bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparative survey of genetic diversity among a set of Caricaceae accessions using microsatellite markers
Authors: Sengupta Samik , Das Basabdatta , Prasad Manoj , Acharyya Pinaki , Ghose Tapas Kumar
Published: July 2013

A preliminary survey of genetic diversity among 34 commercially popularCarica papayacultivars from India and abroad, 6 accessions ofVasconcelleaspecies and 1 accession ofJacaratia spinosa, was done using 20 simple sequence repeat (SSR) markers. The SSR profiles were used to find out total number of alleles, null and rare alleles, Polymorphism Information Content (PIC) values and to calculate similarity matrix using Jaccard’s coefficient. The subsequent dendrogram was made by unweighted pair-group method of arithmetic average (UPGMA) and neighbor-joining method. Based on these parameters a comparison was made between the Indian papaya cultivars and the rest of the accessions. All the markers showed polymorphism and a total of 140 alleles were identified. The average number of alleles was 7 alleles/locus. Categorically theVasconcelleaandJacaratiaspecies had 54 alleles, the 7 non-IndianCarica papayaaccessions had 70 and the 27 Indian accessions had 102 alleles. The average PIC value was 0.735 per marker. A total of 37 rare alleles were identified.Jacaratia spinosahad 17 rare alleles. Nineteen null alleles were detected among theCarica papayaaccessions. ACarica papayaaccession from South Africa, Hortus Gold had 5 null alleles. The genetic similarity among the accessions ranged from 7% to 67%. In the dendrogram, theVasconcellea and Jacaratia spinosaaccessions separated as a distinct cluster from the rest of theCarica papayaaccessions. The study indicated that the accessions of IndianCarica papayacultivars included in this survey are genetically more diverse than the non-IndianCarica papayacultivars.
Gene expression changes with age in skin, adipose tissue, blood and brain
Authors: Glass Daniel , Viñuela Ana , Davies Matthew N , Ramasamy Adaikalavan , Parts Leopold , Knowles David , Brown Andrew A , Hedman Åsa K , Small Kerrin S , Buil Alfonso , Grundberg Elin , Nica Alexandra C , Di Meglio Paola , Nestle Frank O , Ryten Mina ,   the UK Brain Expression consortium,   the MuTHER consortium, Durbin Richard , McCarthy Mark I , Deloukas Panagiotis , Dermitzakis Emmanouil T , Weale Michael E , Bataille Veronique , Spector Tim D
Published: July 2013

Background

Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age.

Results

Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential expression with age in both skin and brain tissue and three common to adipose and brain tissues.

Conclusions

Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.
The strength of genetic interactions scales weakly with mutational effects
Authors: Velenich Andrea , Gore Jeff
Published: July 2013

Background

Genetic interactions pervade every aspect of biology, from evolutionary theory, where they determine the accessibility of evolutionary paths, to medicine, where they can contribute to complex genetic diseases. Until very recently, studies on epistatic interactions have been based on a handful of mutations, providing at best anecdotal evidence about the frequency and the typical strength of genetic interactions. In this study, we analyze a publicly available dataset that contains the growth rates of over five million double knockout mutants of the yeast Saccharomyces cerevisiae.

Results

We discuss a geometric definition of epistasis that reveals a simple and surprisingly weak scaling law for the characteristic strength of genetic interactions as a function of the effects of the mutations being combined. We then utilized this scaling to quantify the roughness of naturally occurring fitness landscapes. Finally, we show how the observed roughness differs from what is predicted by Fisher's geometric model of epistasis, and discuss the consequences for evolutionary dynamics.

Conclusions

Although epistatic interactions between specific genes remain largely unpredictable, the statistical properties of an ensemble of interactions can display conspicuous regularities and be described by simple mathematical laws. By exploiting the amount of data produced by modern high-throughput techniques, it is now possible to thoroughly test the predictions of theoretical models of genetic interactions and to build informed computational models of evolution on realistic fitness landscapes.
Risk of dementia after anaesthesia and surgery
Authors: Chen Pin-Liang , Yang Chih-Wen , Tseng Yi-Kuan , Sun Wei-Zen , Wang Jane-Ling , Wang Shuu-Jiun , Oyang Yen-Jen , Fuh Jong-Ling
Published: July 2013

Background

The potential relationship between anaesthesia, surgery and onset of
dementia remains elusive.

Aims

To determine whether the risk of dementia increases after surgery with
anaesthesia, and to evaluate possible associations among age, mode of
anaesthesia, type of surgery and risk of dementia.

Method

The study cohort comprised patients aged 50 years and older who were
anaesthetised for the first time since 1995 between 1 January 2004 and 31
December 2007, and a control group of randomly selected patients matched
for age and gender. Patients were followed until 31 December 2010 to
identify the emergence of dementia.

