bluuebunny/crossref_metadata_2025_split huggingface dataset:
COLLISION DETECTION FOR CLOTH SIMULATION USING BOUNDING SPHERE HIERARCHY
Authors: Bade Abdullah , Sue Ping Ching , Tanalol Siti Hasnah 
Published: September 2015

For the past 2-decades, the challenges of collision detection on cloth simulation have attracted numerous researchers. Simple mass spring model is used to model the cloth where the movement of the particles within the cloth was controlled by applying the Newton’s second law. After the modeling stage, implementation of the collision detection algorithm took place on cloth has been done. The collision detection technique used is bounding sphere hierarchy. Then, quad tree is being used to partitioning the bounding sphere and the collision search was based on the top-down approach. A prototype of the collision detection system is developed on cloth simulation and several experiments were conducted. Time taken for this system to be executed is around 235.258 milliseconds. Then the frame rate is at the average of 22 frames per second which is close to the real time system. Times taken for the collision detection system travels from root to nodes were 23 seconds. As a conclusion, the computational cost for bounding sphere hierarchy is much higher because the bounding sphere required more vertices for generation process, however the execution time for bounding sphere hierarchy is faster than the AABB hierarchy.
3D RECONSTRUCTION OF BREAST CANCER FROM MAMMOGRAMS USING VOLUME RENDERING TECHNIQUES
Authors: Wei Yong Ho , Bade Abdullah , Muniandy Rajesh Kumar 
Published: September 2015

Over the past thirty years, a number of researchers have investigated on 3D organ reconstruction from medical images and there are a few 3D reconstruction software available on the market. However, not many researcheshave focused on3D reconstruction of breast cancer’s tumours. Due to the method complexity, most 3D breast cancer’s tumours reconstruction were done based on MRI slices dataeven though mammogram is the current clinical practice for breast cancer screening. Therefore, this research will investigate the process of creating a method that will be able to reconstruct 3D breast cancer’s tumours from mammograms effectively. Several steps were proposed for this research which includes data acquisition, volume reconstruction, andvolume rendering. The expected output from this research is the 3D breast cancer’s tumours model that is generated from correctly registered mammograms. The main purpose of this research is to come up with a 3D reconstruction method that can produce good breast cancer model from mammograms while using minimal computational cost.
TURBULENT-FORCED CONVECTIVE HEAT TRANSFER AND PRESSURE DROP ANALYSIS OF FE3O4 MAGNETIC NANOFLUID IN A CIRCULAR MICROCHANNEL
Authors: Che Sidik Nor Azwadi , Yassin M.M. , Musa M.N. 
Published: September 2015

A numerical simulation was accomplished in this study that investigated the turbulent force convective heat transfer and pressure drop in straight circular copper pipe with a hydraulic diameter of 0.0005m and 0.1m in length, as given by Lee and Mudawar [11]. The enhancement of heat transfer for water and nanofluids (Fe3O4) under 100 [W/m2] constant heat flux was applied around the wall of the pipe. In this study, standard k-ɛ turbulence model was employed and was performed at a steady state flow, incompressible turbulent flow, and three-dimensional structure. Various volume concentrations of nanoparticles were conducted in the range of 1% to 15% at constant nanoparticle diameter size, which was 32 nm. The heat transfer enhancement was obtained in the range of Reynolds number from 3000 to 10,000. The results displayed an increase in Reynolds number and volume concentrations, as well as an increase in the Nusselt number. The optimum Nusselt number gained was about 5% to 6% of volume concentration at each Reynolds number tested. Besides, with the increase of Reynolds number, the variation pressure saw a dropped for inlet, whereas an increase in the outlet section. Moreover, the increase in volume concentration also caused a small increment in the pressure drop compared to pure water.
FRACTURE MODELING IN OIL AND GAS RESERVOIRS USING IMAGE LOGS DATA AND PETREL SOFTWARE
Authors: Alizadeh Mostafa , Movahed Zohreh , Junin Radzuan , Mohsin Rahmat , Alizadeh Mehdi , Alizadeh Mohsen 
Published: September 2015

The purpose of modelling the fractures is to create simulation properties with the power to predict the reservoir behaviour. Petrel software is one of the best softwares in the market that can do this task very well, but there is no available educational paper for every researcher. Therefore, in this work, a fracture modelling job was done in one of the most important Iranian fields using Petrel software and image log data. The purpose of this work was to determine the new information of the fractures in Gachsaran field and also to prepare a valuable educational paper for other researchers who are interested to learn about the fracture modelling. This work revealed that in this field, the longitudinal fractures had been parallel to minimum stress (Zagros trend), fracture intensity was the nearest to the major fault and northern flank, fracture porosity was 0-7%, fracture permeability was 0-6000 MD, and more valuable information is provided in this paper.
PENENTUAN SIFAT KEKUKUHAN DAN KETEBALAN LAPISAN PERMUKAAN BERASFALT MENGGUNAKAN KAEDAH PENCARIAN RESONAN TAMBAHAN (ERS)
Authors: Zakaria Nur Mustakiza , Md. Jaffary Muhammad Fakhry , Hassan Muhammad Kamal , Hamim Asmah , Md. Yusoff Nur Izzi , Mohd Nayan Khairul Anuar 
Published: September 2015

