubic symphysis was a frequent phenomenon. These results recommend that the S–B method should be applied with caution in medico‐legal death investigations of Queensland skeletal remains and warrant further investigation of reliable age estimation techniques. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.
Chylous ascites after hepatopancreatobiliary surgery
Authors: Kuboki S , Shimizu H , Yoshidome H , Ohtsuka M , Kato A , Yoshitomi H , Furukawa K , Miyazaki M 
Published: January 2013

AbstractBackgroundPostoperative chylous ascites following abdominal surgery is uncommon. It potentially induces malnutrition and immunodeficiency, contributing to increased mortality. In the field of hepatopancreatobiliary (HPB) surgery, no large studies have been conducted that focused on postoperative chylous ascites. The aim of this study was to determine the incidence, risk factors and management of chylous ascites following HPB surgery, with particular emphasis on pancreatic resection.MethodsConsecutive patients who had HPB surgery between 2000 and 2011 at a single institution were reviewed retrospectively. Chyle leak was defined as 100 ml/day or more of milky, amylase-free peritoneal fluid with a triglyceride concentration of 110 mg/dl or above. Risk factors for chylous ascites associated with pancreatic resection and the clinical efficacy of octreotide in treating chylous ascites were evaluated.ResultsOf 2002 consecutive patients who underwent HPB surgery during the study period, 21 (1·0 per cent) developed chylous ascites. Chylous ascites occurred relatively frequently in patients who had a pancreatic resection, such as pancreaticoduodenectomy (3·3 per cent) or distal pancreatectomy (3·8 per cent). Multivariable analysis revealed that manipulation of the para-aortic area (P &lt; 0·001), retroperitoneal invasion (P = 0·031) and early enteral feeding after operation (P &lt; 0·001) were independent risk factors for chylous ascites following pancreatic resection. Octreotide treatment decreased drainage output of chylous ascites on day 1 after initiation of treatment (P = 0·002).ConclusionChylous ascites is a rare complication following HPB surgery. It is more common after pancreatic resection. Treatment with octreotide combined with total parenteral nutrition is recommended.
Simulation‐based estimates of safety distances for pipeline transportation of carbon dioxide
Authors: Mazzoldi Alberto , Picard David , Sriram Papagudi G. , Oldenburg Curtis M. 
Published: January 2013

AbstractPipeline transportation of fluids is a proven technology for moving large quantities of liquids and gases (e.g. hydrocarbons, hazardous liquids, hydrogen). The anticipated introduction of large‐scale geologic carbon sequestration (GCS) as a means of reducing greenhouse gas (GHG) emissions will require the ability to transport massive amounts of carbon dioxide (CO2) safely and economically. To accommodate GCS demands, the existing US and European CO2 pipeline infrastructure may eventually have to be expanded to be comparable in size to natural gas and oil pipeline systems. Furthermore, the new pipeline infrastructure will inevitably intersect with population centers as it connects sources with sink areas. There are important unanswered questions about pipeline network requirements, regulations, utility cost recovery, economics, regulatory classification of CO2 itself, and pipeline safety. The focus of this research is on this last aspect, i.e. safety of the general public, workers, and property related to the transportation of CO2. We carried out simulations that coupled two computational fluid dynamics (CFD) codes to determine: (i) leakage rates from fully ruptured above‐ground CO2 pipelines for a typical pipeline fluid composition, and (ii) the resulting atmospheric dispersion of the gas near the broken pipe. Using threshold values for atmospheric CO2 concentration, our work shows that concentrations dangerous to human health can extend on the order of hundreds of meters from the ruptured pipeline. This work contributes to the knowledge base needed to establish safety distances for routing CO2 pipelines through inhabited and other sensitive areas. © 2012 Society of Chemical Industry and John Wiley & Sons, Ltd
FEW: A workflow tool for free energy calculations of ligand binding
Authors: Homeyer Nadine , Gohlke Holger 
Published: January 2013

AbstractIn the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.
Multi‐proxy study of Holocene environmental change and human activity in the Central Apennine Mountains, Italy
Authors: Brown A. G. , Hatton J. , Selby K. A. , Leng M. J. , Christie N. 
Published: January 2013