Results

Relative to the control group, patients who underwent anaesthesia and
surgery exhibited an increased risk of dementia (hazard ratio = 1.99) and
a reduced mean interval to dementia diagnosis. The risk of dementia
increased in patients who received intravenous or intramuscular
anaesthesia, regional anaesthesia and general anaesthesia.

Conclusions

The results of our nationwide, population-based study suggest that
patients who undergo anaesthesia and surgery may be at increased risk of
dementia.
Impact of clinical severity on outcomes of mentalisation-based treatment for borderline personality disorder
Authors: Bateman Anthony , Fonagy Peter
Published: July 2013

Background

Evidence of remission from borderline personality disorder (BPD) without specialised treatment is accumulating.

Aims

To establish whether specialised treatments are indicated for patients with clinically severe disorder.

Method

The impact of clinical severity on outcomes of a randomised controlled trial of mentalisation-based treatment (MBT) was contrasted with structured clinical management (SCM). Severity indicators were defined as severity of comorbid psychiatric syndromes, severity of BPD, severity of personality disturbance and severity of symptom distress. Logistic regressions were used to predict the likelihood of recovery at 18 months, and mixed-effects regression analysis was applied to examine the association of severity and rates of improvement across time in the two treatment groups.

Results

None of the severity criteria predicted outcome at the end of treatment on logistic regression. However, testing the significance of distribution of cases of recovery v. non-recovery suggested that multiple Axis II diagnoses and symptom distress influenced outcomes.

Conclusions

Borderline personality disorder with significant Axis II comorbidity is a possible but uncertain indicator for specialist treatment. Patients whose only personality disorder diagnosis is BPD do equally well with SCM. Prospective studies are needed.
Transmission of chimeric HIV by mating in conventional mice: prevention by pre-exposure antiretroviral therapy and reduced susceptibility during estrus
Authors: Hadas Eran , Chao Wei , He Hongxia , Saini Manisha , Daley Eleen , Saifuddin Mohammed , Bentsman Galina , Ganz Eric , Volsky David J. , Potash Mary Jane
Published: July 2013

Heterosexual transmission accounts for the majority of new human immunodeficiency virus (HIV) cases worldwide. The current approach to investigate HIV heterosexual transmission in animals involves application of virus stock to the vaginal surface, a method that does not reproduce the physiological conditions of vaginal intercourse that influence the rate of transmission. We have previously described efficient infection of conventional mice using EcoHIV/NL4-3 and EcoHIV/NDK, chimeric HIV molecular clones constructed to express all HIV structural and regulatory genes except envelope, which is replaced by a rodent-tropic envelope gene. Here we investigated whether EcoHIV/NDK-infected male mice transmit virus to females during coitus, and the sensitivity of this transmission to HIV pre-exposure prophylaxis and the estrus state. Our general approach was to allow mating between EcoHIV/NDK-infected male mice and uninfected females for 1-7 nights. At 1-6 weeks after mating, mice were euthanized and virus burdens were measured by quantitative PCR (qPCR) amplification of HIV RNA or DNA in peritoneal macrophages, inguinal lymph node cells, spleen cells or vas deferens, or by ELISA for antibodies to HIV Gag. We found that 70-100% of female mice mated to EcoHIV/NDK-infected males acquired infection. Pericoital treatment of females with either 2',3'-dideoxcytidine (ddC) or tenofovir largely prevented their EcoHIV/NDK infection by mating (P<0.05 and P<0.003, respectively). In males, T cells were dispensable for virus transmission. The rate of EcoHIV/NDK sexual transmission to females in estrus declined sharply (P=0.003) but their infection by injection was unaffected, indicating that the local environment in the female reproductive tract influences susceptibility to HIV. We conclude that this system of EcoHIV/NDK transmission during mouse mating reproduces key features of heterosexual transmission of HIV in humans and can be used to investigate its biology and control.
Membrane curvature generation by a C-terminal amphipathic helix in peripherin-2/rds, a tetraspanin required for photoreceptor sensory cilium morphogenesis
Authors: Khattree Nidhi , Ritter Linda M. , Goldberg Andrew F. X.
Published: July 2013

