bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient expression of a Paenibacillus barcinonensis endoglucanase in Saccharomyces cerevisiae
Authors: Mormeneo María , Pastor FI Javier , Zueco Jesús
Published: June 2011

The endoglucanase coded by celA (GenBank Access No. Y12512) from Paenibacillus barcinonensis, an enzyme with good characteristics for application on paper manufacture from agricultural fibers, was expressed in Saccharomyces cerevisiae by using different domains of the cell wall protein Pir4 as translational fusion partners, to achieve either secretion or cell wall retention of the recombinant enzyme. Given the presence of five potential N-glycosylation sites in the amino acid sequence coded by celA, the effect of glycosylation on the enzymatic activity of the recombinant enzyme was investigated by expressing the recombinant fusion proteins in both, standard and glycosylation-deficient strains of S. cerevisiae. Correct targeting of the recombinant fusion proteins was confirmed by Western immunoblot using Pir-specific antibodies, while enzymatic activity on carboxymethyl cellulose was demonstrated on plate assays, zymographic analysis and colorimetric assays. Hyperglycosylation of the enzyme when expressed in the standard strain of S. cerevisiae did not affect activity, and values of 1.2 U/ml were obtained in growth medium supernatants in ordinary batch cultures after 24 h. These values compare quite favorably with those described for other recombinant endoglucanases expressed in S. cerevisiae. This is one of the few reports describing the expression of Bacillus cellulases in S. cerevisiae, since yeast expressed recombinant cellulases have been mostly of fungal origin. It is also the first report of the yeast expression of this particular endoglucanase.
Decolorization of Rice Bran Oil Using Modified Kaolin
Authors: Worasith Niramon , Goodman Bernard A. , Jeyashoke Narumon , Thiravetyan Paitip
Published: June 2011

Measurements show that kaolin from Ranong, obtained from a major deposit in southern Thailand, can be modified to produce a material that is suitable for decolorizing rice bran oil. Its sorption properties were determined after various physical and chemical modifications of this kaolin. Physical modification was achieved by grinding via a planetary ball mill (300 rpm for 1 h), and this was followed by chemical treatment using sulfuric or oxalic acids. The optimum decolorization capacity (~80%) was achieved by using 2 M sulfuric acid. With oxalic acid, the best results were obtained with 0.7 M, but these were slightly lower than those obtained with 2 M sulfuric acid. Compared to the original kaolin sample, the specific surface area of the modified clay increased from ~13 to ~244 cm2 g−1, and the total pore volume from 0.06 to 0.43 cm3 g−1. The pore size distribution curves show that most pores are in the mesoporous region with their diameters between 3.0–4.5 nm, and are suitable for adsorption of pigment molecules that are present in rice bran oil. Desorption and spectroscopic studies suggest that both electrostatic and chemical processes are involved in the interaction between pigments and active sites on the clay surface.
Solid Lipid Nanoparticles: Effect of Carrier Oil and Emulsifier Type on Phase Behavior and Physical Stability
Authors: Qian Cheng , Decker Eric Andrew , Xiao Hang , McClements David Julian
Published: June 2011

The impact of surfactant type and carrier oil type on the phase behavior and physical stability of emulsified tripalmitin was investigated. Solid lipid nanoparticles (SLNs) were prepared by homogenizing lipid and aqueous phases at a temperature (≈80 °C) above the melting point of tripalmitin, and then cooling the resulting oil‐in‐water emulsion to induce lipid droplet crystallization. When stored at 37 °C, tripalmitin particles had good long‐term stability (d < 150 nm) when coated with Tween 20, but were prone to aggregation and gelation when coated with modified starch (MS). Conversely, when stored at ≤20 °C tripalmitin particles coated by MS were more stable to aggregation/gelation than those coated by Tween 20. Blending tripalmitin with low melting point lipids (either medium chain triglycerides or orange oil) prior to homogenization led to a considerable alteration in the SLN phase behavior and stability. DSC measurements indicated that the presence of the carrier oils reduced the crystallization temperature, melting temperature, and melting enthalpy of tripalmitin. In addition, the carrier oils improved the stability of SLNs to particle aggregation and gelation, although some particle coalescence still occurred. These results have important implications for formulating colloidal delivery systems for utilization within the food and other industries.
Recurrence after surgery for equinus foot deformity in children with cerebral palsy: Assessment of predisposing factors for recurrence in a long-term follow-up study
Authors: Joo Sun Young , Knowtharapu Durga N. , Rogers Kenneth J. , Holmes Laurens , Miller Freeman
Published: June 2011

Background

Despite the large number of studies on the recurrence after surgery for equinus foot deformity in cerebral palsy (CP) patients, only a few investigations have reported long-term recurrence rates. Furthermore, little is known on the interval between the recurrent surgeries and the factors that lead to early recurrence. This study aimed to assess the overall recurrence after surgery for equinus foot deformity in patients with CP and to assess the factors associated with recurrence. We also aimed to determine the predisposing factors for early recurrence.

Methods

The medical records of 186 patients (308 feet) were reviewed in order to determine the recurrence after surgery for equinus foot deformity. The type of CP, type of surgery, age at surgery, functional mobility, passive dorsiflexion of the ankle at the last follow-up visit, and subsequent treatment were recorded. Kaplan–Meier survival analysis was employed, with the end point defined as reoperation.

