bluuebunny/crossref_metadata_2025 huggingface dataset:
A Study on Variations in Sewerage Construction Projects
Authors: Kassim Mohd Azraai , Lee Jen Loong
Published: January 2013

Perubahan dalam pembinaan telah lama menjadi isu pertikaian antara pelbagai pihak yang terlibat dalam projek pembinaan. Namun, hanya sejumlah kecil kajian yang rasmi telah dijalankan untuk menganalisis sebab-sebab dan kesan-kesannya. Kajian ini tertumpu kepada analisis kekerapan dan keterukan berbagai-bagai faktor yang mengakibatkan perubahan dalam projek pembinaan rangkaian pembetungan. Adalah penting bagi sesebuah syrikat bukan sahaja mengetahui kos perubahan, tetapi juga mengenal pasti perkara-perkara yang perlu diberi perhatian untuk mengurangkan kos-kos sedemikian dalam projek akan datang. Kesemua data dan maklumat yang diperlukan diperolehi dari fail-fail arkib bagi tiga belas projek yang disahkan melalui temubual. Data-data dikategori untuk menganalisis kekerapan dan keterukan faktor-faktor. Jadual dan carta digunakan untuk menunjukkan hasil-hasil kajian. Daripada hasil analisis, keadaan tapak yang berbeza merupakan faktor utama yang mengakibatkan perubahan. Faktor-faktor ini menyumbangkan 49.3% daripada jumlah bilangan perubahan, 56.2% daripada jumlah kos perubahan dan 3.8% daripada jumlah kos projek. Dua ciri projek, iaitu nilai anugerah kontrak dan gred pendaftaran kontraktor dengan Lembaga Pembangunan Industri Pembinaan (mewakili pengkhususan, kedudukan kewangan dan sumber-sumber lain kontraktor) menunjukkan penyebab yang tertentu dengan perubahan.

Kata kunci: perubahan; kekerapan; keterukan; pembetungan; rangkaian; pengkhususan

Variations in construction have long been a debatable issue among the different participants involved in construction projects. However, only a few formal studies have been carried out to analyse its couses and effects. This study is focused on the frequency and severity of various factors causing variations in sewerage networks construction projects. It is important for a company not only to know the variation costs, but also to identify the most likely areas on which to focus in order to reduce these costs for the future projects. All the necessary data and information are obtained from archival files of thirteen projects and verified through interviews. These data are categorised to analyse the frequency and severity of factors. Tables and charts are presented to show the research findings. From the analysis, differing site conditions appear to be the major factors contributing to variations. They average 49.3% of the total number of variations, 56.2% of the total variation costs and 3.8% of the total project costs. Two project characteristics i.e. contract award value and the contractor´s registration grade with the Construction Industry Development Board (which represents the contractor´s specialisation, financial and other resources standing) show certain causal relationships with variations.

Key words: variation; frequency; severity; sewerage; network; specialisation
Urban Development And Changing Patierns Of Night Time Temperatures In The Kuala Lumpur- Petaling Jaya Area Malaysia
Authors: Sani Sham
Published: January 2013

Makalah ini Ielah cuba menonjolkan beberapa ciri penting dalam perkembangan pembandaran di Kuala Lumpur- Petaling Jaya sejak tahun 1970an dan memeriksa cara bagaimana perkembangan ini telah mempengaruhi pola suhu pada waktu malam. Perbandingan po/a suhu bagi tahun-tahun 1972, 1975 dan 1980 menunjukkan bahawa intensiti pulau haba telah bertambah disertai oleh pertambahan kawasan yang mempunyai suhu tinggi. Perbezaan suhu di antara pusat bandar dan kawasan Kebun Bunga telah menjadi berkurangan dan tidak sebegitu ketara seperti yang terdapat pada tahun 1972. Perubahan-perubahan ini adalah disebabkan oleh bertambahnya bilangan kenderaan berinjin di jalan-jalan raya di samping pertambahan kawasan perumahan dan jalan-jalan raya itu sendiri. Selain daripada mempengaruhi suhu dan keselesaan,permukaan-permukaan yang tidak telap air ini juga mempengaruhi haidrologi kawasan bandar. Larian air dari kawasan bandar adalah lebih tinggi daripada kawasan luar-bandar. Makalah ini seterusnya mencadangkan supaya selari dengan rancangan-rancangan perumahan dan jalanraya, rancangan-rancangan menanam pokok juga perlu dijalankan kerana ini akan mengurangkan larian air dan seterusnya kejadian banjir kilat di bandar.

The paper has attempted to highlight some salient features in the growth and development of urbanization in the Kuala Lumpur- Petaling Jaya since the early 1970s and examine the way in which such growth has affected night-time temperature patterns. Comparison of temperatures during 1972,1975 and 1980 indicates that the intensity of the heat island had increased quite considerably followed by an increasingly larger areas having higher temperatures. The steep temperature gradient between the central city and the Lake Garden which was observed in 1972 had by 1980 disappeared. Such changes were attributed to the increased number of motor vehicles on the roads, the opening up of the many new housing estates and road building itself. Apart from affecting temperatures, paved surfaces also affect the hydrology of the area. Studies have shown that increased runoff from urban areas can be quite considerable. It is suggested that along with road construction and housing development programmes those of tree planting must also follow suit immediately. Such programmes will have the effect of decreasing runoff and hence flash floods.
The Role Of UTM In Technology Transfer
Authors: Hussain AKM Moazzem , Abdul Mukti Mohd. Afifi
Published: January 2013

Di dalam proses pembangunannya, Malaysia telah mengimport teknologi dengan kadar yang tinggi.Tetapi pemindahan teknologi yang diimport belum lagi mencapai tahap yang diharapkan.Di sini pengarang cuba mengenalpasti fakta yang menghalang pemindahan teknologi dan mencadangkan tugas positif yang dapat dimainkan oleh UTM untuk mengatasi masalah ini.Perkara yang dibincangkan termasuk peringkat pengembangan teknologi, dan penubuhan sebuah pusat teknologi di UTM.