Vertebrate vision requires photon absorption by photoreceptor outer segments (OSs), structurally elaborate membranous organelles derived from non-motile sensory cilia. OS structure/function depends on a precise stacking of hundreds of membranous disks. Each disk is fully (as in rods) or partially (as in cones) bounded by a rim, at which the membrane is distorted into an energetically unfavorable high curvature bend; however, the mechanism(s) underlying disk rim structure are not established. Here we demonstrate that the intrinsically disordered cytoplasmic C-terminus of the photoreceptor tetraspanin peripherin-2/rds (P/rds) can directly generate membrane curvature. A P/rds C-terminal domain (CTER) and a peptide mimetic of an amphipathic helix (AH) contained within it (CHR) each generated curvature in liposomes with a composition similar to that of OS disks and in liposomes generated from native OS lipids. CTER association with liposomes required conical phospholipids, and was promoted by membrane curvature and anionic surface charge, results suggesting that the P/rds C-terminal AH can partition into the cytosolic membrane leaflet to generate curvature via a hydrophobic insertion (wedging) mechanism. This activity was evidenced in full-length P/rds by its induction of small diameter tubulovesicular membrane foci in cultured cells. In sum, the findings suggest that curvature generation by the P/rds C-terminus may contribute to the distinctive structure of OS disk rims, and provide insight into how inherited defects in P/rds can disrupt organelle structure to cause retinal disease. They also raise the possibility that tethered AHs can function for shaping cellular membranes more generally.
Nuclear PP2A-Cdc55 prevents APC-Cdc20 activation during the spindle assembly checkpoint
Authors: Rossio Valentina , Michimoto Takeshi , Sasaki Takeshi , Ohbayashi Iwai , Kikuchi Yoshiko , Yoshida Satoshi
Published: July 2013

Cdc55, a regulatory B-subunit of protein phosphatase 2A (PP2A) complex, is essential for the spindle assembly checkpoint (SAC) in budding yeast, but the regulation and molecular targets of PP2A-Cdc55 have not been clearly defined or are controversial. Here, we show that an important target of Cdc55 in the SAC is the anaphase-promoting complex (APC) coupled with Cdc20 and that APC-Cdc20 is kept inactive by dephosphorylation by nuclear PP2A-Cdc55 when spindle is damaged. By isolating a new class of Cdc55 mutants specifically defective in the SAC and by artificially manipulating nucleocytoplasmic distribution of Cdc55, we further show that nuclear Cdc55 is essential for the SAC. Because the Cdc55-binding proteins Zds1 and Zds2 inhibit both nuclear accumulation of Cdc55 and SAC activity, we propose that spatial control of PP2A by Zds1 family proteins is important for tight control of SAC and mitotic progression.
Ligand signature in the membrane dynamics of single TrkA receptor molecules
Authors: Marchetti Laura , Callegari Andrea , Luin Stefano , Signore Giovanni , Viegi Alessandro , Beltram Fabio , Cattaneo Antonino
Published: July 2013

The neurotrophin receptor TrkA (also known as NTRK1) is known to be crucially involved in several physio-pathological processes. However, a clear description of the early steps of ligand-induced TrkA responses at the cell plasma membrane is missing. We have exploited single particle tracking and TIRF microscopy to study TrkA membrane lateral mobility and changes of oligomerization state upon binding of diverse TrkA agonists (NGF, NGF R100E HSANV mutant, proNGF and NT-3). We show that, in the absence of ligands, most of the TrkA receptors are fast moving monomers characterized by an average diffusion coefficient of 0.47 µm2/second; about 20% of TrkA molecules move at least an order of magnitude slower and around 4% are almost immobile within regions of about 0.6 µm diameter. Ligand binding results in increased slow and/or immobile populations over the fast one, slowing down of non-immobile trajectories and reduction of confinement areas, observations that are consistent with the formation of receptor dimeric and oligomeric states. We demonstrate that the extent of TrkA lateral mobility modification is strictly ligand dependent and that each ligand promotes distinct trajectory patterns of TrkA receptors at the cell membrane (ligand ‘fingerprinting’ effect). This ligand signature of receptor dynamics results from a differential combination of receptor-binding affinity, intracellular effectors recruited in the signalling platforms and formation of signalling and/or recycling endosome precursors. Thus, our data uncover a close correlation between the initial receptor membrane dynamics triggered upon binding and the specific biological outcomes induced by different ligands for the same receptor.
RNA structural motif recognition based on least-squares distance
Authors: Shen Ying , Wong Hau-San , Zhang Shaohong , Zhang Lin
Published: July 2013

RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.
High-resolution view of compound promiscuity
Authors: Hu Ye , Bajorath Jürgen
Published: July 2013

Compound promiscuity is defined as the ability of a small molecule to specifically interact with multiple biological targets. So-defined promiscuity is relevant for drug discovery because it provides the molecular basis of polypharmacology, which is increasingly implicated in the therapeutic efficacy of drugs. Recent studies have analyzed different aspects of compound promiscuity on the basis of currently available activity data. In this commentary, we present take-home messages from these studies augmented with new results to generate a detailed picture of compound promiscuity that might serve as a reference for further discussions and research activities.
Product-Oriented Web Technologies and Product Returns: An Exploratory Study
Authors: De Prabuddha , Hu Yu (Jeffrey) , Rahman Mohammad S.
Published: July 2013