Results

The mean age at surgery was 6.8 ± 2.5 years (range, 2.2–13.1). With the mean follow-up period of 11.3 years (range, 7.2–17.7), the overall recurrence rate was 43.8%. The recurrence rate was highest among patients with hemiplegia (62.5%). The Kaplan–Meier survival without repeat surgery estimate was shown to be 88.6% at 5 years and 59.6% at 10 years. Among children with hemiplegia and diplegia, the younger children (≤8 years of age) showed a higher rate of recurrence compared with the older children ( P = 0.04 and P = 0.01, respectively). In 41 feet (30.4%), reoperations were performed within 5 years after the primary surgery. Early recurrence was most prevalent among children with hemiplegia (50.0%). In children with diplegia and quadriplegia, the younger children underwent the secondary operation later than the older children ( P = 0.04 and P = 0.02, respectively).

Conclusion

Recurrence after surgery for equinus foot deformity is common and the age at surgery has a significant influence on recurrence. Recurrence can occur at any age while the child is still growing; therefore, it is advised to follow those patients until they reach skeletal maturity.

Level of Evidence

Level III, therapeutic study.
Confirmatory Factor Analysis of the Patient Health Questionnaire‐9: A Study of the Participants From the Spinal Cord Injury Model Systems
Authors: Krause James S. , Saunders Lee L. , Bombardier Charles , Kalpakjian Claire
Published: June 2011

Objective

To examine the factor structure of the Patient Health Questionnaire‐9, a measure of depression, in persons with spinal cord injury (SCI).

Design

Cross‐sectional, confirmatory factor analytic study.

Setting

Community.

Participants

Data for 7296 persons with an SCI who had sustained their injury at least 1 year prior to assessment and who had complete Patient Health Questionnaire‐9 data collected at a follow‐up interview were drawn from the National Spinal Cord Injury Statistical Center Database.

Interventions

None.

Main outcome measures

Factor structure of the Patient Health Questionnaire‐9.

Results

Confirmatory factor analysis indicated a marginal fit for the single factor solution (root mean square error of approximation [RMSEA] = 0.086), whereas the solution with 5 somatic items and 4 nonsomatic items had the best fit (RMSEA = 0.054) among 2‐factor models that used all 9 items. Of the models that used fewer than 9 items, the best fit was for the 6‐item solution with 3 somatic items (sleep, appetite, and fatigue) and 3 nonsomatic items (feeling down, feeling bad about self, and suicidal ideation; RMSEA = 0.043). Similar results were found across the strata except for the Hispanic group (for whom no model fit well).

Conclusions

Given the results of this analysis that support a 2‐factor structure of the Patient Health Questionnaire‐9 in persons with SCI, the next step in this line of research is to validate each of these dimensions against other ways of measuring depression.
High Altitude Ataxia—Its Assessment and Relevance
Authors: Bird Brynn A. , Wright Alexander David , Wilson Mark H. , Johnson Brian G. , Imray Chris H.
Published: June 2011

Ataxia at altitude is reviewed in relation to acute mountain sickness (AMS). The cause of ataxia occurring at altitude is unknown but may be hypoxia affecting basal ganglia and hindbrain activity. Ataxia is an important sign of high altitude cerebral edema (HACE) but is less well-established as a clinical feature of AMS. Assessment of ataxia is part of the Environmental Systems and the Lake Louise questionnaires, together with a heel-to-toe measurement. More precise measures of ataxia include the Sharpened Romberg Test (SRT) and the use of unstable platforms. Isolated ataxia at altitude may not be related to AMS or HACE. Age affects ataxia and careful baseline measurements are essential in older subjects before results at high altitude can be interpreted. Testing for ataxia needs to be standardized with sufficient learning time. Ataxia should be distinguished from weakness or fatigue occurring at altitude. Specialized tests have not been shown to be clinically important. Our results above 5000 m showed that an abnormal SRT may be specific for AMS but with relatively poor sensitivity. Wobble board results have not correlated with AMS scores consistently. Other authors using an unstable platform in a chamber and static posturography during 3 days of exposure to 4559 m also found no relationship with AMS scores. Ataxia is a common and important clinical feature of HACE but is unhelpful in the assessment of mild or even moderate AMS in the absence of an altered mental state. The simple heel-to-toe test remains a useful part of the assessment of more severe AMS bordering on HACE.
Wilderness Medical Society Practice Guidelines for the Prevention and Treatment of Frostbite
Authors: McIntosh Scott E. , Hamonko Matthew , Freer Luanne , Grissom Colin K. , Auerbach Paul S. , Rodway George W. , Cochran Amalia , Giesbrecht Gordon , McDevitt Marion , Imray Christopher H. , Johnson Eric , Dow Jennifer , Hackett Peter H.
Published: June 2011

