bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete mitochondrial genome of a carabid beetle, Damaster mirabilissimus mirabilissim (Coleoptera: Carabidae)
Authors: WAN Xinlong , HONG Mee Yeon , LIAO Aimei , KIM Man Il , KIM Ki‐Gyoung , HAN Yeon Soo , KIM Iksoo
Published: December 2011

In the present study, we report the 16 823‐bp long complete mitochondrial genome (mitogenome) of a carabid beetle, Damaster mirabilissimus mirabilissim (Coleoptera: Carabidae), which is endangered in Korea. The gene arrangement of D. m. mirabilissim mitogenome is identical to the most common type found in insects. The start codon of the D. m. mirabilissim COI gene is a typical ATN codon. On the other hand, the initiation codon for ND1 gene is TTG, instead of ATN. All transfer RNAs (tRNAs) exhibit a stable canonical clover‐leaf structure, except for tRNASer(AGN), the dihydrouridine arm of which forms a simple loop. The 1703‐bp long A+T‐rich region is the second longest among the complete adephagan mitogenome sequences, next to Macrogyrus oblongus belonging to Gyrinoidea. One of the unusual features of the genome is the presence of a tRNALeu(UUR)‐like sequence in the A+T‐rich region. This sequence displays the proper anticodon sequence and the potential to form secondary structures, but also harbors many mismatches in the stems.
Prediction of Crop Production using Drought indices at Different Time Scales and Climatic Factors to Manage Drought Risk1
Authors: Sadat Noori S.M. , Liaghat A.M. , Ebrahimi K.
Published: December 2011

Sadat Noori, S.M., A.M. Liaghat, and K. Ebrahimi, 2011. Prediction of Crop Production Using Drought Indices at Different Time Scales and Climatic Factors to Manage Drought Risk. Journal of the American Water Resources Association (JAWRA) 48(1): 1‐9. DOI: 10.1111/j.1752‐1688.2011.00586.x

Abstract:  Drought causes great damage to rainfed and irrigated farming. Therefore, prediction of crop production during the drought period is essential in order to manage drought risk. Thus, proceeding to agricultural drought risk management can be very useful. This study shows the results of early crop prediction using the combination of climate factors and drought indices at different time scales. The study region was Hamadan, a semiarid region in Iran. The methodology demonstrated here has allowed the prediction of production several months before harvest. Moreover, the predictive models constructed have explained 89% of the temporal variability of wheat production. This method could be very efficient for managing crop production. Moreover, having clear prediction, decision makers can plan better for overcoming drought impacts to reduce crop uncertainty for farmers in insurance companies.
Miss Milner's Return from the Crypt: Mourning in Elizabeth Inchbald's A Simple Story
Authors: O'CONNELL MICHELLE
Published: December 2011

This article argues that focusing more closely on the character of Elmwood in Elizabeth Inchbald's A Simple Story, particularly in volumes III and IV, offers new insights into the novel and demonstrates great sophistication on Inchbald's part in the creation of this figure. The article discloses Inchbald's complex exploration of Elmwood's frustrated grief, which is illuminated by reading it in the light of Freud's and Derrida's observations on the processes of mourning. This mourning is, in part, read in the light of recent critical investigations into eighteenth‐century masculinity and masculine sensibility.
A Matter of Honour: The Duel in Thomas Moore's Life of Richard Brinsley Sheridan
Authors: JONES ROBERT W.
Published: December 2011

Shortly after Sheridan's death in 1816, Thomas Moore (without previous experience in the field) agreed to write his biography. This was no small undertaking, as Sheridan had a reputation for sexual, political and financial infidelity. Moore's first task, however, was to account for Sheridan's early duels, memories of which had been revived in the Tory press. This essay examines how Moore attempted, using unpublished documents, to defend his protagonist. While the politics of this endeavour are important, attention is also paid to how Moore exploited a private archive to establish his own status as an author, confidant and moral guide.
Universal COI primers for DNA barcoding amphibians
Authors: CHE JING , CHEN HONG‐MAN , YANG JUN‐XIAO , JIN JIE‐QIONG , JIANG KE , YUAN ZHI‐YONG , MURPHY ROBERT W. , ZHANG YA‐PING
Published: December 2011

DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large‐scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.
PCR enrichment techniques to identify the diet of predators
Authors: O’RORKE R. , LAVERY S. , JEFFS A.
Published: December 2011

The increasing sensitivity of PCR has meant that in the last two decades PCR has emerged as a major tool in diet studies, enabling us to refine our understanding of trophic links and to elucidate the diets of predators whose prey is as yet uncharacterized. The achievements and methods of PCR‐based diet studies have been reviewed several times, but here we review an important development in the field: the use of PCR enrichment techniques to promote the amplification of prey DNA over that of the predator. We first discuss the success of using group‐specific primers either in parallel single reactions or in multiplex reactions. We then concentrate on the more recent use of PCR enrichment techniques such as restriction enzyme digests, peptide nucleic acid clamping, DNA blocking and laser capture microdissection. We also survey the vast literature on enrichment techniques in clinical biology, to ascertain the pitfalls of enrichment techniques and what refinements have yielded some highly sensitive methods. We find that while there are several new approaches to enrichment, peptide nucleic acid clamping and DNA blocking are generally sufficient techniques for the characterization of diets of predators and highlight the most important considerations of the approach.
Multiplexed microsatellite markers for genetic studies of beech
Authors: LEFÈVRE S. , WAGNER S. , PETIT R. J. , De LAFONTAINE G.
Published: December 2011