Internet retailers have been making significant investments in Web technologies, such as zoom, alternative photos, and color swatch, that are capable of providing detailed product-oriented information and, thereby, mitigating the lack of “touch and feel,” which, in turn, is expected to lower product returns. However, a clear understanding of the relationship between these technologies and product returns is still lacking. Our study attempts to fill this gap by using several econometric models to explore the said relationship. Our unique and rich data set from a women's clothing company allows us to measure technology usage at the product level for each consumer. The results show that, in this context, zoom usage has a negative coefficient, suggesting that a higher use of the zoom technology is associated with fewer returns. Interestingly, we find that a higher use of alternative photos is associated with more returns and, perhaps more importantly, with lower net sales. Color swatch, on the other hand, does not seem to have any effect on returns. Thus, our findings show that different technologies have different effects on product returns. We provide explanations for these findings based on the extant literature. We also conduct a number of tests to ensure the robustness of the results.
Installation, Calibration, and Application of Dielectric Sensors in Laboratory Studies of Compacted Unsaturated Granular Materials
Authors: de Carteret Ryan , Buzzi Olivier , Fityus Stephen
Published: July 2013

The use of small-scale, instrumented laboratory columns for the study of moisture content and electrical conductivity response of soils has historically been restricted primarily to fine-grained materials because of the size of available instrumentation and probe installation difficulties. This study explores the suitability of capacitance-type dielectric sensors for studies of coarse-grained granular materials by assessing installation and calibration requirements. A number of different methods for installing a Hydra Probe dielectric sensor in a gravelly granular material were assessed and their repeatability compared with sensor installation in a fine-grained material. Typical installation methods were found to result in highly inconsistent installation in the compacted granular material, with poor repeatability. An alternative installation method is presented for gravelly granular materials, which resulted in an acceptable level of repeatability for both components of sensor measurement, consistent with that achieved by direct sensor insertion in fine-grained materials. It was also found necessary to develop a material-specific volumetric moisture content calibration relationship for the granular material as the manufacturer-supplied relationships were found to have very-low accuracy. This material-specific calibration was found to improve the accuracy of the dielectric sensor to ±0.03 m3/m3. To demonstrate the potential of dielectric sensors for use in the study of compacted granular materials, two laboratory experiments are described: one monitoring changes in moisture content with time and the other changes in electrical conductivity. General recommendations for use of dielectric sensors with granular materials are also presented.
Monitoring Field Lift Thickness Using Compaction Equipment Instrumented with Global Positioning System (GPS) Technology
Authors: Meehan Christopher L. , Khosravi Mohammad , Cacciola Daniel V.
Published: July 2013

When constructing earthen embankments, it is essential that the soil be placed and spread in uniform lifts prior to compaction. To ensure that the resulting soil lifts are evenly compacted, typical compaction specification approaches place restrictions on the thickness that is acceptable for each soil lift. In current practice, it can be extremely difficult for a field inspector to verify that lift thickness requirements are being met when soil is being placed and spread over a large area, without the use of frequent surveying (which adds both costs and delays to earthwork projects). Recent advances in compaction control include the development of continuous compaction control (CCC) and intelligent compaction (IC) systems, which provide real-time monitoring and feedback about the operation and performance of soil compaction. Typically, CCC and IC compaction equipment is outfitted with a real-time kinematic global positioning system (RTK-GPS) that monitors and records the position of the compacter as the soil lift is being compacted. This paper suggests that geotechnical engineers use field RTK-GPS measurements that are made by CCC or IC equipment to monitor and control the thickness of compacted soil lifts. Data collected from a full-scale field study is used to illustrate the practical issues with using GPS measurements for field monitoring of lift thickness during construction of a roadway embankment, such as varying roller position from lift-to-lift and the measurement uncertainty associated with RTK-GPS measurement data. The use of both simple and sophisticated spatial analysis techniques are explored for interpolating measured field elevation data onto a uniform grid for lift thickness assessment. The resulting methodology that is presented can be utilized to build spatial maps of compacted soil lift thickness, a process that can be used to great benefit by field engineers who are trying to ensure the quality of compacted soil lifts.
Determination of Soil Stabilizer Content Using X-Ray Fluorescence
Authors: Cerato A. B. , Miller G. A.
Published: July 2013

Currently, there are no simple methods routinely used to quantify the amount of chemical additive mixed into the soil during subgrade stabilization. Such a method was developed and validated for commonly used chemical additives including lime, cement kiln dust, and Class C fly ash mixed with different fine-grained soil types. The method employs the well-established x-ray fluorescence (XRF) technique. X-ray fluorescence was used to detect the amount of stabilizer, in the form of calcium oxide (CaO), in several stabilized subgrade soils. This technique was validated using four soils of different mineralogy and classification stabilized with three chemical stabilizers, and successfully implemented on several roadway stabilization projects. The results show that XRF accurately measures the amount of CaO in various soils, using different stabilizers, and can be a valuable tool for not only quality control, but forensic geotechnical investigations as well.
Calibration of Roller-Integrated Machine Drive Power Measurements Using Soil Compaction Forecasting Model
Authors: Thompson Mark J. , Schmitt Robert L.
Published: July 2013