In the process of development, Malaysia has been importing technology in massive proportions during the recent years. But it is reported that the extent of transfer of the imported technology to form Malaysia's own technology is far below the target of expectation.In this paper, the authors have tried to identify the problems which are hindering the expected technology transfer and suggested a positive role that UTM can play in overcoming these problems. The different stages in the process of technology development have been discussed and the establishment of a technology centre, in UTM having multifunction activities contributing to the transfer of technology has been emphasized.
Flow Profile Around Bluff Body
Authors: Ibrahim Abdul Aziz
Published: January 2013

This paper presents the results of an analytical study on local scour around bluff bodies. An equation has been developed which allowed the velocity distribution of the vertical component of velocity induced by the presence of a body to be predicted. The equation, equation (16) was obtained by re-organising known facts and incorporating them in a new fashion e.g. the logarithmic velocity profile was modified to include turbulence effect. Much of this has been done before but it is believed that this is the first time that the particular combination of turbalence effects, roughness effects, etc has been presented. Equation ( 16) is a modification of equation (16) in reference (7).The predicted vertical velocity distributions have been compared with analytically obtained data from previous investigations. The results of the comparison are encouraging but unfortunately not conclusive due to the lack of sufficient reliable experimental data.
The Establishment Of A Gravity Base Network In Peninsular Malaysia
Authors: A. Kadir Abd. Majid
Published: January 2013

A gravity basenet has been established in Peninsular Malaysia to meet the requirements of geophysics, geology, metrology and geodesy. The net comprises of 31 stations covering the entire country. The observations of this national gravity base net has been adjusted within the framework of the International Gravity Standardization Net 1971 (IGSN 71). The final adjustment showed a point standard error of better than ±O.05mGal. The procedures and the results of the adjustment have been reported along with the plans for future work.
Comparison Between Perforating System And Study Of Perforating Efficiency
Authors: Md Yassin Dr. Abu Azam , Hwa Chiew Tan
Published: January 2013

The major objective of perforating is to provide an effective flow communication between wellbore and formation, and achieve adequate well productivity. Perforating techniques and equipment that are used play an important role in determining the production that results. This paper describes the various perforating system used in the oil industry, with tile guns and techniques that are commonly used, applications and limitations of each. Studies also include factors that affect the well productivity as well as other parameters that influence the decision making in chosing the right perforator/gun under existing conditions. Actual data from a local oil field are used as a case study and the performance of different shaped charge are simulated using the Schlumberger SPAN OIL software. The results agree with the previous findings, guns having high shot density. deepest penetration, best phase angle under reversepressure condition give the best productivity.
On the Computation of Output Bounds for Compartmental In-Series Models under Parametric Uncertainty
Authors: De Pereda Diego , Romero-VivГі Sergio , Ricarte Beatriz , Bondia Jorge
Published: December 2012

In this work, the problem of obtaining tight output bounds for compartmental in-series models under parametric uncertainty is addressed. It is well-known that current methods used to compute a solution envelope may produce a significant overestimation. However, monotonicity analysis enables us to estimate a tight solution envelope. Our main aim is to get an equivalent model to the initial one, which is usually non-monotone, by means of a suitable combination of equations. In this new model the system monotonicity with respect to the uncertain parameters depends on the elimination rate values of the original model. If the equivalent model is monotone, no overestimation occurs in the computation of the output bounds.
Predicting and Scoring Links in Anatomical Ontology Mapping
Authors: Petrov Peter , Krachounov Milko , Kulev Ognyan , Nisheva Maria , Vassilev Dimitar
Published: December 2012

The paper presents a work performed in the area of automatic and semi-automatic ontology mapping. A method for inferring additional cross-ontology links while mapping anatomical ontologies is described and the results of some experiments performed with various external knowledge sources and scoring schemes are discussed as well.
Second-Order Mixed Convective Flow in a Long Vertical Microchannel
Authors: Jian Shih-Jie , Weng Huei Chu
Published: January 2013

The present investigation is concerned with the role of second-order slip in the mixed convection through a long heated vertical planar microchannel with asymmetric wall temperatures. The fully developed solutions of fields and the corresponding characteristics are analytically derived on the basis of second-order Maxwell–Smoluchowski–Burnett (MSB) slip/jump boundary conditions. Results reveal that second-order slip has an appreciable effect on the flow but a negligible effect on the heat transfer. The effect is to raise the gas motion speeds near the heated walls and to enlarge the pressure gradient required to drive the flow. It then leads to the reduction of local flow drag, except for the case where a reversed flow region exists. The second-order effect could be magnified by increasing the mixed convection number, the ratio of the Grashof number to the Reynolds number.
A spacing compensation factor for the optimization of guided wave annular array transducers
Authors: Borigo Cody , Rose Joseph L. , Yan Fei
Published: January 2013