European beech (Fagus sylvatica L.) is one of the economically most important broadleaved tree species in Europe and has become a model for studying climate change effects on forests. Multiplex PCR of microsatellites is a fast and cost‐effective technique allowing high‐throughput genotyping. Here we present the procedure used to develop two multiplex kits (8‐plexes) for European beech. We paid particular attention to quality control throughout all steps of the multiplex kits development (null allele detection, error rate measurements, linkage disequilibrium). Preliminary assays suggest that the 16 amplified loci are largely devoid of null alleles and allow rapid and cost‐effective genotyping of beech with low error rates. The two kits, which differ in their levels of polymorphism, most likely due to marker origin, were also informative in seven other beech species tested.
Lateral Elbow Pain in a 21-year-old Pregnant Female
Authors: Amanatullah Derek F. , Bozzio Anthony E. , Mallon Zachary O. , Mak Walter H. , Borys Darius , Tamurian Robert M.
Published: December 2011

The present case report highlights the diagnosis and modern surgical techniques involved when treating an aggressive benign bone tumour in a skeletally mature patient. It also stresses the importance of a broad differential when examining a patient. An increase in circulating growth hormones during pregnancy could play a role in the rapid growth of particular tumours. For example, certain transforming growth factor (TGF)-β receptors have been identified in cells of aneurysmal bone cysts and a rat model has demonstrated that TGF-β isoforms are regulated differently in pregnancy, and also could have an important role in apoptosis and cell survival. The occurrence of aneurysmal bone cysts during pregnancy suggests a possible link between the pregnancy and tumour growth.
Aliskiren as a novel therapeutic agent for hypertension and cardio-renal diseases
Authors: Rashikh Azhar , Ahmad Shibli Jameel , Pillai Krishna Kolappa , Najmi Abul Kalam
Published: December 2011

Objectives

High blood pressure (BP) is a major risk factor for cardiovascular and renal complications. A majority of treated hypertensive patients still complain of high BP. The renin-angiotensin aldosterone system (RAAS) has been a centre-stage target for all the cardiovascular and cardio-renal complications. Aliskiren, is the first direct renin inhibitor (DRI) to be approved by the US FDA. Renin controls the rate-limiting step in the RAAS cascade and hence is the most favorable target for RAAS suppression.

Key findings

This review article strives to summarize the pharmacokinetic, preclinical and clinical studies done so far pertaining to the efficacy of aliskiren. Further, the pharmacology of aliskiren has been comprehensively dealt with to enhance understanding so as to further research in this unfathomed area in the multitude of cardiovascular disorders and renal diseases.

Aliskiren has been shown to have comparable BP-lowering effects to other RAAS inhibitors. Recent clinical trials have indicated that it might contribute significantly in combination with other agents for the protection of end-organ diseases.
Single injection of ONO-1301-loaded PLGA microspheres directly after ischaemia reduces ischaemic damage in rats subjected to middle cerebral artery occlusion
Authors: Hazekawa Mai , Sakai Yoshiki , Yoshida Miyako , Haraguchi Tamami , Uchida Takahiro
Published: December 2011

Objectives

ONO-1301 was developed as a novel long-acting prostacyclin agonist with thromboxane synthase inhibitory activity. In this study, we investigated the therapeutic time window of oral ONO-1301 and the effect of a single subcutaneous injection of ONO-1301-loaded poly(lactide-co-glycolide) (PLGA) microspheres (ONO-1301 PLGA MS) on infarction volume, functional deficits and plasma ONO-1301 levels following a 1 h middle cerebral artery occlusion (MCAO) in rats.

Methods

Rats were treated with ONO-1301 (3 mg/kg) orally twice-daily starting 1 (directly), 6 or 24 h after MCAO. Rats received a single subcutaneous injection of ONO-1301 PLGA MS (10 mg/kg) directly after MCAO. Neurological scores were evaluated directly after, 1 and 6 h, 1, 2, and 3 days after MCAO. Infarct volume, oedema and plasma ONO-1301 levels were measured three days after MCAO.

Key findings

Neurological scores, oedema and infarct volume were all significantly improved in rats repeatedly treated with oral ONO-1301 and subcutaneous ONO-1301 PLGA MS directly after MCAO. Plasma ONO-1301 levels were significantly lower in rats treated directly after MCAO (either with ONO-1301 or ONO-1301 PLGA MS) than in rats treated 6 h or 24 h after MCAO.

Conclusions

ONO-1301 PLGA MS subcutaneous treatment directly after MCAO showed a neuroprotective effect as well as oral ONO-1301. This treatment should be clinically more convenient than ONO-1301 oral administration since it is delivered as a single treatment after MCAO.
Pharmacokinetic profile of Oncofid-S after intraperitoneal and intravenous administration in the rat
Authors: Tringali Giuseppe , Bettella Fabio , Greco Maria Cristina , Campisi Monica , Renier Davide , Navarra Pierluigi
Published: December 2011

Objectives

Oncofid-S is a bio-conjugate molecule obtained from the binding of campthotecin, SN-38, to hyaluronic acid. In view of a possible clinical development for loco-regional treatment of peritoneal carcinomatosis, this study aimed to establish the pharmacokinetic profile of Oncofid-S after single intraperitoneal or intravenous administration in the rat.