Calibration of roller-integrated machine drive power (MDP) measurements is a necessary step for implementing the continuous compaction control technology into practice. State-of-the-practice calibration procedures use univariate or multivariate regression analysis of roller machine values with traditional compaction indices, such as modulus or soil unit weight. In this paper, a new calibration technique for estimating dry unit weight from MDP measurements was developed through investigation of the relationship between roller-integrated MDP and the inferred compactive effort associated with the corresponding moisture-density state of soil. Based on field data from eight test strips, linear trends were observed between compactive effort and cumulative MDP, and the proposed approach was able to detect how moisture content (a changing variable between test strips) substantially influences soil compactive effort and the soil–roller interaction affecting MDP measurements. Identifying slopes and intercepts of these moisture-dependent correlations allows for estimating roller-achieved compactive effort, and then converting estimated compactive effort to soil dry unit weight through a unified soil compaction model that is calibrated using traditional laboratory Proctor test data. The proposed forecasting calibration technique is based on accepted and defensible geotechnical principles on which earthworks practice is based, not relying solely on regression models. Observing the correlation of roller machine values and dry unit weight in the context of soil compaction behavior is expected to improve confidence in the continuous compaction control technology and ultimately result in more widespread acceptance and use.
Centrifuge Modeling of Deep Excavations and Their Interaction With Adjacent Buildings
Authors: Elshafie M. Z. E. B. , Choy C. K. C. , Mair R. J.
Published: July 2013

Major cities in the world are experiencing a rapid growth in population while becoming increasingly overcrowded and congested. In recent years, this has created a huge demand for underground infrastructure, which often involves the design of major mass transit tunnel systems; these tunnel systems (underground tunnels and metro stations) are becoming increasingly necessary to construct in very close proximity to existing buildings. The prediction of excavation-induced deformations, therefore, becomes a key issue in the planning and design process for these schemes. However, current design approaches are conservative and often lead to unnecessary concern and expenditure in the design and provision of protective measures. A better understanding of the mechanisms involved in the excavation soil–structure interaction could reduce costs and help avoid potential problems. A series of small-scale model tests was carried out in the geotechnical centrifuge at Cambridge University to investigate the interaction between excavations and model buildings. Excavations (simulated by adopting a novel two-fluid technique) in a “free field” were also undertaken to assess the difference between free-field ground movements and those affected by a stiff model building. A detailed description of the centrifuge models and test procedures is presented in this paper, followed by the presentation of test results that demonstrate the effect of the stiffness of the model building on the excavation-induced displacements.
A Large-Scale Soil-Structure Interface Testing Device
Authors: Vogelsang Jakob , Huber Gerhard , Triantafyllidis Theodoros
Published: July 2013

A large-scale testing device for the experimental investigation of soil-structure interactions was developed. It allows an observation of the evolution of deformations and the measurement of the stresses in the soil-structure contact zone under 1 g-conditions. The tests are designed as boundary value problems for benchmark tests of numerical simulations. They can be used to validate contact formulations and constitutive equations for the soil. The dimensions (soil height >1.5 m) provide a sufficiently high stress level for simulations with constitutive models for soil. The major part of the device is an instrumented wall section with modifiable surface roughness representing, e.g., a part of a pile shaft or a steel sheet. This wall can be displaced quasi-statically relative to an adjacent soil body. The distribution of shear and normal stress and the wall displacements are measured. Digital image correlation (DIC) is used to evaluate the soil deformations. The paper focuses on the basic concept, the design, and the instrumentation details of the testing device. Additionally, some selected test results are shown.
Evaluation of Bouwer-Rice Large-Particle Correction Procedure for Soil Water Characteristic Curves
Authors: Bareither Christopher A. , Benson Craig H.
Published: July 2013

The Bouwer-Rice correction method to account for large particles excluded during laboratory testing to measure the soil water characteristic curve (SWCC) was evaluated on samples of well-graded alluvium. A large-scale hanging column apparatus was used so that tests could be conducted on specimens containing all particle sizes. The analyses show that SWCCs measured on the fraction of alluvium finer than the No. 4 U.S. sieve (4.8 mm) can be corrected reliably to represent the SWCC of bulk soil or fractions of bulk soil corresponding to different large-particle thresholds. The method can also be used reliably to correct SWCCs measured on soils prepared with different large-particle thresholds (e.g., finer than 25 mm, 12.5 mm, or 4.8 mm). Dry density of the finer fraction being tested must be carefully controlled to match the dry density of the finer fraction in the soils containing large particles. An equation is described for computing the dry density of the finer fraction in a bulk soil. A simplified version of the Bouwer-Rice method is also proposed and evaluated. In this method, a SWCC test is conducted on the finer soil fraction with dry density matching that anticipated in the field, the van Genuchten equation is fit to the measured SWCC to define the shape parameters α and n, and then the SWCC for the field application is computed using the fitted α and n from the test on the finer fraction, saturated volumetric water content of the bulk soil in the field, and a residual water content of zero. Analyses show that this modified Bouwer-Rice method is simpler and results in an accurate representation of the SWCC of soil containing large particles.
An Experimental Framework for BGP Security Evaluation
Authors: Perouli Debbie , Maennel Olaf , Phillips Iain , Fahmy Sonia , Bush Randy , Austein Rob
Published: July 2013