Transducer arrays can be utilized in ultrasonic guided wave applications to achieve preferential excitation of particular points on a dispersion curve. These arrays are designed according to the principles of wave interference and the influence of the wavelength excitation spectrum. This paper develops the relationships between the peak wavelength in the excitation spectra and the element spacing of linear comb and annular arrays. The excitation spectra are developed by applying Fourier and Hankel transforms to the spatial loading distribution functions of the comb and annular arrays, respectively. Although the peak wavelength of excitation of a comb array is typically assumed to be equal to the element spacing, it is shown that this can be an inaccurate assumption for annular arrays. The ratio of element spacing to the peak wavelength in the excitation spectrum is termed the spacing compensation factor, and is dependent on the number of array elements and the inner radius. It is determined that the compensation factor is negligible for comb arrays but is crucial for annular arrays in order to achieve optimal mode selection. Finite element analyses and experimental data are used to verify the calculations and demonstrate the significance of the compensation factor.
Horizontal ducting of sound by curved nonlinear internal gravity waves in the continental shelf areas
Authors: Lin Ying-Tsong , McMahon Kara G. , Lynch James F. , Siegmann William L.
Published: January 2013

The acoustic ducting effect by curved nonlinear gravity waves in shallow water is studied through idealized models in this paper. The internal wave ducts are three-dimensional, bounded vertically by the sea surface and bottom, and horizontally by aligned wavefronts. Both normal mode and parabolic equation methods are taken to analyze the ducted sound field. Two types of horizontal acoustic modes can be found in the curved internal wave duct. One is a whispering-gallery type formed by the sound energy trapped along the outer and concave boundary of the duct, and the other is a fully bouncing type due to continual reflections from boundaries in the duct. The ducting condition depends on both internal-wave and acoustic-source parameters, and a parametric study is conducted to derive a general pattern. The parabolic equation method provides full-field modeling of the sound field, so it includes other acoustic effects caused by internal waves, such as mode coupling/scattering and horizontal Lloyd's mirror interference. Two examples are provided to present internal wave ducts with constant curvature and meandering wavefronts.
Acoustical and perceptual assessment of water sounds and their use over road traffic noise
Authors: Galbrun Laurent , Ali Tahrir T.
Published: January 2013

This paper examines physical and perceptual properties of water sounds generated by small to medium sized water features that have applications for road traffic noise masking. A large variety of water sounds were produced in the laboratory by varying design parameters. Analysis showed that estimations can be made on how these parameters affect sound pressure levels, frequency content, and psychoacoustic properties. Comparisons with road traffic noise showed that there is a mismatch between the frequency responses of traffic noise and water sounds, with the exception of waterfalls with high flow rates, which can generate large low frequency levels comparable to traffic noise. Perceptual assessments were carried out in the context of peacefulness and relaxation, where both water sounds and noise from dense road traffic were audible. Results showed that water sounds should be similar or not less than 3 dB below the road traffic noise level (confirming previous research), and that stream sounds tend to be preferred to fountain sounds, which are in turn preferred to waterfall sounds. Analysis made on groups of sounds also indicated that low sharpness and large temporal variations were preferred on average, although no acoustical or psychoacoustical parameter correlated well with the individual sound preferences.
Using Zebra-speech to study sequential and simultaneous speech segregation in a cochlear-implant simulation
Authors: Gaudrain Etienne , Carlyon Robert P.
Published: January 2013

Previous studies have suggested that cochlear implant users may have particular difficulties exploiting opportunities to glimpse clear segments of a target speech signal in the presence of a fluctuating masker. Although it has been proposed that this difficulty is associated with a deficit in linking the glimpsed segments across time, the details of this mechanism are yet to be explained. The present study introduces a method called Zebra-speech developed to investigate the relative contribution of simultaneous and sequential segregation mechanisms in concurrent speech perception, using a noise-band vocoder to simulate cochlear implants. One experiment showed that the saliency of the difference between the target and the masker is a key factor for Zebra-speech perception, as it is for sequential segregation. Furthermore, forward masking played little or no role, confirming that intelligibility was not limited by energetic masking but by across-time linkage abilities. In another experiment, a binaural cue was used to distinguish the target and the masker. It showed that the relative contribution of simultaneous and sequential segregation depended on the spectral resolution, with listeners relying more on sequential segregation when the spectral resolution was reduced. The potential of Zebra-speech as a segregation enhancement strategy for cochlear implants is discussed.
Unique Meteorite from Early Amazonian Mars: Water-Rich Basaltic Breccia Northwest Africa 7034
Authors: Agee Carl B. , Wilson Nicole V. , McCubbin Francis M. , Ziegler Karen , Polyak Victor J. , Sharp Zachary D. , Asmerom Yemane , Nunn Morgan H. , Shaheen Robina , Thiemens Mark H. , Steele Andrew , Fogel Marilyn L. , Bowden Roxane , Glamoclija Mihaela , Zhang Zhisheng , Elardo Stephen M.
Published: January 2013

So Different and So Similar

Most known meteorites from Mars fit into one class.

Agee
et al.