The Wilderness Medical Society convened an expert panel to develop a set of evidence-based guidelines for the prevention and treatment of frostbite. We present a review of pertinent pathophysiology. We then discuss primary and secondary prevention measures and therapeutic management. Recommendations are made regarding each treatment and its role in management. These recommendations are graded based on the quality of supporting evidence and balance between the benefits and risks/burdens for each modality according to methodology stipulated by the American College of Chest Physicians.
Practical Introduction to Greek Prose Composition
Authors: Arnold Thomas Kerchever
Published: June 2011

Thomas Kerchever Arnold's Practical Introduction to Greek Prose Composition first appeared in 1838 and was reprinted in several editions due to popular demand, being adopted as a textbook in leading public schools. Ordained as a priest in 1827 after graduating from Trinity College, Cambridge in 1821, Arnold had studied both theology and classics, and wrote prolifically on both subjects. His first school textbook was published in 1836 and others followed steadily until his death in 1853. One of the chief merits of Arnold's classical publications was his use of contemporary works of German scholarship, to which he readily acknowledged his debt. He produced, alongside Latin and Greek textbooks, grammars of English, French, German, Italian, and Hebrew, and editions of many Greek and Latin authors. This introduction was designed to provide students with the basic tools with which to construct sentences and includes exercises on syntax and a vocabulary index.
Slavery, Disease, and Suffering in the Southern Lowcountry
Authors: McCandless Peter
Published: June 2011

On the eve of the Revolution, the Carolina lowcountry was the wealthiest and unhealthiest region in British North America. Slavery, Disease, and Suffering in the Southern Lowcountry argues that the two were intimately connected: both resulted largely from the dominance of rice cultivation on plantations using imported African slave labor. This development began in the coastal lands near Charleston, South Carolina, around the end of the seventeenth century. Rice plantations spread north to the Cape Fear region of North Carolina and south to Georgia and northeast Florida in the late colonial period. The book examines perceptions and realities of the lowcountry disease environment; how the lowcountry became notorious for its 'tropical' fevers, notably malaria and yellow fever; how people combated, avoided or perversely denied the suffering they caused; and how diseases and human responses to them influenced not only the lowcountry and the South, but the United States, even helping to secure American independence.
Fatty acid content, vitamins and selenium in bulk tank milk from organic and conventional Swedish dairy herds during the indoor season
Authors: Fall Nils , Emanuelson Ulf
Published: June 2011

Fatty acids, vitamins and minerals in milk are important for the human consumer, the calf and the cow. Studies indicate that milk from organic and conventional dairy herds may differ in these aspects. The aim of this study was therefore to investigate whether there are differences in the fatty acid composition and concentration of vitamins and selenium in milk between organic and conventional herds in Sweden. Bulk tank milk was sampled in 18 organic and 19 conventional dairy herds on three occasions during the indoor season 2005–2006. Herd characteristics were collected by questionnaires and from the official milk recording scheme. Multivariable linear mixed models were used to evaluate the associations between milk composition and type of herd, while adjusting for potential confounders and the repeated observations within herd. In addition to management type, variables included in the initial models were housing type, milk fat content, herd size, average milk yield and time on pasture during summer. The median concentration of conjugated linoleic fatty acids (CLA) was 0·63% in organic compared with 0·48% in conventional herds, the content of total n-3 fatty acids was 1·44% and 1·04% in organic and conventional milk, respectively, and the content of total n-6 fatty acids was 2·72% and 2·20% in organic and conventional milk, respectively. The multivariable regression models indicated significantly higher concentrations of CLA, total n-3 and n-6 fatty acids in organic milk and a more desirable ratio of n-6 to n-3 fatty acids, for the human consumer, in organic milk. The multivariable models did not demonstrate any differences in retinol, α-tocopherol, β-carotene or selenium concentrations between systems. Median concentrations of α-tocopherol were 0·80 μg/ml in organic and 0·88 μg/ml in conventional milk, while for β-carotene the median concentrations were 0·19 and 0·18 μg/ml, respectively; for retinol, the median concentration was 0·32 μg/ml in both groups; the median concentrations of selenium were 13·0 and 13·5 μg/kg, respectively, for organic and conventional systems.
Optimal design of a class of generalized symmetric Gough–Stewart parallel manipulators with dynamic isotropy and singularity-free workspace
Authors: Tong Zhizhong , He Jingfeng , Jiang Hongzhou , Duan Guangren
Published: June 2011

In this paper, the definition of generalized symmetric Gough–Stewart parallel manipulators is presented. The concept of dynamic isotropy is proposed and the singular values of the bandwidth matrix are introduced to evaluate dynamic isotropy and solved analytically. Considering the payload's mass-geometry characteristics, the formulations for completely dynamic isotropy are derived in close form. It is proven that a generalized symmetric Gough–Stewart parallel manipulator is easer to achieve dynamic isotropy and applicable in engineering applications. An optimization procedure based on particle swarm optimization is proposed to obtain better dexterity and large singularity-free workspace, which guarantees the optimal solution and gives mechanically feasible realization.
The role of drinking water in the transmission of antimicrobial-resistantE. coli
Authors: COLEMAN B. L. , SALVADORI M. I. , McGEER A. J. , SIBLEY K. A. , NEUMANN N. F. , BONDY S. J. , GUTMANIS I. A. , McEWEN S. A. , LAVOIE M. , STRONG D. , JOHNSON I. , JAMIESON F. B. , LOUIE M. ,   ARO Water Study Group
Published: June 2011