Internet routing is based on implicit trust assumptions. Given the critical importance of the Internet and the increasing security threats, such simple trust relationships are no longer sufficient. Over the past decade, significant research has been devoted to securing the Internet routing system. The Internet Engineering Task Force (IETF) is well along in the process of standardizing routing security enhancements (Secure Inter-Domain Routing — SIDR, Keying and Authentication for Routing Protocols — KARP, etc.). However, the research challenges are not over: not only do these new protocols need to be tested for protocol conformance and interoperability, they also need to be evaluated both for their security properties and scaling performance. The purpose of this paper is two-fold: we outline the main security challenges in inter-domain routing and argue that research in this area has barely begun; and we take a closer look at a production implementation of one component and evaluate it at a fairly large scale. We discuss the difficulties we experienced and lessons learned; we also present some initial results.
Die Herausbildung des biblischen Kanons im antiken Judentum und im frühen Christentum
Authors: Frey Jörg
Published: July 2013

Starting with the observation that the canon of the Bible differs among the Christian denominations (Lutheran, Reformed, Roman Catholic), and that definitive decisions on the canon were not made before the 16th century, the author gives a brief account of the process of the development of both the Jewish and the bipartite Christian canon. Due to more recent textual discoveries, earlier views of the making of the Jewish or the Christian canon have undergone significant changes. For the Jewish canon, the discovery of the Dead Sea Scrolls (Qumran texts) provided the opportunity to study the making of the canon from manuscript evidence, and to alter the overall view from the pattern of a three stage canonization to the pattern of a “canonical process”, leading to the Hebrew canon and, later and in Christian circles, to the canon of the Septuagint. This pattern is also useful for studying the making of the bipartite Christian canon or the New Testament canon. Here, the author focuses on the challenge provided by Marcion’s “canon”, the early beginning of the canonical process and its late closure, and the various factors in the process, which can be studied by including the manuscript evidence and taking into account the character of several apocryphal texts and the context and intention of the various lists of canonical texts. The biblical canon as presupposed throughout the Middle Ages is the result of a complicated and variegated canonical process. But in spite of the problems of the criteria and factors involved, the biblical canon is theologically valuable and “well-chosen”.
Toter Buchstabe – lebendiger Geist. Bibelauslegung als Lektüreereignis
Authors: Prica Aleksandra
Published: July 2013

There is scarcely a sentence in the New Testament that could have unleashed a wider reception history than Paul‘s comparison of the letter and the spirit in the third chapter of the Second Epistle to the Corinthians: “For the letter killeth, but the spirit giveth life.” In Patristics two diverging lines of reception can be identified, which, depending on the perspective, emphasise the hermeneutic or the soteriological side of the formula more strongly. This paper investigates the antithesis of spirit and letter at various stations of its reception history from Late Antiquity to the late Middle Ages and ventures to profile the contrast primarily as the hermeneutic relationship between the object and the reading event.
Lebendige Bücher. Materielle und mediale Aspekte der Heilsvermittlung in der mittelalterlichen Gedenküberlieferung
Authors: Hugener Rainer
Published: July 2013

Throughout the Middle Ages, documents commemorating the names of dignitaries and benefactors in monasteries and churches were characterized as liber vitae, just as the heavenly book mentioned in the Bible. Those whose names were inscribed in such a list were promised eternal life through commemoration. The paper discusses material and medial aspects of the mediation of salvation within such documents as well as the shifts between different sorts of bookkeeping arising between the 9th and the 15th century by focusing on writing strategies, document organization, and layout in Carolingian confraternity books, monastic necrologies, and late medieval obituaries or anniversary books from collegiate and parish churches. Their differing structures show how concepts and places of liturgical commemoration changed over the centuries.
Von Göttern und Gesteinen. Zur Interpretation dreier bemerkenswerter Kultobjekte im Tempel von Tôd
Authors: von Lieven Alexandra
Published: July 2013

In the scene 284 II in the crypts of the temple of Tôd, there is a unique depiction of three hippopotamus-like lumps of jasper. Up to now their strange iconography has eluded an explanation. In this paper, it is argued that indeed these were mere lumps of stone of peculiar shape, into which the Egyptians “saw” hippopotamuses. To back this interpretation up, other examples of similar cases of religious interest in odd-shaped stones or the like are presented. Finally, it is discussed why these “hippopotamuses” were believed to be forms of Tjenenet, as the inscriptions clearly state, when otherwise this goddess is not attested to have been associated with this kind of animal.
Nodjmet A, Daughter of Amenhotep, Wife of Piankh and Mother of Herihor
Authors: Thijs Ad
Published: July 2013