(p.
780
, published online 3 January; see the Perspective by

Humayun

) describe a meteorite, NWA 7034, which shares some characteristics with other martian meteorites but does not fit within the usual classification. NWA 7034 matches the composition of Mars' surface but is also richer in water than other martian meteorites, and has different oxygen isotope composition, which suggests the existence of multiple oxygen isotopic reservoirs within Mars. Its radiometric age of 2.1 billion years makes it a unique sample of the Amazonian period on Mars.
A Strategy for Modulation of Enzymes in the Ubiquitin System
Authors: Ernst Andreas , Avvakumov George , Tong Jiefei , Fan Yihui , Zhao Yanling , Alberts Philipp , Persaud Avinash , Walker John R. , Neculai Ana-Mirela , Neculai Dante , Vorobyov Andrew , Garg Pankaj , Beatty Linda , Chan Pak-Kei , Juang Yu-Chi , Landry Marie-Claude , Yeh Christina , Zeqiraj Elton , Karamboulas Konstantina , Allali-Hassani Abdellah , Vedadi Masoud , Tyers Mike , Moffat Jason , Sicheri Frank , Pelletier Laurence , Durocher Daniel , Raught Brian , Rotin Daniela , Yang Jianhua , Moran Michael F. , Dhe-Paganon Sirano , Sidhu Sachdev S.
Published: January 2013

Modifying Deubiquitinases

Protein ubiquitination is a widespread mechanism for cellular regulation, and new regulators are valuable research tools and may help to generate therapeutic small molecules.

Ernst
et al.

(p.
590
, published online 3 January) used known crystal structures to roughly define the interaction domain between a ubiquitin-specific protease and a ubiquitinated substrate and then screened ubiquitin variants with changes in these residues to find variants that acted as potent and specific regulators that could modify ubiquitin pathway regulation in cells.
Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents
Authors: Prota Andrea E. , Bargsten Katja , Zurwerra Didier , Field Jessica J. , Díaz José Fernando , Altmann Karl-Heinz , Steinmetz Michel O.
Published: January 2013

Dissecting Microtubule Stability

Microtubule-stabilizing agents (MSAs), like taxol, inhibit cell division and are widely used in cancer chemotherapy.

Prota
et al.

(p.
587
, published online 3 January) present structural data on the molecular mechanism of action of antimitotic drugs. Tubulin structures in complex with the MSAs zampanolide and epothilone A, revealed a general mechanism for how MSAs promote microtubule assembly and stability by affecting lateral tubulin interactions.
Identification of Novel Inhibitors of Human Immunodeficiency Virus Type 1 Replication by
In Silico
Screening Targeting Cyclin T1/Tat Interaction
Authors: Hamasaki Takayuki , Okamoto Mika , Baba Masanori
Published: December 2012

Human immunodeficiency virus type 1 (HIV-1) transcription is essential for viral replication and the only step for viral genome amplification. Cyclin T1 (CycT1) interacts with HIV-1 Tat and transactivation-responsive (TAR) RNA, leading to the activation of viral transcription through the hyperphosphorylation of RNA polymerase II (RNAPII). Thus, the CycT1/Tat/TAR RNA interaction represents a novel target for inhibition of HIV-1 replication. In this study, we conducted
in silico
screening of compounds targeting the CycT1/Tat/TAR RNA complex and found that two structurally related compounds (C1 and C2) had high docking scores for a model of the complex. These compounds proved inhibitory to HIV-1 replication in tumor necrosis factor alpha-stimulated chronically infected cells. In addition, C3, a derivative of C1 and C2, was found to be a more potent inhibitor of HIV-1 replication in chronically infected cells. C3 also inhibited HIV-1 replication in acutely infected cells. The compound could suppress Tat-mediated HIV-1 long terminal repeat-driven gene expression and phosphorylation of RNAPII through inhibition of Tat binding to CycT1. Furthermore, the docking pose of C3 was defined by analyses for its
in silico
docking energy and
in vitro
antiviral activity, which indicates that C3 interacts with Tat-binding amino acids of CycT1. Thus, a series of compounds described herein are novel inhibitors of HIV-1 transcription through inhibition of CycT1/Tat interaction.
A Staphylococcus xylosus Isolate with a New
mecC
Allotype
Authors: Harrison Ewan M. , Paterson Gavin K. , Holden Matthew T. G. , Morgan Fiona J. E. , Larsen Anders Rhod , Petersen Andreas , Leroy Sabine , De Vliegher Sarne , Perreten Vincent , Fox Lawrence K. , Lam Theo J. G. M. , Sampimon Otlis C. , Zadoks Ruth N. , Peacock Sharon J. , Parkhill Julian , Holmes Mark A.
Published: December 2012

Recently, a novel variant of
mecA
known as
mecC
(
mecA
LGA251
) was identified in
Staphylococcus aureus
isolates from both humans and animals. In this study, we identified a
Staphylococcus xylosus
isolate that harbors a new allotype of the
mecC
gene,
mecC1
. Whole-genome sequencing revealed that
mecC1
forms part of a class E
mec
complex (
mecI-mecR1-mecC1-blaZ
) located at the
orfX
locus as part of a likely staphylococcal cassette chromosome
mec
element (SCC
mec
) remnant, which also contains a number of other genes present on the type XI SCC
mec
.
Combination Treatment with Hepatitis C Virus Protease and NS5A Inhibitors Is Effective against Recombinant Genotype 1a, 2a, and 3a Viruses
Authors: Gottwein Judith M. , Jensen Sanne B. , Li Yi-Ping , Ghanem Lubna , Scheel Troels K. H. , Serre Stéphanie B. N. , Mikkelsen Lotte , Bukh Jens
Published: December 2012