Methods

Single-dose intraperitoneal or intravenous administrations of Oncofid-S were performed. Groups of six rats were sacrificed at various times (up to 24 and 72 h in i.p. and i.v. study, respectively) after drug injection. Trunk blood, livers and spleens were collected for subsequent analysis. Total SN-38 was assayed by HPLC.

Key findings

We found that Oncofid-S was poorly absorbed after intraperitoneal injection, the estimated AUC0–72 being less than2%. The drug was distributed in liver, but not spleen, and was eliminated with a terminal half-life of 16 h. After intravenous dosing, Oncofid-S was found in liver as well as in spleen.

Conclusions

Here we have demonstrated that Oncofid-S administered intraperitoneally in the rat was poorly absorbed into the systemic circulation, even after the administration of an extremely high dose. This finding reinforces the rationale for developing Oncofid-S in the loco-regional intraperitoneal treatment of peritoneal carcinomatosis in man.
Finite Element Simulation of Welding Sequences Effect on Residual Stresses in Multipass Butt-Welded Stainless Steel Pipes
Authors: Feli S. , Aalami Aaleagha M. E. , Foroutan M. , Borzabadi Farahani E.
Published: December 2011

In this paper, a finite element simulation, based on abaqus software is presented for analyzing the temperature history and the residual stress states in multipass welds in stainless steel pipe. The uncoupled thermal–mechanical a three-dimensional (3D) model and a two-dimensional (2D) model are developed. The volumetric heat source with double ellipsoidal distribution for front and rear heat source, proposed by Goldak and Akhlaghi, has also been used. Furthermore, a moving heat source has been modeled by abaqus subroutine DFLUX. A user subroutine FILM has also been used to simulate the combined thermal boundary conditions. The results of both a 3D model and a 2D axisymmetric model which are compared with the available experimental measurements show good agreements. Predictions show that the axial and hoop residual stresses in a 3D model and a 2D axisymmetric model have the same distributions in all locations except the starting point of welding. The effects of welding sequences on the thermal and structural analysis are also investigated. Four types of welding sequences for circular welds of pipe have been used and thermal history and axial and hoop residual stresses are compared. Predictions show that for other locations (except the starting point of welding) there are no important differences of axial and hoop residual stresses for welding sequences and they have the same distribution along axial direction.
Analysis of Postbuckling Drillstring Vibrations in Rotary Drilling of Extended-Reach Wells
Authors: Tikhonov Vadim S. , Safronov Alexander I.
Published: December 2011

One of the most serious concerns of extended-reach drilling is the dynamic behavior of the drillstring and the cleaning of well. Good cleaning requires an increased angular velocity. This paper presents a 3D nonlinear dynamic model of drillstring in a wellbore of 3D profile. The model suggests possible contact/lift-off of drill pipes with/from the wellbore wall. The interaction of lateral, torsional, and axial vibrations is taken into account. The relation between the normal component of contact force and the deformation of the wellbore wall is taken as quadratic-elastic. The friction force is described based on a hysteretic dynamic model. The friction force model also takes into account, the transition from a sliding to whirling. The equations of drillstring dynamics are solved numerically using the method of lines. The DYNTUB software is developed to analyze the drillstring time-varying processes under different loads. The program is used to study the effects of angular velocity, compression load, torque, friction factor, well profile, and availability of connectors on the drillstring dynamic behavior. From the study follows the key conclusions: (1) The friction factor has a considerable effect on the drillstring rotational behavior in the wellbore; (2) no whirling of drillstring at real value of rolling friction factor in a horizontal well in the discussed examples could be seen at all; (3) when whirling takes place, the contact force shows a dramatic times increase; and (4) snaking can be seen in any wells at moderate compressive load and angular velocity.
Lithography-patterning-fidelity-aware electron-optical system design optimization
Authors: Chen Sheng-Yung , Ng Hoi-Tou , Ma Shiau-Yi , Chen Hsing-Hong , Liu Chun-Hung , Tsai Kuen-Yu
Published: December 2011

Low-energy electron beam lithography is a promising patterning solution for the 21 nm half-pitch node and beyond due to its high resolution, low substrate damage, and increased resist sensitivities. To ensure a successful electron-optical system (EOS) design, many factors such as focusing properties (FPs) and patterning fidelity (PF) have to be considered. In traditional EOS optimization flow, FPs are typical performance indices selected when optimizing the EOS design parameters. In each numerical iteration, the EOS FP simulation results are compared with specified performance index values. The differences are reduced by adjusting the EOS design parameters until convergence. However, the performance indices related to FPs may have no direct relation to lithography PF, which is judged by the quality of the developed resist patterns. A new EOS design methodology which directly incorporates lithography PF metrics into the optimization flow is proposed. The EOS design parameters are first optimized while meeting the geometric constraints by using the traditional design flow to obtain acceptable FPs. In order to ensure lithography PF, writing patterns are selected and writing parameters are optimized. Then, constraints and cost functions related to PF are selected to further optimize the EOS design parameters to obtain acceptable PF. In each numerical iteration, the simulated lithography patterning results are compared against specified PF metric values. Their differences are reduced by adjusting the EOS design parameters until all constraints are met and PF cost functions are converged. The proposed method is applied to an EOS structure design for a 5 keV electron beam lithography system which includes a single-gate source and a focusing lens. Initial values of EOS design parameters and geometric constraints are selected based on previous studies. A drawn layout for a 22 nm isolated line pattern is used for verifying the lithography PF specifications based on the International Technology Roadmap of Semiconductors. The developed resist pattern after applying the proposed method clearly indicates that the PF is significantly improved from the value of corresponding critical dimension (CD) and the value of gate CD control.
Manipulatives-Based Laboratory for Majors Biology – a Hands-On Approach to Understanding Respiration and Photosynthesis
Authors: Boomer Sarah M. , Latham Kristin L.
Published: December 2011