For Queen Nodjmet two funeral papyri are known. In this article it is argued that both should be ascribed to the mother of Herihor (Nodjmet A) rather than to his wife (Nodjmet B). This would make Nodjmet A the wife of HPA Piankh, and her mother, Hrere, the wife of HPA Amenhotep. Hrere, who is attested with the title “king’s mother”, is here interpreted as the mother of king Khakheperre Pinuzem and as the grandmother of both Nodjmet B and HPA Masaharta. This model is discussed in the light of the Late Ramesside Letters, the Oracle of Herihor, the Banishment Stele, the Procession scene from the Temple of Khonsu and several other sources.
Global engineers thinking locally: creating kindergartens for Africa
Authors: Gryc Hayley , da Silva Jo
Published: July 2013

This paper reflects on the wider benefits that civil engineers can bring to individual communities when undertaking design services through engaging with local stakeholders and understanding the environment, context and culture in which they work. A sustainable kindergarten complex in Ghana is used as a case study to illustrate the benefits of civil engineers adopting a broader perspective, combining global expertise with local knowledge. The paper explains the design approach taken by the team and the key features of the design and construction, which offers a sustainable solution to the shortfall in facilities for early-years learning in Ghana and potentially throughout Africa.
Developments in UK flood forecasting will lead to major reduction in flash-flood risk
Authors: Pollard Oliver , Harrison Tim
Published: July 2013

In the decade since the dramatic flash floods in Boscastle, Cornwall there have been major developments in UK flood-forecasting techniques and systems, particularly for ‘rapid-response’ catchments. Oliver Pollard and Tim Harrison of the Environment Agency explain.
EU spreads the net for waste electrical and electronic equipment
Authors: Huber-Humer Marion
Published: July 2013

The EU has revised its 10-year-old directive on waste electrical and electronic equipment, with wider definitions and higher collection and recovery targets. Stefan Salhofer and Marion Huber-Humer of the University of Natural Resources and Life Sciences in Vienna report.
How a diver saved Winchester Cathedral, UK: and today's solution?
Authors: Roberts Gwilym
Published: July 2013

In 1905 there were concerns about the dangerous state of Britain's Winchester Cathedral, some walls having subsided significantly while others were leaning out dangerously or had cracks and voids. A trial hole confirmed a high water table with compressible peat overlying a gravel bed. Francis Fox was consulted and recommended grouting the cavities, installing tie-rods and the temporary shoring up of some walls before underpinning them down to the gravel bed. Pits dug to start the underpinning operation rapidly filled with black peaty water thereby reducing visibility to almost nil. Conventional pumping being considered too dangerous, a diver excavated and then bottom-sealed pits dug under the walls, thus enabling the remainder of the underpinning work to be completed by others. Eventually the work was extended to virtually all the cathedral's walls, the diver remaining on site for 5 years, carrying out most of his work underwater in a diving suit and by feel and touch. Studies undertaken in 2006–2007 confirmed that the structure was stable but suggested that, before deciding to underpin the walls, Fox might have instituted more investigations. It was also thought that, if foundation strengthening was considered necessary now, it would probably comprise some form of micropiling.
Classical writers and ancient construction works
Authors: Parry Richard H. G.
Published: July 2013

Construction works were no less important in the ancient world than they are today in creating the infrastructure consistent with a settled way of life. The importance of these works was not lost on the writers of the time: many are mentioned or described in classical texts. Works variously described or mentioned in these texts range from those associated with the control and utilisation of water, thus providing the basic essential for life, to structures associated with travel and trade, administration, military activities, cultural customs and spiritual beliefs. Taken together with remains of these works and contemporary inscriptions, these descriptions by classical writers reveal much about the motivations and capabilities of people in the ancient world.
The challenge of building the Buda-Pesth Chain Bridge across the icebound Danube
Authors: Vaci Sandor P. , Vignoles John
Published: July 2013

The freezing of the Danube over the winter months was a critical influence in the provision and method of construction of what is now the Széchenyi Chain Bridge in Budapest, Hungary, between 1839 and 1849. The bridge of boats connection between the former towns of Buda and Pesth could not operate in the winter months and it was imperative that a permanent structure be built. The major considerations in building the bridge related to the dangers posed by the river freezing over: in particular, choosing a chain bridge with the least number of piers and locating it to take account of the dangers of inundation from river ice. In describing the challenges faced and overcome, the paper makes use of a wealth of material from archives in both Budapest and London. These include the original contract for building the cofferdams, the drawings referred to in the contract, British engineer, William Tierney Clark's own comments and correspondence (particularly with his superintendent engineer Adam Clark) and vivid contemporary accounts of the freezing Danube. It is therefore an amalgam of contract history, civil engineering and cultural history.
Development of expedient military concrete airfield pavement repairs
Authors: Priddy Lucy P. , Tingle Jeb S.
Published: July 2013