With the development of directly acting antivirals, hepatitis C virus (HCV) therapy entered a new era. However, rapid selection of resistance mutations necessitates combination therapy. To study combination therapy in infectious culture systems, we aimed at developing HCV semi-full-length (semi-FL) recombinants relying only on the JFH1 NS3 helicase, NS5B, and the 3′ untranslated region. With identified adaptive mutations, semi-FL recombinants of genotypes(isolates) 1a(TN) and 3a(S52) produced supernatant infectivity titers of ∼4 log
10
focus-forming units/ml in Huh7.5 cells. Genotype 1a(TN) adaptive mutations allowed generation of 1a(H77) semi-FL virus. Concentration-response profiles revealed the higher efficacy of the NS3 protease inhibitor asunaprevir (BMS-650032) and the NS5A inhibitor daclatasvir (BMS-790052) against 1a(TN and H77) than 3a(S52) viruses. Asunaprevir had intermediate efficacy against previously developed 2a recombinants J6/JFH1 and J6cc. Daclatasvir had intermediate efficacy against J6/JFH1, while low sensitivity was confirmed against J6cc. Using a cross-titration scheme, infected cultures were treated until viral escape or on-treatment virologic suppression occurred. Compared to single-drug treatment, combination treatment with relatively low concentrations of asunaprevir and daclatasvir suppressed infection with all five recombinants. Escaped viruses primarily had substitutions at amino acids in the NS3 protease and NS5A domain I reported to be genotype 1 resistance mutations. Inhibitors showed synergism at drug concentrations reported
in vivo
. In summary, semi-FL HCV recombinants, including the most advanced reported genotype 3a infectious culture system, permitted genotype-specific analysis of combination treatment in the context of the complete viral life cycle. Despite differential sensitivity to lead compound NS3 protease and NS5A inhibitors, genotype 1a, 2a, and 3a viruses were suppressed by combination treatment with relatively low concentrations.
Biomass Conversion Inhibitors Furfural and 5-Hydroxymethylfurfural Induce Formation of Messenger RNP Granules and Attenuate Translation Activity in Saccharomyces cerevisiae
Authors: Iwaki Aya , Kawai Takao , Yamamoto Yosuke , Izawa Shingo
Published: December 2012

Various forms of stress can cause an attenuation of bulk translation activity and the accumulation of nontranslating mRNAs into cytoplasmic messenger RNP (mRNP) granules termed processing bodies (P-bodies) and stress granules (SGs) in eukaryotic cells. Furfural and 5-hydroxymethylfurfural (HMF), derived from lignocellulosic biomass, inhibit yeast growth and fermentation as stressors. Since there is no report regarding their effects on the formation of cytoplasmic mRNP granules, here we investigated whether furfural and HMF cause the assembly of yeast P-bodies and SGs accompanied by translational repression. We found that furfural and HMF cause the attenuation of bulk translation activity and the assembly of cytoplasmic mRNP granules in
Saccharomyces cerevisiae
. Notably, a combination of furfural and HMF induced the remarkable repression of translation initiation and SG formation. These findings provide new information about the physiological effects of furfural and HMF on yeast cells, and also suggest the potential usefulness of cytoplasmic mRNP granules as a warning sign or index of the deterioration of cellular physiological status in the fermentation of lignocellulosic hydrolysates.
Molecular Characterization of “Candidatus Parilichlamydia carangidicola,” a Novel Chlamydia-Like Epitheliocystis Agent in Yellowtail Kingfish, Seriola lalandi (Valenciennes), and the Proposal of a New Family, “Candidatus Parilichlamydiaceae” fam. nov. (Order Chlamydiales)
Authors: Stride M. C. , Polkinghorne A. , Miller T. L. , Groff J. M. , LaPatra S. E. , Nowak B. F.
Published: December 2012

Three cohorts of farmed yellowtail kingfish (Seriola lalandi) from South Australia were examined forChlamydia-like organisms associated with epitheliocystis. To characterize the bacteria, 38 gill samples were processed for histopathology, electron microscopy, and 16S rRNA amplification, sequencing, and phylogenetic analysis. Microscopically, the presence of membrane-enclosed cysts was observed within the gill lamellae. Also observed was hyperplasia of the epithelial cells with cytoplasmic vacuolization and fusion of the gill lamellae. Transmission electron microscopy revealed morphological features of the reticulate and intermediate bodies typical of members of the orderChlamydiales. A novel 1,393-bp 16S chlamydial rRNA sequence was amplified from gill DNA extracted from fish in all cohorts over a 3-year period that corresponded to the 16S rRNA sequence amplified directly from laser-dissected cysts. This sequence was only 87% similar to the reported “CandidatusPiscichlamydia salmonis” (AY462244) from Atlantic salmon and Arctic charr. Phylogenetic analysis of this sequence against 35ChlamydiaandChlamydia-like bacteria revealed that this novel bacterium belongs to an undescribed family lineage in the orderChlamydiales. Based on these observations, we propose this bacterium of yellowtail kingfish be known as “CandidatusParilichlamydia carangidicola” and that the new family be known as “CandidatusParilichlamydiaceae.”
Bacterial Cytochrome P450 System Catabolizing the Fusarium Toxin Deoxynivalenol
Authors: Ito Michihiro , Sato Ikuo , Ishizaka Masumi , Yoshida Shin-ichiro , Koitabashi Motoo , Yoshida Shigenobu , Tsushima Seiya
Published: December 2012