The first course in our year-long introductory series for Biology majors encompasses four learning units: biological molecules and cells, metabolism, genetics, and evolution. Of these, the metabolism unit, which includes respiration and photosynthesis, has shown the lowest student exam scores, least interest, and lowest laboratory ratings. Consequently, we hypothesized that modeling metabolic processes in the laboratory would improve student content learning during this course unit. Specifically, we developed manipulatives-based laboratory exercises that combined paper cutouts, movable blocks, and large diagrams of the cell. In particular, our novel use of connecting LEGO blocks allowed students to move model electrons and phosphates between molecules and within defined spaces of the cell. We assessed student learning using both formal (content indicators and attitude surveys) and informal (the identification of misconceptions or discussions with students) approaches. On the metabolism unit content exam, student performance improved by 46% over pretest scores and by the end of the course, the majority of students rated metabolism as their most-improved (43%) and favorite (33%) subject as compared with other unit topics. The majority of students rated manipulatives-based labs as very helpful, as compared to non-manipulatives-based labs. In this report, we will demonstrate that students made learning gains across all content areas, but most notably in the unit that covered respiration and photosynthesis.
Assessment of Microbiology Students’ Progress With an Audience Response System
Authors: Chaudhry M. Ahmad
Published: December 2011

The development of new approaches to teaching of large lecture courses is needed. Today’s classroom has a wide range of students including high-achieving motivated learners, students struggling to understand basic concepts, and learning-challenged students. Many of these students can be lost in large classes under the shadow of the high-achieving extroverted students who dominate classroom question-and-answer sessions. Measuring a student’s understanding and achievement of content standards becomes difficult until an assessment has been done. To close this gap, an audience response system was introduced in an introductory Principles of Microbiology course. This technology specifically addressed the goal of individualizing instruction to the needs of the students. The evaluation of this project indicated an overall positive impact on student learning.
Introductory Biology Textbooks Under-Represent Scientific Process
Authors: Duncan Dara B. , Lubman Alexandra , Hoskins Sally G.
Published: December 2011

Attrition of undergraduates from Biology majors is a long-standing problem. Introductory courses that fail to engage students or spark their curiosity by emphasizing the open-ended and creative nature of biological investigation and discovery could contribute to student detachment from the field. Our hypothesis was that introductory biology books devote relatively few figures to illustration of the design and interpretation of experiments or field studies, thereby de-emphasizing the scientific process.

To investigate this possibility, we examined figures in six Introductory Biology textbooks published in 2008. On average, multistep scientific investigations were presented in fewer than 5% of the hundreds of figures in each book. Devoting such a small percentage of figures to the processes by which discoveries are made discourages an emphasis on scientific thinking. We suggest that by increasing significantly the illustration of scientific investigations, textbooks could support undergraduates’ early interest in biology, stimulate the development of design and analytical skills, and inspire some students to participate in investigations of their own.
Early Embryonic Development Role-Playing in a Large Introductory Biology Lecture
Authors: Geiser John R.
Published: December 2011

Animal development in introductory biology texts is generally described as a series of four coordinated and controlled phases of cell growth and movement: Body Axis, Segmentation, Segment Structures/Characteristics and, finally, Differentiation. In an ongoing effort to reform my teaching practices and place my introductory biology lectures within the context of student’s lives, I began teaching the development chapter as one possible outcome of the transcription and translational processes. During this process, I realized that students were having difficulty visualizing what was happening during early embryonic development. This activity was created to expose students to early embryonic development by making them move and change in a manner similar to what a cell in the embryo might undergo.
A Review of
Allies and Enemies: How the World Depends on Bacteria
Review of:
Allies and Enemies: How the World Depends on Bacteria
; 1st edition; Anne Maczulak; (2011). FT Press, Upper Saddle River, NJ. 210 pages.
Authors: Kavouras Jerry H.
Published: December 2011

Review of:
Allies and Enemies: How the World Depends on Bacteria
; 1st edition; Anne Maczulak; (2011). FT Press, Upper Saddle River, NJ. 210 pages.
A Review of EDVOTEK - The Biotechnology Education Company
Authors: Stein Scott
Published: December 2011

Review of:
EDVOTEK - The Biotechnology Education Company, a science equipment and supplies vendor specializing in biotechnology materials for middle school, high school and undergraduate college students.
Bedtime Stories From the Viral UniverseReview of:
Planet of Viruses;
Carl Zimmer; (2011). University of Chicago Press, Chicago, IL. Hardcover, 128 pages. ISBN-10: 0226983358.
Authors: Govindan Brinda
Published: December 2011