To determine whether drinking water contaminated with antimicrobial-resistantE. coliis associated with the carriage of resistantE. coli, selected households sending water samples to Ontario and Alberta laboratories in 2005–2006 were asked to participate in a cross-sectional study. Household members aged ⩾12 years were asked to complete a questionnaire and to submit a rectal swab. In 878 individuals, 41% carried a resistant strain ofE. coliand 28% carried a multidrug-resistant strain. The risk of carriage of resistantE. coliwas 1·26 times higher for users of water contaminated with resistantE. coli. Other risk factors included international travel [prevalence ratio (PR) 1·33], having a child in nappies (PR 1·33), being male (PR 1·33), and frequent handling of raw red meats (PR 1·10). Protecting private water sources (e.g. by improving systems to test and treat them) may help slow the emergence of antimicrobial resistance inE. coli.
Right bundle branch block as a marker for interatrial septal abnormalities
Authors: Bakalli Aurora , Koçinaj Dardan , Georgievska-Ismail Ljubica , Bekteshi Tefik , Pllana Ejup , Sejdiu Basri
Published: June 2011

Background

Interatrial septal anomalies, which include atrial septal defect, patent foramen ovale, and atrial septal aneurysm, are common disorders among adult patients. Early detection of interatrial septal anomalies is important in order to prevent haemodynamic consequences and/or thromboembolic events. Electrocardiogram offers some clues that should serve as hints for detection of interatrial abnormalities. The aim of our study was to analyse the interatrial septum by transoesophageal echocardiography in patients with electrocardiogram signs of right bundle branch block and in those without right bundle branch block.

Methods and results

In a prospective study, 87 adult patients were included, that is, 41 with electrocardiogram signs of right bundle branch block forming the first group and 46 without right bundle branch block forming the second group. Interatrial septal anomalies were present in 80.5% of the patients with right bundle branch block, with patent foramen ovale (39.02%) being the most prevalent disorder, followed by atrial septal aneurysm (21.9%) and atrial septal defect (19.5%). Interatrial septal abnormalities were significantly more frequent in the first group compared with the second group (80.5% versus 6.5%, p value less than 0.001). Independently, patent foramen ovale was significantly more prevalent in patients with right bundle branch block (39.02% versus 4.3%, p value less than 0.001), as were atrial septal aneurysm (21.9% versus 2.2%, p value equal 0.01) and atrial septal defect (19.5% versus 0%, p value equal 0.004).

Conclusions

Right bundle branch block should serve as a valuable indicator to motivate a detailed search for interatrial septal abnormalities.
Objectively assessed physical activity and sedentary behaviour does not differ between children and adolescents with and without a congenital heart defect: a pilot examination
Authors: Ewalt Lauren A. , Danduran Michael J. , Strath Scott J. , Moerchen Victoria , Swartz Ann M.
Published: June 2011

Objectives

To objectively evaluate and describe physical activity levels in children with a stable congenital heart defect and compare those levels with children who do not have a congenital heart defect.

Methods

We matched 21 pairs of children for gender and grade in school and gave them an accelerometer-based motion sensor to wear for 7 consecutive days.

Results

Physical activity levels did not differ between children with and without a congenital heart defect. During the 7 days of monitoring, children in this study spent most of their time in sedentary behaviours, that is, 6.7 hours of the 13 monitored hours, 54 minutes in moderate-intensity physical activity, and 12 minutes in vigorous-intensity physical activity. Less than one-fifth of all participants, with or without a congenital heart defect, accumulated sufficient physical activity to meet current physical activity recommendations for children and adolescents.

Conclusion

Children with a stable congenital heart defect have activity behaviours that are similar to children without a congenital heart defect. Habitual physical activity in children with a congenital heart defect should be encouraged early on in life to develop strong physical activity habits that will hopefully follow them across their lifespan.
Symptomatic myocardial bridges in children: a case report with review of literature
Authors: Sharma Jayendra , Hellenbrand William , Kleinman Charles , Mosca Ralph
Published: June 2011

Myocardial bridge is a rare congenital coronary anomaly in children, usually seen in the setting of hypertrophic cardiomyopathy and in left ventricular hypertrophy. Most myocardial bridges are believed to represent a benign anatomical variant; however, symptomatic myocardial bridge is a distinct subgroup of pathological variant, linked to myocardial ischaemia, ventricular arrhythmia, and sudden cardiac death. We present a case of a symptomatic myocardial bridge in a 5-year-old boy with mild hypertrophic cardiomyopathy who underwent supra-arterial myotomy, automatic defibrillator placement, and long-term Beta-blocker therapy. We also present 10 years of follow-up with a review of literature regarding symptomatic myocardial bridges in the paediatric age group.
OWNERSHIP AND SOCIAL SOLIDARITY: A Kantian Alternative
Authors: Katz Larissa
Published: June 2011