Deoxynivalenol (DON) is a natural toxin of fungi that causeFusariumhead blight disease of wheat and other small-grain cereals. DON accumulates in infected grains and promotes the spread of the infection on wheat, posing serious problems to grain production. The elucidation of DON-catabolic genes and enzymes in DON-degrading microbes will provide new approaches to decrease DON contamination. Here, we report a cytochrome P450 system capable of catabolizing DON inSphingomonassp. strain KSM1, a DON-utilizing bacterium newly isolated from lake water. The P450 geneddnAwas cloned through an activity-based screening of a KSM1 genomic library. The genes of its redox partner candidates (flavin adenine dinucleotide [FAD]-dependent ferredoxin reductase and mitochondrial-type [2Fe-2S] ferredoxin) were not found adjacent toddnA; the redox partner candidates were further cloned separately based on conserved motifs. The DON-catabolic activity was reconstitutedin vitroin an electron transfer chain comprising the three enzymes and NADH, with a catalytic efficiency (kcat/Km) of 6.4 mM−1s−1. The reaction product was identified as 16-hydroxy-deoxynivalenol. A bioassay using wheat seedlings revealed that the hydroxylation dramatically reduced the toxicity of DON to wheat. The enzyme system showed similar catalytic efficiencies toward nivalenol and 3-acetyl deoxynivalenol, toxins that frequently cooccur with DON. These findings identify an enzyme system that catabolizes DON, leading to reduced phytotoxicity to wheat.
Polyketide Synthase Gene Diversity within the Microbiome of the Sponge Arenosclera brasiliensis, Endemic to the Southern Atlantic Ocean
Authors: Trindade-Silva Amaro E. , Rua Cintia P. J. , Andrade Bruno G. N. , Vicente Ana Carolina Paulo , Silva Genivaldo G. Z. , Berlinck Roberto G. S. , Thompson Fabiano L.
Published: December 2012

Microbes associated with marine sponges are considered important producers of bioactive, structurally unique polyketides. The synthesis of such secondary metabolites involves type I polyketide synthases (PKSs), which are enzymes that reach a maximum complexity degree in bacteria. The Haplosclerida spongeArenosclera brasiliensishosts a complex microbiota and is the source of arenosclerins, alkaloids with cytotoxic and antibacterial activity. In the present investigation, we performed high-throughput sequencing of the ketosynthase (KS) amplicon to investigate the diversity of PKS genes present in the metagenome ofA. brasiliensis. Almost 4,000 ketosynthase reads were recovered, with about 90% annotated automatically as bacterial. A total of 235 bacterial KS contigs was rigorously assembled from this sequence pool and submitted to phylogenetic analysis. A great diversity of six type I PKS groups has been consistently detected in our phylogenetic reconstructions, including a novel andA. brasiliensis-exclusive group. Our study is the first to reveal the diversity of type I PKS genes inA. brasiliensisas well as the potential of its microbiome to serve as a source of new polyketides.
Real-Time PCR Assays for Quantification of
qnr
Genes in Environmental Water Samples and Chicken Feces
Authors: Marti Elisabet , Balcázar José Luis
Published: December 2012

Real-time PCR assays were developed for the enumeration of plasmid-mediated quinolone resistance (PMQR) determinants, such as the
qnrA
,
qnrB
, and
qnrS
genes, in different water samples and chicken feces. The results indicate that the developed assays are specific and sensitive for the quantification of
qnr
genes in complex samples.
Upgrading Fungal Gene Expression on Demand: Improved Systems for Doxycycline-Dependent Silencing in Aspergillus fumigatus
Authors: Helmschrott Christoph , Sasse Anna , Samantaray Sweta , Krappmann Sven , Wagener Johannes
Published: December 2012

Conditional gene expression is key for functional studies in any given microorganism. To allow tight regulation in the pathogenic mold
Aspergillus fumigatus
, improved versions of the doxycycline-dependent Tet-On system were generated by replacing functional elements of the precursor module, thereby circumventing the former problem of leakiness due to intramolecular recombination.
Malignant peritoneal mesothelioma (MPM) who responded to rechallenge with cisplatin and pemetrexed with current literature review
Authors: Gilani Shahid Nazir , Gridley Rebecca , Searle Gemma , Jegannathen Apurna
Published: January 2013

Peritoneal mesothelioma is an aggressive malignancy which is indeed very rare. Due to rarity, experience among many physicians surrounding the treatment of peritoneal mesothelioma is limited. Recently, we have received a patient who was initially treated palliatively with a combination of pemetrexd and cisplatin showing good response. On progression of his disease, he was again treated with the same drugs. This is not the strategy commonly used. We consider rechallenging cisplatin and pemetrexd to such patients who respond for the first time.
Oesophageal rupture: a tough diagnosis to swallow
Authors: Pillinger Toby , Rogers Angela , Barnes Simon
Published: January 2013

An elderly gentleman presented with acute dyspnoea and right-sided pleuritic chest pain. Two-weeks previously an oesophageal stent had been inserted for dysphagia secondary to oesophageal carcinoma. With low PaO2, a neutrophilic leucocytosis, raised inflammatory markers and a right-sided pleural effusion, antibiotics were prescribed for pneumonia. Computed tomographic pulmonary angiogram (CTPA) ruled out pulmonary embolus. The patient rallied transiently and his effusion improved. His respiratory distress returned 14 days later. A chest x-ray revealed a right-sided hydropneumothorax, and a chest drain-released stomach contents from the pleural cavity. A gastrografin swallow and endoscopy demonstrated malignant oesophageal rupture. An attempt to re-stent failed, and the patient returned to the ward for palliation. His initial presentation was likely that of an oesophageal leak, and not pneumonia. Oesophageal rupture is difficult to diagnose due to ambiguous signs, symptoms and radiological findings. Swift diagnosis significantly improves the outcome, therefore clinicians presented with similar cases should consider the diagnosis early.
Cardiac type of total anomalous pulmonary venous connection: diagnosis and demonstration by multidetector CT angiography
Authors: Singh Neha , Singh Ragini , Aga Pallavi , Singh Shailesh Kumar
Published: January 2013