Review of:
Planet of Viruses;
Carl Zimmer; (2011). University of Chicago Press, Chicago, IL. Hardcover, 128 pages. ISBN-10: 0226983358.
Using LabPaq Kits to Perform Science Labs at Home
Authors: Newman Jeffrey D.
Published: December 2011

Review of:
mail-order kits called LabPaqs, which are sold by Hands-On-Labs Inc., and are primarily designed to provide laboratory experiences for students enrolled in online science courses. The kits include all non-household materials necessary to perform the experiments and a full color lab manual on CD.
A Review of The Mirage Man: Bruce Ivins, the anthrax attacks, and America’s rush to warReview of:
The Mirage Man: Bruce Ivins, the anthrax attacks, and America’s rush to war
; David Willman; (2011). Bantam Books, Random House, Inc., New York, NY. 448 pages.
Authors: Frederick Gregory (Greg)
Published: December 2011

Review of:
The Mirage Man: Bruce Ivins, the anthrax attacks, and America’s rush to war
; David Willman; (2011). Bantam Books, Random House, Inc., New York, NY. 448 pages.
What the 7th Grader Should Know About Microbes — Or, Is That “What the College Student Should Know?”Review of:
Bacteria: A Class of Their Own
; Judy Wearing; (2010). Crabtree Publishing Company, New York, NY. 43 pages (48 with glossary and index). ISBN 978-0-7787-5388-9.
Archaea: A Class of Their Own
; David M. Barker; (2010). Crabtree Publishing Company, New York, NY. 43 pages (48 with glossary and index). ISBN 978-0-7787-5387-2.
Authors: Katz Sue
Published: December 2011

Review of: Bacteria:
A Class of Their Own ;
Judy Wearing; (2010). Crabtree Publishing Company, New York, NY. 43 pages (48 with glossary and index). ISBN 978-0-7787-5388-9.

and

Archaea: A Class of Their Own ;
David M. Barker; (2010) . Crabtree Publishing Company, New York, NY. 43 pages (48 with glossary and index). ISBN 978-0-7787-5387-2.
A Comparative Review of Three Microbiology Student Study ResourcesReview of:
Let’s Get Ready For Microbiology
; 1st ed.; Lorri K. Garrett and Judy M. Penn; (2009). Benjamin Cummings Publishers, San Francisco, CA. 240 pages. ISBN-13: 978-0321592507.
Authors: Dustman Wendy A.
Published: December 2011

Review of:
Let’s Get Ready For Microbiology
; 1st ed.; Lorri K. Garrett and Judy M. Penn; (2009). Benjamin Cummings Publishers, San Francisco, CA. 240 pages. ISBN-13: 978-0321592507.
Outer Membrane Targeting of Pseudomonas aeruginosa Proteins Shows Variable Dependence on the Components of Bam and Lol Machineries
Authors: Hoang Hanh H. , Nickerson Nicholas N. , Lee Vincent T. , Kazimirova Anastasia , Chami Mohamed , Pugsley Anthony P. , Lory Stephen
Published: December 2011

In Gram-negative bacteria, the Lol and Bam machineries direct the targeting of lipidated and nonlipidated proteins, respectively, to the outer membrane (OM). Using
Pseudomonas aeruginosa
strains with depleted levels of specific Bam and Lol proteins, we demonstrated a variable dependence of different OM proteins on these targeting pathways. Reduction in the level of BamA significantly affected the ability of the β-barrel membrane protein OprF to localize to the OM, while the targeting of three secretins that are functionally related OM proteins was less affected (PilQ and PscC) or not at all affected (XcpQ). Depletion of LolB affected all lipoproteins examined and had a variable effect on the nonlipidated proteins. While the levels of OprF, PilQ, and PscC were significantly reduced by LolB depletion, XcpQ was unaffected and was correctly localized to the OM. These results suggest that certain β-barrel proteins such as OprF primarily utilize the complete Bam machinery. The Lol machinery participates in the OM targeting of secretins to variable degrees, likely through its involvement in the assembly of lipidated Bam components. XcpQ, but not PilQ or PscC, was shown to assemble spontaneously into liposomes as multimers. This work raises the possibility that there is a gradient of utilization of Bam and Lol insertion and targeting machineries. Structural features of individual proteins, including their β-barrel content, may determine the propensity of these proteins for folding (or misfolding) during periplasmic transit and OM insertion, thereby influencing the extent of utilization of the Bam targeting machinery, respectively.