The article considers what Kant's theory of property, as set out in Arthur Ripstein's Force and Freedom, contributes to contemporary property theory. I argue that by drawing our attention to a new set of questions concerning the basis of the state's authority, a Kantian approach provides an important alternative to the dominant instrumentalist approach to the moral problems that private ownership introduces (specifically, the problems of poverty and dependence). I consider the extent to which the Kantian framework is normative appealing. After raising a number of objections to the Kantian division of labor in response to the problem of material dependence, I suggest a way to restore some harmony between the rights of owners and the interests of others within a Kantian framework.
Development and Validation of a Brief Measure of Therapeutically-Induced Change
Authors: Schutte Nicola S. , Malouff John M.
Published: June 2011

Background: A premise of cognitive behavioural treatment is that individuals make cognitive, behavioural and situational changes prompted by interventions and that these changes bring about improvements in targeted outcomes. Aims: The present project set out to provide reliability and validity information for a brief measure of therapeutically induced change. Methods: A total of 281 participants, comprising three samples who took part in three different intervention studies, completed items relating to cognitive, behavioural and situational changes and completed measures relating to the intervention in which they participated. Results: The internal consistency of the scale assessing therapeutically induced change was high in the three samples. The scale showed evidence of validity through association with (1) more involvement in an intervention (2) reporting that an intervention was meaningful (3) being instructed to incorporate insights gained from an intervention into one's daily life (4) greater decreases in psychological distress and negative affect from pre-intervention to post-intervention, and (5) greater increases in positive affect from pre-intervention to post-intervention. Conclusions: The therapeutically-induced change scale may have utility as a process measure in various interventions.
The Healthy Eating Index and the Alternate Healthy Eating Index as predictors of 10-year CHD risk in Cuban Americans with and without type 2 diabetes
Authors: Huffman Fatma G , Zarini Gustavo G , Mcnamara Elizabeth , Nagarajan Aarthi
Published: June 2011

Objective

To examine the relationship between dietary patterns, as measured by the Healthy Eating Index (HEI) and the Alternate Healthy Eating Index (AHEI), and 10-year predicted CHD risk in Cuban Americans with and without type 2 diabetes (T2D).

Design

In a cross-sectional study participants were selected from two randomly generated mailing lists of individuals with and without T2D. HEI and AHEI scores were calculated from a self-reported FFQ. CHD risk was determined using the 10-year CHD risk calculator of the Adult Treatment Panel III.

Setting

Miami Dade and Broward Counties, FL, USA.

Subjects

Cuban Americans (n358) aged ≥30 years.

Results

Participants with T2D had a higher waist circumference (P= 0·001) and 10-year CHD risk score (P= 0·008) compared with those without T2D. Participants without T2D had a higher energy intake (P= 0·034), total blood cholesterol (P= 0·007), HDL cholesterol (P= 0·001) and HEI score (P= 0·006) compared with participants with T2D. AHEI score was a significant predictor of 10-year CHD risk (F(1,351)= 4·44,P= 0·036). An association between AHEI and 10-year CHD risk was found only for participants with T2D (β= −0·244,se= 0·049,P= 0·001).

Conclusion

The present study showed that only participants with T2D with significantly higher AHEI scores had lower scores for 10-year predicted CHD risk. No association was found between HEI score and CHD risk among Cuban Americans. Individuals with T2D are advised to follow the AHEI dietary pattern.
Structure and Chemistry across Interfaces at Nanoscale of a Ge Quantum Well Embedded within Rare Earth Oxide Layers
Authors: Das Tanmay , Bhattacharyya Somnath
Published: June 2011

Structure and chemistry across the rare earth oxide-Ge interfaces of a Gd2O3-Ge-Gd2O3 heterostructure grown on p-Si (111) substrate using encapsulated solid phase epitaxy method have been studied at nanoscale using various transmission electron microscopy methods. The structure across both the interfaces was investigated using reconstructed phase and amplitude at exit plane. Chemistry across the interfaces was explored using elemental mapping, high-angle annular dark-field imaging, electron energy loss spectroscopy, and energy dispersive X-ray spectrometry. Results demonstrate the structural and chemical abruptness of both the interfaces, which is most essential to maintain the desired quantum barrier structure.
Exploring the transfer of Earth surface materials from source to sink
Authors: Kuehl Steven A. , Nittrouer Charles A.
Published: June 2011

AGU Chapman Conference on Source to Sink Systems Around the World and Through Time: Recent Advances in Understanding Production, Transfer, and Burial of Terrestrial and Marine Materials on the Earth Surface; Oxnard, California, 24–27 January 2011; The source‐to‐sink (S2S) holistic approach examines the dispersal of material (particulate and dissolved) across the Earth's surface, with a focus on how material is transferred between segments of a dispersal system (e.g., uplands, river, coastal ocean, deep margin). Past studies primarily examined sedimentary processes within individual segments of dispersal systems. Although these processes are still recognized as important, the timing, intensity, and operative transfer mechanisms controlling sediment input and output are now accepted as fundamental parts of the dispersal process. A group of 150 scientists and students from six continents met in California to synthesize and integrate S2S research and to initiate the creation of a digital text (Web‐accessible publication with enhanced content) and educational resources. Broad participation by academic and federal sedimentary research communities, energy industry scientists, and geoscience educators provided a rich opportunity to explore the many dimensions of S2S research and its impact on society.
The law through the eye of a needle
Authors: Ricceri Laura , Vitale Augusto
Published: June 2011