Pulmonary venous developmental anomalies have been evaluated conventionally with echocardiography and catheter angiography, multidetector CT angiography (MDCTA) and MR angiography are playing increasing roles in their characterisation. Here, we report a rare case of a 15-year-old boy, who presented with cyanosis and dyspnoea which he had had since childhood. Cardiac type of total anomalous pulmonary venous connection (TAPVC) was diagnosed and demonstrated using MDCTA in this case. Only a few case reports describing the MDCTA findings in cardiac TAPVC are available in the published literature.
Validity of theInternational Classification of Diseases 10th revisioncode for hyperkalaemia in elderly patients at presentation to an emergency department and at hospital admission
Authors: Fleet Jamie L , Shariff Salimah Z , Gandhi Sonja , Weir Matthew A , Jain Arsh K , Garg Amit X
Published: December 2012

Objectives

Evaluate the validity of theInternational Classification of Diseases, 10th revision(ICD-10) code for hyperkalaemia (E87.5) in two settings: at presentation to an emergency department and at hospital admission.

Design

Population-based validation study.

Setting

12 hospitals in Southwestern Ontario, Canada, from 2003 to 2010.

Participants

Elderly patients with serum potassium values at presentation to an emergency department (n=64 579) and at hospital admission (n=64 497).

Primary outcome

Sensitivity, specificity, positive-predictive value and negative-predictive value. Serum potassium values in patients with and without a hyperkalaemia code (code positive and code negative, respectively).

Results

The sensitivity of the best-performing ICD-10 coding algorithm for hyperkalaemia (defined by serum potassium >5.5 mmol/l) was 14.1% (95% CI 12.5% to 15.9%) at presentation to an emergency department and 14.6% (95% CI 13.3% to 16.1%) at hospital admission. Both specificities were greater than 99%. In the two settings, the positive-predictive values were 83.2% (95% CI 78.4% to 87.1%) and 62.0% (95% CI 57.9% to 66.0%), while the negative-predictive values were 97.8% (95% CI 97.6% to 97.9%) and 96.9% (95% CI 96.8% to 97.1%). In patients who were code positive for hyperkalaemia, median (IQR) serum potassium values were 6.1 (5.7 to 6.8) mmol/l at presentation to an emergency department and 6.0 (5.1 to 6.7) mmol/l at hospital admission. For code-negative patients median (IQR) serum potassium values were 4.0 (3.7 to 4.4) mmol/l and 4.1 (3.8 to 4.5) mmol/l in each of the two settings, respectively.

Conclusions

Patients with hospital encounters who were ICD-10 E87.5 hyperkalaemia code positive and negative had distinct higher and lower serum potassium values, respectively. However, due to very low sensitivity, the incidence of hyperkalaemia is underestimated.
Differences between acute myocardial infarction and unstable angina: a longitudinal cohort study reporting findings from the Register of Information and Knowledge about Swedish Heart Intensive Care Admissions (RIKS-HIA)
Authors: Dudas Kerstin , Björck Lena , Jernberg Tomas , Lappas Georgios , Wallentin Lars , Rosengren Annika
Published: January 2013

Objectives

The aim of this study was to compare risk factors and comorbidities in patients with a first episode of acute coronary syndrome (ACS), being either acute myocardial infarction (AMI) or unstable angina pectoris (UAP).

Design

Cross-sectional and prospective.

Setting

The Swedish population.

Participants

A total of 145 346 consecutive patients aged 25–105 years included in the Swedish Register of Cardiac Intensive Care Admission (Register of Information and Knowledge about Swedish Heart Intensive Care) and admitted to hospital between 1 January 1996 and 30 June 2009 with a first episode of either AMI or UAP.

Primary and secondary outcome measures

Type of ACS and 1-year outcome.

Results

Compared with patients with UAP, AMI patients were more likely to be older; men; and former or current smokers; they were also more likely to have had diabetes and peripheral artery disease, but had lower rates of prior heart failure (HF) and fewer cardioprotective medications on admission. Among patients aged <65 years, 1.4% of men and 1.6% of women with UAP died within 1 year in 2003–2006 compared with 4.2% of men and 3.1% of women AMI patients (multiple-adjusted OR 3.54 (99% CI 2.29 to 5.48) in women and 2.65 (99% CI 2.11 to 3.34) in men). Corresponding proportions in patients aged ≥65 years was 7.5% in men and 7.6% in women with UAP and 21.5% in men and 17.8% in women with AMI.

Conclusions

In patients with a first-time ACS episode, male sex, slightly older age, smoking, diabetes and peripheral arterial disease (PAD), but fewer cardioprotective medications, were major determinants for presenting with AMI. Despite increasingly active treatment in AMI and more inclusive diagnostic criteria in recent years, persistently worse prognosis was observed in AMI patients.
Introduction to Special Issue ofCanadian Journal of Earth Sciences: Canadian contributions to planetary geoscience
Authors: Williamson Marie-Claude , Johnson Catherine L. , Sylvester Paul J.
Published: January 2013