IMPORTANCE
Targeting of lipidated and nonlipidated proteins to the outer membrane (OM) compartment in Gram-negative bacteria involves the transfer across the periplasm utilizing the Lol and Bam machineries, respectively. We show that depletion of Bam and Lol components in
Pseudomonas aeruginosa
does not lead to a general OM protein translocation defect, but the severity (and therefore, Lol and Bam dependence), varies with individual proteins. XcpQ, the secretin component of the type II secretion apparatus, is translocated into the OM without the assistance of Bam or Lol machineries. The hypothesis that XcpQ, after secretion across the cytoplasmic membrane, does not utilize the OM targeting machineries was supported by demonstrating that
in vitro
-synthesized XcpQ (but not the other
P. aeruginosa
secretins) can spontaneously incorporate into lipid vesicles. Therefore, the requirement for ancillary factors appears to be, in certain instances, dictated by the intrinsic properties of individual OM proteins, conceivably reflecting their propensities to misfold during periplasmic transit.
Synthesis, physico-chemical and biological properties of DNA and RNA oligonucleotides containing short alkylamino internucleotide bond
Authors: Sobczak Milena , Kubiak Katarzyna , Janicka Magdalena , Sierant Malgorzata , Mikolajczyk Barbara , Nawrot Barbara
Published: December 2011

The condensation of the 5′-O-DMT-3′-deoxy-3′-aminothymidine with 3′-O-TBDMS-thymidine- 5′-aldehyde, followed by reduction of the resultant imine derivative and removal of tert-butyldimethylsilyl (TBDMS) protecting group, provided a dimer (denoted as TNHT), which is a congener of dithymidine phosphate with the phosphate linkage 3′-O-P(O)(OH)-O-5′ replaced with an amino group (–NH–). After phosphitylation of the 3′-OH group, the dimer TNHT was introduced (by the standard phosphoramidite approach) into a central part of the nonadecathymidylate. This oligomer exhibited lower affinity to the complementary single and double stranded DNA complements as compared to unmodified T19 oligonucleotide. The cleavage of modified oligomer with the snake venom and calf spleen phosphodiesterases was completely suppressed at the site of modification. RNA oligomers containing the TNHT dimer were used for preparation of siRNA molecules directed towards mRNA of BACE1 (beta-site amyloid precursor protein cleaving enzyme). The presence of the TNHT units at the 3′-ends of the RNA strands of the siRNA molecule (the siRNA itself is an effective gene expression inhibitor for BACE1) preserved the gene silencing activity and improved the stability of the modified siRNA in 10% fetal bovine serum.
The value of intervening for intimate partner violence in South African primary care: project evaluation
Authors: Joyner Kate , Mash Robert James
Published: December 2011

Objectives

Intimate partner violence (IPV) is an important contributor to the burden of disease in South Africa. Evidence-based approaches to IPV in primary care are lacking. This study evaluated a project that implemented a South African protocol for screening and managing IPV. This article reports primarily on the benefits of this intervention from the perspective of women IPV survivors.

Design

This was a project evaluation involving two urban and three rural primary care facilities. Over 4–8 weeks primary care providers screened adult women for a history of IPV within the previous 24 months and offered referral to the study nurse. The study nurse assessed and managed the women according to the protocol. Researchers interviewed the participants 1 month later to ascertain adherence to their care plan and their views on the intervention.

Results

In total, 168 women were assisted and 124 (73.8%) returned for follow-up. Emotional (139, 82.7%), physical (115, 68.5%), sexual (72, 42.9%) and financial abuse (72, 42.9%) was common and 114 (67.9%) were at high/severe risk of harm. Adherence to the management plan ranged from testing for syphilis 10/25 (40.0%) to consulting a psychiatric nurse 28/58 (48.3%) to obtaining a protection order 28/28 (100.0%). Over 75% perceived all aspects of their care as helpful, except for legal advice from a non-profit organisation. Women reported significant benefits to their mental health, reduced alcohol abuse, improved relationships, increased self-efficacy and reduced abusive behaviour. Two characteristics seemed particularly important: the style of interaction with the nurse and the comprehensive nature of the assessment.

Conclusion

Female IPV survivors in primary care experience benefit from an empathic, comprehensive approach to assessing and assisting with the clinical, mental, social and legal aspects. Primary care managers should find ways to integrate this into primary care services and evaluate it further.
Selection bias and patterns of confounding in cohort studies: the case of the NINFEA web-based birth cohort
Authors: Pizzi Costanza , De Stavola Bianca L , Pearce Neil , Lazzarato Fulvio , Ghiotti Paola , Merletti Franco , Richiardi Lorenzo
Published: December 2011

Background

Several studies have examined the effects of sample selection on the exposure–outcome association estimates in cohort studies, but the reasons why this selection may induce bias have not been fully explored.

Aims

To investigate how sample selection of the web-based NINFEA birth cohort may change the confounding patterns present in the source population.

Methods

The characteristics of the NINFEA participants (n=1105) were compared with those of the wider source population—the Piedmont Birth Registry (PBR)—(n=36 092), and the association of two exposures (parity and educational level) with two outcomes (low birth weight and birth by caesarean section), while controlling for other risk factors, was studied. Specifically the associations among measured risk factors within each dataset were examined and the exposure–outcome estimates compared in terms of relative ORs.

Results

The associations of educational level with the other risk factors (alcohol consumption, folic acid intake, maternal age, pregnancy weight gain, previous miscarriages) partly differed between PBR and NINFEA. This was not observed for parity. Overall, the exposure–outcome estimates derived from NINFEA only differed moderately from those obtained in PBR, with relative ORs ranging between 0.74 and 1.03.