The new European Directive covering animal research only applies if the procedure is more painful than the insertion of a needle. Pain varies between species and individuals, so how can we judge when this is the case, and who is responsible?
Biophysical visual virtual reality in retinotopic visual areas
Authors: Bókkon István , Tuszynski Jack , Salari Vahid
Published: June 2011

Previously, we have pointed out that biophoton production can be a controlled process that originates from regulated redox/radical reactions. Our biophoton experiments support the notion that various visual related phenomena such as discrete retinal noise, retinal phosphenes as well as negative afterimages are due to biophotons. We have also suggested a new model, stating that the brain is able to create biophysical pictures in retinotopic visual areas via redox regulated biophotons of synchronized neurons. According to our interpretation, visualization (imagery) is a special kind of representation i.e., visual imagery requires peculiar inherent biophysical processes. Our idea of biophysical visual virtual reality in retinotopic areas may be a possible biophysical basis of Kosslyn's reality simulation principle in the case of visual imagery. Long-term visual memories are not stored as biophysical pictures but as epigenetic codes. During visual imagery, top-down processes control the epigenetic encoded long-term visual information. Then, according to retrieved epigenetic information, synchronized retinotopic neurons generate dynamic patterns of biophotons via redox reactions that can produce biophysical pictures. We have also presented an iterative model involving a biophysical picture-representation without homunculus during visual imagery.
Transcriptional Metabolic Inflexibility in Skeletal Muscle Among Individuals With Increasing Insulin Resistance
Authors: Jans Anneke , Sparks Lauren M. , van Hees Anneke M.J. , Gjelstad Ingrid M.F. , Tierney Audrey C. , Risérus Ulf , Drevon Christian A. , Roche Helen M. , Schrauwen Patrick , Blaak Ellen E.
Published: June 2011

Disturbances in skeletal muscle lipid metabolism may play an important role in development of insulin resistance (IR). The aim was to investigate transcriptional control of skeletal muscle fatty acid (FA) metabolism in individuals with the metabolic syndrome (MetS) with varying degrees of insulin sensitivity (SI). 122 individuals with MetS (NCEP‐ATP III criteria) at age 35–70 years, BMI 27–38 kg/m2 were studied (subgroup EU‐LIPGENE study). Individuals were divided into quartiles of SI measured during a frequently sampled insulin modified intravenous glucose tolerance test. Skeletal muscle normalized mRNA expression levels of genes important in skeletal muscle FA handling were analyzed with quantitative real‐time PCR. The expression of sterol regulatory element binding protein 1c (SREBP1c), acetyl‐CoA carboxylase 2 (ACC2), diacylglycerol acyltransferase (DGAT1), and nuclear respiration factor (NRF) was higher in the lowest two quartiles of SI (<50th) compared with the highest two quartiles of SI (>50th). Interestingly, peroxisome proliferator‐activated receptor coactivator 1α (PGC1α), peroxisome proliferator‐activated receptor α (PPARα), and muscle carnitine palmitoyl transferase 1b (mCPT1), important for oxidative metabolism, showed a complex mRNA expression profile; levels were lower in both the most “insulin sensitive” (IS) as well as the most “IR” individuals. Lipoprotein lipase (LPL) mRNA was reduced in the lowest quartile of SI. Enhanced gene expression of SREBP1c and ACC2 in the IR state suggests a tendency towards FA storage rather than oxidation. From the lower expression of PGC1α, PPARα, and mCPT1 in both the most “IS” as well as the most “IR” individuals, it may be speculated that “IS” subjects do not need to upregulate these genes to have a normal FA oxidation, whereas the most “IR” individuals are inflexible in upregulating these genes.
Genome‐Wide Association of BMI in African Americans
Authors: Ng Maggie C.Y. , Hester Jessica M. , Wing Maria R. , Li Jiang , Xu Jianzhao , Hicks Pamela J. , Roh Bong H. , Lu Lingyi , Divers Jasmin , Langefeld Carl D. , Freedman Barry I. , Palmer Nichole D. , Bowden Donald W.
Published: June 2011

Recent genome‐wide association studies (GWAS) have identified multiple novel loci associated with obesity in Europeans but results in other ethnicities are less convincing. Here, we report a two‐stage GWAS of BMI in African Americans. The GWAS was performed using the Affymetrix 6.0 platform in 816 nondiabetic and 899 diabetic nephropathy subjects. 746,626 single‐nucleotide polymorphisms (SNPs) were tested for association with BMI after adjustment for age, gender, disease status, and population structure. Sixty high scoring SNPs that showed nominal association in both GWAS cohorts were further replicated in 3,274 additional subjects in four replication cohorts and a meta‐analysis was computed. Meta‐analysis of 4,989 subjects revealed five SNPs (rs6794092, rs268972, rs2033195, rs815611, and rs6088887) at four loci showing consistent associations in both GWAS (P < 0.0001) and replication cohorts (P < 0.05) with combined P values range from 2.4 × 10−6 to 5 × 10−5. These loci are located near PP13439‐TMEM212, CDH12, MFAP3‐GALNT10, and FER1L4 and had effect sizes between 0.091 and 0.167 s.d. unit (or 0.67–1.24 kg/m2) of BMI for each copy of the effect allele. Our findings suggest the presence of novel loci potentially associated with adiposity in African Americans. Further replication and meta‐analysis in African Americans and other populations will shed light on the role of these loci in different ethnic populations.
B Cell‐Activating Factor Controls the Production of Adipokines and Induces Insulin Resistance
Authors: Hamada Maho , Abe Masanori , Miyake Teruki , Kawasaki Keitarou , Tada Fujimasa , Furukawa Shinya , Matsuura Bunzo , Hiasa Yoichi , Onji Morikazu
Published: June 2011