Recent military operations have highlighted the need for modernisation of airfield damage repair capabilities for concrete pavements to eliminate long closure periods. Damaged or distressed military airfield pavements must be repaired using expedient methods and durable materials to minimise the time the pavement is removed from service, and to reduce or eliminate additional closure times for subsequent repairs. As a result of this need, extensive research was conducted to develop multiple concrete pavement repair techniques that could be applied across the full spectrum of military airfield repair operations. Developed methods included placing rapid-setting cementitious materials, foreign object debris covers and precast concrete panels over various backfill materials. Newly developed backfill techniques included poured and injected polyurethane foams and dry-placed, rapid-setting flowable fill. The combination of these materials resulted in several new repair techniques that could return a damaged pavement to aircraft traffic within 4–6 h of initiation of the repair. This paper summarises the development of these repair technologies, and describes their performances under accelerated pavement testing and aircraft validation tests. The paper also includes recommendations as to the suitability of each technique for specific operational scenarios, based on field evaluations.
Risk allocation in construction contracts – Irish public works
Authors: Mooney Conor , Mooney Emma
Published: July 2013

A properly executed contract is generally understood to be enforceable, regardless of the balance of risk contained in the contract. Allocating risk appropriately between employer and contractor in construction projects is therefore of prime importance, since, once agreed, there are very limited opportunities to reapportion that balance. Standard forms of contract differ primarily in how they allocate the balance of risk between employer and contractor, and some are considered more contractor-onerous than others. This article looks at optimal risk allocation, and compares the Irish government's recent approach to risk allocation in public works with the contractor-onerous FIDIC Silver Book form of contract. It is observed that the Irish government's approach attempts to place more risk onto the contractor than does the FIDIC Silver Book, does so without scope for amendments to the contract clauses, and this has occurred simultaneously with a significant drop in tender prices and an environment in which data is not yet readily available on the critical test of out-turn contract performance.
Comparison of plant preference hierarchies of male and female moths and the impact of larval rearing hosts
Authors: Thöming Gunda , Larsson Mattias C. , Hansson Bill S. , Anderson Peter
Published: July 2013

Selection of a suitable host plant is essential for the fitness of herbivorous insects. For polyphagous insects the underlying proximate mechanisms for host plant selection, including phenotypic plasticity, remain only partially understood. We established an experimental protocol evaluating preferences to five plant species in males and females of the polyphagous mothSpodoptera littoralis. Female preference hierarchies were assessed by oviposition decisions; those of males were assessed by the attraction to female sex pheromones in background odors of different plant species. The experiments revealed clear preference hierarchies in both males and females, which were partly overlapping in spite of the different behavioral contexts of the respective assays. Furthermore, we demonstrated strong effects of the larval rearing host on adult plant preference, where the larval host plant species was generally elevated to the most preferred plant in both sexes, without otherwise affecting the overall preference hierarchy. Our results suggest that both sexes are involved in host plant choice and that experience‐based convergent intersexual plant preferences may confer selective advantages. The host plant choice is guided by a stable plant preference hierarchy, which can be modified by the larval rearing host, permitting fast adaptation to variation in local conditions and to novel environments. It may also provide a mechanism for reducing costs associated with polyphagy by functional plasticity in plant choice.
Parsing handling time into its components: implications for responses to a temperature gradient
Authors: Sentis A. , Hemptinne J.-L. , Brodeur J.
Published: July 2013

The functional response is a key element of predator–prey interactions, and variations in its parameters influence interaction strength and population dynamics. Recent studies have used the equation of the metabolic theory of ecology (MTE) to quantify the effect of temperature on the parameter Th, called “handling time,” and then predict the responses of predators and communities to climate change. However, our understanding of the processes behind Th and how they vary with temperature remains limited. Using a ladybeetle–aphid system, we compared estimates of Th to direct observations of handling time across a temperature gradient. We found estimated Th values to be greater than observed Th values, suggesting that predation rate is not limited by the time available for handling prey. We next estimated the corrected digestion time, i.e., digestion time corrected for gut capacity, by subtracting observed to estimated Th values. We finally plotted the relationships between temperature and handling or digestion rates. As predicted by MTE, the corrected digestion rate increased exponentially with warming whereas, in contrast to MTE prediction, the relationship between handling rate and temperature was hump shaped. The parameter Th is thus confusing because it combines handling and digestive processes that have different thermal responses. This may explain why general patterns in the relationship between Th and temperature have been difficult to identify in previous studies.