Conclusions

Sample selection in cohort studies may alter the confounding patterns originally present in the general population. However, this does not necessarily introduce selection bias in the exposure–outcome estimates, as sample selection may reduce some of the residual confounding present in the general population.
Effort and potential efficiencies for aquatic non-native species early detection
Authors: Hoffman Joel C. , Kelly John R. , Trebitz Anett S. , Peterson Greg S. , West Corlis W.
Published: December 2011

Our objective was to determine the effort required for high-probability early detection of non-native zooplankton, benthic invertebrates, and fish using Duluth–Superior Harbor — a Great Lakes port under intense non-native species introduction pressure — as a case study. Initially, we allocated samples using a spatially balanced random design. We then resampled the harbor, but allocated samples to a few targeted areas. We detected 21 non-native invertebrate and 10 non-native fish species; however, many rare zooplankton and benthic invertebrates were likely missed. The two designs did not have significantly different species accumulation curves, but the targeted area design samples had higher species richness and detected non-native species with a significantly higher probability. It was possible to reduce the effort required to detect established non-native species. In contrast, the effort required to detect an ultra-rare, newly arrived species remained large. Based on statistical estimation theory, the effort required to detect 95% or more of species present could exceed enumerating 750 zooplankton samples (~500 000 individuals, ~90 species), 150 benthic invertebrate samples (~100 000 individuals, ~250 species), and 100 fish samples (~75 000 individuals, ~40 species).
Identification of putative migratory pheromones from Pacific lamprey (Lampetra tridentata)
Authors: Yun Sang-Seon , Wildbill Andrew J. , Siefkes Michael J. , Moser Mary L. , Dittman Andrew H. , Corbett Stephen C. , Li Weiming , Close David A.
Published: December 2011

Pacific lamprey, Lampetra tridentata , has declined precipitously throughout their range in the Columbia River basin of North America. Tribal Nations and Federal and State agencies are engaged in efforts to restore these fish. Understanding whether Pacific lamprey emit and detect migratory pheromones is particularly important for these restoration efforts. Using behavioural assays, we demonstrated that migratory adult Pacific lamprey are attracted to odors emanating from their larval conspecifics. We then identified putative pheromones released by larval Pacific lamprey. Chemical analysis of the conditioned water from larval lamprey using liquid chromatography – mass spectrometry (LC–MS) revealed that the Pacific lamprey can release petromyzonamine disulfate (PADS), petromyzosterol disulfate (PSDS), and petromyzonol sulfate (PZS). Electro-olfactogram studies further demonstrated that adult Pacific lamprey can smell those bile acid compounds. Our data strongly indicate that the Pacific lamprey employ a chemical communication system mediated by a mixture of bile acids, as evidenced by pheromonal functions of the bile acid compounds in guiding migratory adult sea lamprey to the spawning streams. Comprehensive understanding of the chemical communications involved in lamprey migratory behavior may lead to improved scientific approaches for restoration efforts.
HIGH ACCURACY METHOD FOR TURBULENT FLOW PROBLEMS
Authors: GUNZBURGER M. , LABOVSKY A.
Published: December 2011

We present a method of high-order temporal and spatial accuracy for flow problems with high Reynolds number. The method presented is stable, computationally cheap and gives an accurate approximation to the quantities sought. The direct numerical simulation of turbulent flows is computationally expensive or not even feasible. Hence, the method employs turbulence modeling. The two key ingredients are the temporal deferred correction, combined with the family of Approximate Deconvolution models, which allows for arbitrarily high order of accuracy in both spatial and temporal variables. We prove stability and accuracy for the two-step method; the method is shown to be second order accurate in time and in the filtering width.
ROLL-WAVES IN BI-LAYER FLOWS
Authors: BOUTOUNET MARC , NOBLE PASCAL , VILA JEAN-PAUL
Published: December 2011

We derive consistent shallow water equations (so-called Saint Venant equations) for the superposition of two Newtonian fluids flowing down a ramp. We carry out a complete spectral analysis of steady flows in the low frequency/long wavelength regime and show the occurrence of hydrodynamic instabilities, so-called roll-waves, when steady flows are unstable.
SOME PROPERTIES OF THE "STRING GAS" WITH THE EQUATION OF STATE $p = -\frac{1}{3} \rho$
Authors: KAMENSHCHIK ALEXANDER YU. , KHALATNIKOV ISAAK M.
Published: December 2011

We show that the string gas — a perfect fluid with the equation of state [Formula: see text] possesses rather interesting properties. In Friedmann universes its presence can change the observable topology of the space; in the spherically symmetric spacetimes it produces rather bizzare geometries and in a way its influence on the rotation curves mimics the dark matter effects.
SCREENING OF COSMOLOGICAL CONSTANT IN NON-LOCAL COSMOLOGY
Authors: ZHANG YING-LI , SASAKI MISAO
Published: December 2011

We consider a model of non-local gravity with a large bare cosmological constant, Λ, and study its cosmological solutions. The model is characterized by a function f(ψ) = f0eαψ, where ψ = □-1R and α is a real dimensionless parameter. In the absence of matter, we find an expanding universe solution a ∝ tn with n < 1, that is, a universe with decelerated expansion without any fine-tuning of the parameter. Thus the effect of the cosmological constant is effectively shielded in this solution. It has been known that solutions in non-local gravity often suffer from the existence of ghost modes. In the present case, we find the solution is ghost-free if α > αcr ≈ 0.17. This is quite a weak condition. We argue that the solution is stable against the inclusion of matter fields. Thus our solution opens up new possibilities for solution to the cosmological constant problem.
AN OSMOTICALLY INFLATABLE SEAL TO TREAT ENDOLEAKS OF TYPE 1, FOLLOWING ENDOVASCULAR ANEURYSM REPAIR
Authors: CHAGNON GREGORY , GAUDIN VINCENT , FAVIER DENIS , ORGEAS LAURENT , CINQUIN PHILIPPE
Published: December 2011