Visceral adipose tissue (VAT) inflammation has been linked to the pathogenesis of insulin resistance and metabolic syndrome. VAT has recently been established as a new component of the immune system and is involved in the production of various adipokines and cytokines. These molecules contribute to inducing and accelerating systemic insulin resistance. In this report, we investigated the role of B cell‐activating factor (BAFF) in the induction of insulin resistance. We investigated BAFF levels in the sera and VAT of obese mice. In obese mice, the BAFF levels were preferentially increased in VAT and sera compared to these levels in normal control mice. Next, we treated mice with BAFF to analyze its influence on insulin sensitivity. BAFF impaired insulin sensitivity in normal mice. Finally, we investigated the mechanisms underlying insulin resistance induced by BAFF in adipocytes. BAFF also induced alterations in the expression levels of genes related to insulin resistance in adipocytes. In addition, BAFF directly affected the glucose uptake and phosphorylation of insulin receptor substrate‐1 in adipocytes. We propose that autocrine or paracrine BAFF and BAFF‐receptor (BAFF‐R) interaction in VAT leads to impaired insulin sensitivity via inhibition of insulin signaling pathways and alterations in adipokine production.
A Genome‐Wide Association Study of BMI in American Indians
Authors: Malhotra Alka , Kobes Sayuko , Knowler William C. , Baier Leslie J. , Bogardus Clifton , Hanson Robert L.
Published: June 2011

Numerous studies have been done to understand genetic contributors to BMI, but only a limited number of studies have been done in nonwhite groups such as American Indians. A genome‐wide association study (GWAS) for BMI was therefore performed in Pima Indians. BMI measurements from a longitudinal study of 1,120 Pima Indians and 454,194 single‐nucleotide polymorphisms (SNPs) from the 1 million Affymetrix SNP panel were used (35% of SNPs were excluded due to minor allele frequency <0.05). Data included BMI measured at multiple examinations collected from 1965 to 2004, as well as the maximum BMI at one of these visits. General and within‐family tests were performed using a maximum‐likelihood based mixed model procedure. No SNP reached a genome‐wide significance level (estimated at P < 4.94 × 10−7). For repeated measures analyses, the strongest associations for general and within‐family tests mapped to two different regions on chromosome 6 (rs9342220 (P = 1.39 × 10−6) and rs7758764 (P = 2.51 × 10−6), respectively). For maximum BMI, the strongest association for the general tests mapped to chromosome 4 (rs17612333; P = 1.98 × 10−6) and to chromosome 3 (rs11127958; P = 1.53 × 10−6) for the within‐family tests. Further analysis is important because only a few of these regions have been previously implicated in a GWAS and genetic susceptibility may differ by ethnicity.
Striatal origin of the pathologic beta oscillations in Parkinson's disease
Authors: McCarthy M. M. , Moore-Kochlacs C. , Gu X. , Boyden E. S. , Han X. , Kopell N.
Published: June 2011

Enhanced oscillations at beta frequencies (8–30 Hz) are a signature neural dynamic pathology in the basal ganglia and cortex of Parkinson's disease patients. The mechanisms underlying these pathological beta oscillations remain elusive. Here, using mathematical models, we find that robust beta oscillations can emerge from inhibitory interactions between striatal medium spiny neurons. The interaction of the synaptic GABAa currents and the intrinsic membrane M-current promotes population oscillations in the beta frequency range. Increased levels of cholinergic drive, a condition relevant to the parkinsonian striatum, lead to enhanced beta oscillations in the striatal model. We show experimentally that direct infusion of the cholinergic agonist carbachol into the striatum, but not into the neighboring cortex, of the awake, normal rodent induces prominent beta frequency oscillations in the local field potential. These results provide evidence for amplification of normal striatal network dynamics as a mechanism responsible for the enhanced beta frequency oscillations in Parkinson's disease.
Plasma-assisted partial oxidation of methane at low temperatures: numerical analysis of gas-phase chemical mechanism
Authors: Goujard Valentin , Nozaki Tomohiro , Yuzawa Shuhei , Ağiral Anil , Okazaki Ken
Published: June 2011