AbstractThis paper describes a multi‐proxy palaeoecological investigation undertaken in conjunction with an archaeological survey of the Upper Sangro Valley in the Abruzzo National Park, Central Italy. Despite being a biodiversity hotspot and regarded as a near‐pristine area, the pollen, spore and diatom data all show major changes in the vegetation extending to over 2000 m a.s.l. during the mid to late Holocene. Although there are changes in ecological composition earlier in the Holocene they are different in type and magnitude from the changes which began about 800 cal a BC. The pollen and diatom evidence do not correlate well with regional palaeoclimate data, or on‐site isotopic evidence, but do appear to be related to Samnite (later Iron Age) clearance and upland grazing associated with transhumance and later annexation (and centuriation) of the lower slopes by Roman surveyors. The greatest change in vegetation was during the period c. AD 500–600 and corresponds with the Byzantine–Gothic Wars, and Lombard–Carolingian settlement reorganization into nucleated hilltop settlements which managed upland grazing. This pattern of intensive land use at all altitudes persisted until the early 20th century and only changed following rural depopulation after World War II. These data illustrate how cultural factors had a profound effect on this mountainous region which, in this case, far outweighed the effects of climatic fluctuations which are known to have occurred from both this study area and the region. Copyright © 2012 John Wiley & Sons, Ltd.
Barcode DNA high‐resolution melting (Bar‐HRM) analysis as a novel close‐tubed and accurate tool for olive oil forensic use
Authors: Ganopoulos Ioannis , Bazakos Christos , Madesis Panagiotis , Kalaitzis Panagiotis , Tsaftaris Athanasios 
Published: January 2013

AbstractBACKGROUNDThe adulteration of high‐priced olive oil with low‐cost oils and the fraudulent labelling of oil products make the identification and traceability of vegetable oil species in the food chain very important. This paper describes a high‐resolution melting analysis‐based method using chloroplast barcoding regions as target (Bar‐HRM) to obtain barcoding information for the major vegetable oil species and to quantitatively identify the botanical origin of plant oils. The detection of adulteration of olive oil with canola oil was used as a case study.RESULTSThe proposed method was capable of distinguishing among different vegetable oil species and detecting a level of 1% (w/w) of canola oil in olive oil.CONCLUSIONBar‐HRM analysis is a more accurate, faster and less costly alternative method to authenticate vegetable oils, including olive oil, and to detect mixtures of oils. © 2013 Society of Chemical Industry
Associations of body fat percent and body mass index with childhood asthma by age and gender
Authors: Yiallouros Panayiotis K. , Lamnisos Demetris , Kolokotroni Ourania , Moustaki Maria , Middleton Nicos 
Published: January 2013

ObjectiveHigh body mass index (BMI) has been shown to be associated with asthma, but the pattern of this association is still unclear and may differ by gender or stage of puberty. BMI is only a proxy of adiposity, whereas estimation of body fat percent (BF%) by the bioimpedance technique is considered an accurate measure of adiposity. We investigated whether BMI and BF% behave differently in their association with asthma between genders, before and during adolescence.Design and MethodsIn this cross‐sectional study of 10,981 schoolchildren, we used logistic regression models to examine the pattern of association of BMI and BF% with asthma.ResultsIn the case of BF%, both the highest (odds ratio [OR]: 1.68, 95% confidence interval [95% CI]: 1.21‐2.30) and lowest (OR: 1.59, 95% CI: 1.13‐2.23) z‐score categories conferred an increased adjusted risk for active asthma. The likelihood ratio test (LRT) of nonlinearity yielded significant results (P < 0.01) for BF%. In contrast, the LRT for BMI yielded a nonsignificant result (P = 0.45) indicating a linear association of asthma with BMI. A unit increase in BMI z‐score conferred an increase in the adjusted odds of active asthma (OR: 1.14, 95% CI: 1.02‐1.27). In the case of BF%, the adjusted ORs for active asthma at the highest and lowest z‐score categories in both genders, before and during adolescence, were similarly elevated, exhibiting a U‐shape pattern.ConclusionsIn contrast to the linear association observed with BMI, BF% displayed a U‐shaped association with asthma and may be the preferred measure of adiposity in epidemiological studies of asthma in children.
Knockdown of diacylglycerol kinase delta inhibits adipocyte differentiation and alters lipid synthesis
Authors: Lowe Christopher E. , Zhang Qifeng , Dennis Rowena J. , Aubry Evelyne M. , O'Rahilly Stephen , Wakelam Michael J.O. , Rochford Justin J. 
Published: January 2013

ObjectiveDecreased expression of diacylglycerol kinase delta (DGKδ) has been linked to insulin resistance in humans and mice and it is abundantly expressed in adipose tissue. Therefore, its role in adipogenesis was examined.Design and Methods3T3‐L1 pre‐adipocytes were generated in which DGKδ expression had been knocked down and the effect of this on adipogenesis was determined. Lipidomic analyses were performed to determine levels of the DGKδ product phosphatidic acid (PA), its substrate diacylglycerol (DAG) and triglyceride (TG).ResultsInhibiting DGKδ expression prevents adipogenesis. DGKδ knockdown in differentiating adipocytes blunted the increase in total levels of PA and DAG but did not affect the early rise in TG levels. DAG or PA species acting as TG precursors were only modestly reduced by DGKδ knockdown which significantly impaired the accumulation of DAG or PA species implicated in intracellular signaling. The DAG activated kinase PKCδ was also stimulated in DGKδ knockdown cells, despite no increase in detectable species of DAG.ConclusionsDGKδ is a novel regulator of adipogenesis and phosphorylates a quantitatively small pool of signaling DAG important for differentiation and indirectly affects overall levels of signaling DAG and PA species distinct from those acting as precursors for TG synthesis.
The relationship between measures of obesity and incident heart failure: The multi‐ethnic study of atherosclerosis
Authors: Ebong Imo A. , Goff David C. , Rodriguez Carlos J. , Chen Haiying , Bluemke David A. , Szklo Moyses , Bertoni Alain G. 
Published: January 2013