Stent-grafts of various designs are currently used in endoluminal treatment of abdominal aortic aneurysm. Two of the remaining possible complications are endoleaks and stent migrations. To treat endoleaks of type 1, a new system is studied here: An inflatable osmotic seal. It is set up at the extremities of the endograft and swollen using osmotic process against the vessels in case of endoleak without any invasive re-intervention. Mechanical modeling of the device and finite element simulations are performed to evaluate the efficiency of the seal and the consequences on the arteries as function of the osmotic pressure.
IONIC OSMOTIC EFFECTS INCREASE FLUID FLOW DURING PERMEATION TESTS
Authors: FARRELL M. D. , RICHES P. E.
Published: December 2011

Fluid flow is essential for the transport of metabolites to, from and within the intervertebral disc (IVD). By applying quadriphasic mixture theory experimentally, this study relates fluid flow within the bovine nucleus pulposus (NP) to the applied fluid pressure gradients and fixed charge and mobile ion concentration gradients. 24 plugs of NP tissue (diameter 10 mm, height 1020 ± 122 μm (mean ± SD)), orientated in the axial direction, were harvested from bovine tail discs. The plugs were permeated with either; 0 M NaCl , 0.15 M NaCl or 3 M NaCl solutions by subjecting them to 30, 45 and 60 kPa fluid pressure gradients applied in a random sequence. The hypertonic solution was assumed to render all non-fluid pressure gradients negligible, whilst the hypotonic solution was assumed to render the mobile ion concentration gradient negligible. The effects of these gradients on fluid flow were expressed as a percentage of the applied fluid pressure. Fluid velocity was significantly increased through the tissue in the isotonic case compared to the hypertonic case by up to 55% of the applied fluid pressure. The fixed charges accounted for between 26% and 43% and the mobile ion gradient responsible for 12–26% of this increased fluid flow. These results highlight the importance of using a constitutive equation for permeability that includes mobile ions and fixed charges as separate phases when modeling cartilaginous tissue in order to better describe fluid flow, and thus convective transfer of metabolites, within the tissue.
SUBTLE ELECTROMYOGRAPHIC PATTERN RECOGNITION FOR FINGER MOVEMENTS: A PILOT STUDY USING BSS TECHNIQUES
Authors: NAIK GANESH R. , KUMAR DINESH K.
Published: December 2011

In the recent past, blind source separation (BSS) algorithms using multivariate statistical data analysis technique have been successfully used for source identification and separation in the field of biomedical and statistical signal processing. Recently numbers of different BSS techniques have been developed. With BSS methods being the feasible method for source separation and decomposition of biosignals, it is important to compare the different techniques and determine the most suitable method for the applications. This paper presents the performance of five BSS algorithms (SOBI, TDSEP, FastICA, JADE and Infomax) for decomposition of sEMG to identify subtle finger movements. It is observed that BSS algorithms based on second-order statistics (SOBI and TDSEP) gives better performance compared to algorithms based on higher-order statistics (FastICA, JADE and infomax).
MECHANICAL PROPERTIES OF THE HUMAN METATARSAL BONES
Authors: DANESI VALENTINA , CRISTOFOLINI LUCA , JUSZCZYK MATEUSZ MARIA , ERANI PAOLO , VICECONTI MARCO
Published: December 2011

Despite the incidence of metatarsal fractures and the associated risk of significant disability, little is known about the biomechanical properties (strength and stiffness) of metatarsal bones. In most cases a single metatarsal bone (first, second and fifth) has been investigated. An extensive investigation of the biomechanical properties of the metatarsal bones is essential in the understanding and prevention of metatarsal injuries. Entire sets of metatarsal bones from four feet were tested. The first foot was used to fine-tune the testing set-ups. To measure the stiffness, each metatarsal bone was subjected to non-destructive four-point-bending in the sagittal and transverse planes, axial compression and torsion. Strain was measured at two locations. To measure the strength, each metatarsal bone was tested to failure in torsion. Significant differences (p < 0.0001) existed among the stiffness of the five metatarsal bones: (i) in torsion the first metatarsal bone was 2–3 times stiffer than the others; (ii) in four-point-bending and axial compression this difference was less pronounced than in torsion; (iii) differences were smaller among the other metatarsal bones; (iv) the second metatarsal bone was less stiff than the third and fourth in bending. The second, third and fourth metatarsal bones were stiffer in the sagittal than in the transverse plane (p < 0.0001). Conversely, there was no significant difference between the two planes of bending for the first and fifth bones. During destructive testing, all metatarsal bones exhibited a linear elastic behavior and brittle failure. The torsional strength at failure ranged between 1.9 Nm and 6.9 Nm. The first metatarsal bone was stronger than all the others. Stiffness in different loading conditions and failure were measured and compared for all metatarsal bones. These data corroborate previous biomechanical studies concerning the role and load sharing of the different metatarsal bones.