Methane partial oxidation was investigated using a plasma microreactor. The experiments were performed at 5 and 300 °C. Microreactor configuration allows an efficient evacuation of the heat generated by methane partial oxidation and dielectric barrier discharges, allowing at the same time a better temperature control. At 5 °C, liquid condensation of low vapour pressure compounds, such as formaldehyde and methanol, occurs. 1H-NMR analysis allowed us to demonstrate significant CH3OOH formation during plasma-assisted partial oxidation of methane. Conversion and product selectivity were discussed for both temperatures. In the second part of this work, a numerical simulation was performed and a gas-phase chemical mechanism was proposed and discussed. From the comparison between the experimental results and the simulation it was found that CH3OO· formation has a determinant role in oxygenated compound production, since its fast formation disfavoured radical recombination. At 5 °C the oxidation leads mainly towards oxygenated compound formation, and plasma dissociation was the major phenomenon responsible for CH4 conversion. At 300 °C, higher CH4 conversion resulted from oxidative reactions induced by ·OH radicals with a chemistry predominantly oxidative, producing CO, H2, CO2 and H2O.
Enriching targeted sequencing experiments for rare disease alleles
Authors: Edwards Todd L. , Song Zhuo , Li Chun
Published: June 2011

Motivation: Next-generation targeted resequencing of genome-wide association study (GWAS)-associated genomic regions is a common approach for follow-up of indirect association of common alleles. However, it is prohibitively expensive to sequence all the samples from a well-powered GWAS study with sufficient depth of coverage to accurately call rare genotypes. As a result, many studies may use next-generation sequencing for single nucleotide polymorphism (SNP) discovery in a smaller number of samples, with the intent to genotype candidate SNPs with rare alleles captured by resequencing. This approach is reasonable, but may be inefficient for rare alleles if samples are not carefully selected for the resequencing experiment.

Results: We have developed a probability-based approach, SampleSeq, to select samples for a targeted resequencing experiment that increases the yield of rare disease alleles substantially over random sampling of cases or controls or sampling based on genotypes at associated SNPs from GWAS data. This technique allows for smaller sample sizes for resequencing experiments, or allows the capture of rarer risk alleles. When following up multiple regions, SampleSeq selects subjects with an even representation of all the regions. SampleSeq also can be used to calculate the sample size needed for the resequencing to increase the chance of successful capture of rare alleles of desired frequencies.

Software:  http://biostat.mc.vanderbilt.edu/SampleSeq

Contact:  chun.li@vanderbilt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of novel transcripts in annotated genomes using RNA-Seq
Authors: Roberts Adam , Pimentel Harold , Trapnell Cole , Pachter Lior
Published: June 2011

Summary: We describe a new ‘reference annotation based transcript assembly’ problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation.

Availability: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license.

Contact:  cole@broadinstitute.org; lpachter@math.berkeley.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A procedure to statistically evaluate agreement of differential expression for cross-species genomics
Authors: Pounds Stan , Gao Cuilan Lani , Johnson Robert A. , Wright Karen D. , Poppleton Helen , Finkelstein David , Leary Sarah E. S. , Gilbertson Richard J.
Published: June 2011

Motivation: Animal models play a pivotal role in translation biomedical research. The scientific value of an animal model depends on how accurately it mimics the human disease. In principle, microarrays collect the necessary data to evaluate the transcriptomic fidelity of an animal model in terms of the similarity of expression with the human disease. However, statistical methods for this purpose are lacking.

Results: We develop the agreement of differential expression (AGDEX) procedure to measure and determine the statistical significance of the similarity of the results of two experiments that measure differential expression across two groups. AGDEX defines a metric of agreement and determines statistical significance by permutation of each experiment's group labels. Additionally, AGDEX performs a comprehensive permutation-based analysis of differential expression for each experiment, including gene-set analyses and meta-analytic integration of results across studies. As an example, we show how AGDEX was recently used to evaluate the similarity of the transcriptome of a novel model of the brain tumor ependymoma in mice to that of a subtype of the human disease. This result, combined with other observations, helped us to infer the cell of origin of this devastating human cancer.

Availability: An R package is currently available from www.stjuderesearch.org/site/depts/biostats/agdex and will shortly be available from www.bioconductor.org.

Contact:  stanley.pounds@stjude.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
Authors: Grant Jason R. , Arantes Adriano S. , Liao Xiaoping , Stothard Paul
Published: June 2011

Summary: NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons can, for example, identify SNPs that affect conserved residues, or alter residues or genes linked to phenotypes in another species.

Availability: NGS-SNP is available both as a set of scripts and as a virtual machine. The virtual machine consists of a Linux operating system with all the NGS-SNP dependencies pre-installed. The source code and virtual machine are freely available for download at http://stothard.afns.ualberta.ca/downloads/NGS-SNP/.

Contact:  stothard@ualberta.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
MetaABC—an integrated metagenomics platform for data adjustment, binning and clustering
Authors: Su Chien-Hao , Hsu Ming-Tsung , Wang Tse−Yi , Chiang Sufeng , Cheng Jen-Hao , Weng Francis C. , Kao Cheng−Yan , Wang Daryi , Tsai Huai-Kuang
Published: June 2011

Summary: MetaABC is a metagenomic platform that integrates several binning tools coupled with methods for removing artifacts, analyzing unassigned reads and controlling sampling biases. It allows users to arrive at a better interpretation via series of distinct combinations of analysis tools. After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams.

Availability: MetaABC source code and documentation are available at http://bits2.iis.sinica.edu.tw/MetaABC/

Contact:  dywang@gate.sinica.edu.tw; hktsai@iis.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.