Objective: To evaluate the strength of association of body mass index (BMI) and waist circumference (WC) with incident heart failure (HF), exploring our associations by ethnicity and age.Design and Methods: 6,809 participants, aged 45‐84 years old, without clinical cardiovascular disease (2000–2002), from the Multi‐Ethnic Study of Atherosclerosis were included. Cox‐Proportional hazards models were used to examine associations of BMI and WC with incident HF. The predictive abilities of BMI and WC were compared using receiver operating characteristic curves.Results: Over a median follow‐up of 7.6 years, there were 176 cases. BMI and WC were associated with incident HF in men (1.33 [1.10‐1.61] and 1.38 [1.18‐1.62], respectively] and women (1.70 [1.33‐2.17] and 1.64 [1.29‐2.08], respectively). These associations became non‐significant after adjusting for obesity‐related conditions (hypertension, dysglycemia, hypercholesterolemia, left ventricular hypertrophy, kidney disease, and inflammation). The associations of BMI and WC did not vary significantly by ethnicity or age‐group, but were inverse in Hispanic men. The area under the curve for BMI and WC was 0.749 and 0.750, respectively, in men and 0.782 and 0.777, respectively, in women.Conclusions: The association between obesity and incident HF is largely mediated by obesity‐related conditions. BMI and WC have similar predictive abilities for incident HF.
Increased autophagy in the placental territory of selective intrauterine growth‐restricted monochorionic twins
Authors: Chang Yao‐Lung , Wang Tzu‐Hao , Chang Shuenn‐Dyh , Chao An‐Shine , Hsieh Peter C. C. , Wang Chao‐Nin 
Published: January 2013

ABSTRACTSubjectThis study investigates the placental autophagic activity in growth‐restricted fetuses in the monochorionic (MC) twin model.Patients and methodsForty MC twins were prospectively enrolled in this study, including 21 with and 19 without selective intrauterine growth restriction (sIUGR), defined as birth weight below the tenth percentile. The sIUGR group was subdivided on the basis of present versus absent or reversed umbilical artery end‐diastolic flow at Doppler. Placenta samples were taken after delivery from each twin placenta territories. After protein extraction, Western blot was used to determine light chain 3 (LC3)‐II placental protein expression in sIUGR and appropriately grown (appropriate‐for‐gestational age, AGA) twins.ResultsThe LC3‐II was significantly higher in the sIUGR twin placental territory than in their AGA counterparts. In the sIUGR group, LC3‐II fold change was significantly increased compared with that in the AGA cotwins (2.28 vs 1.04, p < 0.05). Placental LC3‐II protein expression was particularly stimulated in the MC sIUGR group with abnormal umbilical artery Doppler flow compared with AGA controls (p < 0.05, one‐way analysis of variance test).ConclusionsIn MC twins, the placental autophagic activity is different between sIUGR and AGA cotwins. The placenta territory with the least blood flow perfusion has the highest autophagic activity. © 2013 John Wiley & Sons, Ltd.
A review of pharmaceutical labeling for overdose treatment and toxicity data
Authors: Mazer‐Amirshahi Maryann , Sokol Gerald , van den Anker John , Cantilena Louis 
Published: January 2013

ABSTRACTPurposeAdverse drug reactions, including overdose are a major cause of morbidity and mortality, yet clinical toxicology data is limited at the time of drug approval. This study was conducted to determine the quality of clinical toxicology data available for newly approved pharmaceuticals and time to labeling revisions.MethodsThe labeling data of 100 new molecular entities (NMEs) approved between 2005 and 2011 was systematically reviewed. Initial approval data and subsequent labeling revisions were evaluated. The type and quality of clinical toxicology data present at the time of approval as well as the time to any labeling revisions was recorded. The presence of black box warnings and Risk Evaluation and Mitigation Strategies (REMS) was noted.ResultsOf the NMEs reviewed, 27 had agent‐specific toxicology data at approval. General recommendations for overdose management were made in 45 cases. Eight pharmaceuticals had toxicology updates during the study period. The average time to labeling revision was 27.4 months. Expanded adverse effects from case reports comprised 7/8 of the updates, and animal data was added in one case. Over a third of the NMEs had a black box warning or REMS status, suggesting potential for significant human toxicity.ConclusionsOur study suggests there is a paucity of clinical toxicology data at the time of drug approval, with a notable lag time between initial approval and labeling revisions. This lack of toxicology data limits the ability of providers to optimally care for poisoned patients. Copyright © 2013 John Wiley & Sons, Ltd.