The first Special Issue published by the Canadian Journal of Earth Sciences in the field of planetary sciences consists of a collection of nine papers on astromaterials, planetary geology, and Earth-based analogues. We describe the milestones that led to the development of the planetary geology and geophysics (PG&G) community in Canada over the past 5 years, which culminated in record-breaking attendance at a special session of the 2011 GAC–MAC–SEG–SGA Joint Annual Meeting held in Ottawa. The idea of a Special Issue was met with enthusiasm by delegates from coast to coast. By connecting the fields of earth and planetary sciences, the Canadian Journal of Earth Sciences pioneers a new vision for geoscience that expands the options available to Canadians who wish to publish their research at home.
ECONOMIC REPLENISHMENT PLAN WITH IMPERFECT PRODUCTION PROCESS AND BUSINESS-RETURN DEPENDENT DEMAND
Authors: CHUNG CHUN-JEN , WEE HUI-MING
Published: January 2013

This study considers the supplier's warranty return and the buyer's rebate policy as business-return policy in the supplier–buyer supply chain. The policy as well as the displayed stock level influences the behavior of the buyer. Distinct from the traditional single-stage inventory model, we investigate a two-stage replenishment policy model for deteriorating item considering the effect of imperfect production process, product design, stock level and business-return. A mathematical model utilizing the time weighted inventory (TWI) approach and two-variables fixed point optimization technique is developed to derive the optimal inspection starting time, the number of deliveries, the optimal delivery-time interval and the optimal business-return period. A numerical example is presented to illustrate the model developed. The result shows that the fixed demand rate, the unit holding cost and the unit inspection cost are the critical factors affecting the scheduling and performance of the two-stage supply chain.
EFFECTS OF MINIJETS ON COMMON OBSERVABLES IN HEAVY-ION COLLISIONS WITH UNCOMMON IMPLICATION
Authors: HWA RUDOLPH C.
Published: January 2013

In this brief review of the observable effects of minijets in heavy-ion collisions, the main points emphasized are that the quadruple moment v2(pT, b) and the hadronic (π and p) spectra at low pT can both be reproduced by minijet contributions to the recombination of thermal and shower partons. Without using hydrodynamics the minijet approach does not trace the evolution of the expanding system. The thermal distribution of the medium partons at the time of hadronization is assumed, but rapid thermalization initially is not required so as to allow minijets to leave their footprints on the system in the final state. Azimuthal anisotropy due to minijets is directly calculated in the momentum space without any fluid assumption relating the spatial eccentricity to v2. There are no more parameters used and compared to the hydro approach in fitting the data on v2 and pT spectra. Thus both approaches satisfy the sufficiency condition for a viable description of the dynamical process involved.
Detrital zircon data reveal the origin of Australia’s largest delta system
Authors: MacDonald Justin D. , Holford Simon P. , Green Paul F. , Duddy Ian R. , King Rosalind C. , Backé Guillaume
Published: January 2013

The Late Cretaceous Ceduna Delta is the largest deltaic system on the Australian continent, yet its source is unknown. Apatite fission-track data reveal widespread Late Cretaceous exhumation across the southern Australian margin. New detrital zircon analysis of 786 grains from the Gnarlyknots-1 well, which penetrated the offshore delta top, show that the upper part of the delta (Santonian–Maastrichtian) was sourced largely from recycled Permian to Early Cretaceous cover and underlying basement eroded from the margin, proximal to the basin. This challenges the widely accepted model involving distal provenance of >2000 km from the eastern margin of Australia.

Supplementary material

The 2D seismic reflection data, results for detrital zircon LA-ICP-MS and zircon fission-track analyses, including the LA-ICP-MS method, and a list of sample intervals and ages are available at
www.geolsoc.org.uk/SUP18582
.
Involvement of the NO-cGMP-KATP channel pathway in the mesenteric lymphatic pump dysfunction observed in the guinea pig model of TNBS-induced ileitis
Authors: Mathias Ryan , von der Weid Pierre-Yves
Published: December 2012

Mesenteric lymphatic vessels actively transport lymph, immune cells, fat, and other macromolecules from the intestine via a rhythmical contraction-relaxation process called lymphatic pumping. We have previously demonstrated that mesenteric lymphatic pumping was compromised in the guinea pig model of 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced ileitis, corroborating clinical and experimental observations of a dilated and/or obstructed phenotype of these vessels in inflammatory bowel disease. Many mediators released during the inflammatory process have been shown to alter lymphatic contractile activity. Among them, nitric oxide (NO), an inflammatory mediator abundantly released during intestinal inflammation, decreases the frequency of lymphatic contractions through activation of ATP-sensitive potassium (KATP) channels. The objective of this study was to investigate the role of NO and KATP channels in the lymphatic dysfunction observed in the guinea pig model of TNBS-induced ileitis. Using quantitative real-time PCR, we demonstrated that expression of Kir6.1, SUR2B, and inducible NO synthase (iNOS) mRNAs was significantly upregulated in TNBS-treated animals. Pharmacological studies performed on isolated, luminally perfused mesenteric lymphatic vessels showed that the KATP channels blocker glibenclamide, the selective iNOS inhibitor 1400W, and the guanylyl cyclase inhibitor ODQ (1 H-[1,2,4]oxadiazolo[4,3- a]quinoxalin-1-one) significantly improved lymphatic pumping in quiescent lymphatic vessels from TNBS-treated animals. Membrane potential measurement with intracellular microelectrodes revealed that vessels from TNBS-treated animals were hyperpolarized compared with their sham counterpart and that the hyperpolarization was significantly attenuated in the presence of glibenclamide and ODQ. Our findings suggest that NO and KATP play a major role in the lymphatic contractile dysfunction that occurred as a consequence of the intestinal inflammation caused by TNBS.