This study was conducted to investigate the stiffness and thicknesses of asphalt surface layer using the Enhance Resonance Search (ERS) technique. A total of fifteen locations in the Universiti Kebangsaan Malaysia (UKM) Campus have been identified to carry out this experiment. The results were then compared with standards provided by the Malaysian Public Works Department (PWD), Jabatan Pembangunan dan Penyelenggaraan (JPP) UKM and Kumpulan IKRAM Sdn. Bhd. The computation found that the range of elastic moduli values of asphalt layer is between 3928.877 and 17726.012 MPa. A comparison between the experiment results and JPP UKM standard on pavement thickness showed that the different is between 20% to 60%, with the average thickness of 44.13 mm. However, the average value of thickness is still in good agreement with the JKR and JPP UKM standards. Some stiffness values obtained are higher than the standard, probably due to the quality of materials used, the influence of the traffic load and the age of the pavement construction.
Objective assessment in digital images of skin erythema caused by radiotherapy
Authors: Matsubara H. , Matsufuji N. , Tsuji H. , Yamamoto N. , Karasawa K. , Nakajima M. , Takahashi W. , Karube M. 
Published: September 2015

Purpose:Skin toxicity caused by radiotherapy has been visually classified into discrete grades. The present study proposes an objective and continuous assessment method of skin erythema in digital images taken under arbitrary lighting conditions, which is the case for most clinical environments. The purpose of this paper is to show the feasibility of the proposed method.Methods:Clinical data were gathered from six patients who received carbon beam therapy for lung cancer. Skin condition was recorded using an ordinary compact digital camera under unfixed lighting conditions; a laser Doppler flowmeter was used to measure blood flow in the skin. The photos and measurements were taken at 3 h, 30, and 90 days after irradiation. Images were decomposed into hemoglobin and melanin colors using independent component analysis. Pixel values in hemoglobin color images were compared with skin dose and skin blood flow. The uncertainty of the practical photographic method was also studied in nonclinical experiments.Results:The clinical data showed good linearity between skin dose, skin blood flow, and pixel value in the hemoglobin color images; their correlation coefficients were larger than 0.7. It was deduced from the nonclinical that the uncertainty due to the proposed method with photography was 15%; such an uncertainty was not critical for assessment of skin erythema in practical use.Conclusions:Feasibility of the proposed method for assessment of skin erythema using digital images was demonstrated. The numerical relationship obtained helped to predict skin erythema by artificial processing of skin images. Although the proposed method using photographs taken under unfixed lighting conditions increased the uncertainty of skin information in the images, it was shown to be powerful for the assessment of skin conditions because of its flexibility and adaptability.
GS-5806 Inhibits Pre- to Postfusion Conformational Changes of the Respiratory Syncytial Virus Fusion Protein
Authors: Samuel Dharmaraj , Xing Weimei , Niedziela-Majka Anita , Wong Jinny S. , Hung Magdeleine , Brendza Katherine M. , Perron Michel , Jordan Robert , Sperandio David , Liu Xiaohong , Mackman Richard , Sakowicz Roman 
Published: September 2015

ABSTRACT

GS-5806 is a small-molecule inhibitor of human respiratory syncytial virus fusion protein-mediated viral entry. During viral entry, the fusion protein undergoes major conformational changes, resulting in fusion of the viral envelope with the host cell membrane. This process is reproduced
in vitro
using a purified, truncated respiratory syncytial virus (RSV) fusion protein. GS-5806 blocked these conformational changes, suggesting a possible mechanism for antiviral activity.
Artemisinin Resistance at the China-Myanmar Border and Association with Mutations in the K13 Propeller Gene
Authors: Wang Zenglei , Wang Yingna , Cabrera Mynthia , Zhang Yanmei , Gupta Bhavna , Wu Yanrui , Kemirembe Karen , Hu Yue , Liang Xiaoying , Brashear Awtum , Shrestha Sony , Li Xiaolian , Miao Jun , Sun Xiaodong , Yang Zhaoqing , Cui Liwang 
Published: September 2015

ABSTRACT

Artemisinin resistance in
Plasmodium falciparum
parasites in Southeast Asia is a major concern for malaria control. Its emergence at the China-Myanmar border, where there have been more than 3 decades of artemisinin use, has yet to be investigated. Here, we comprehensively evaluated the potential emergence of artemisinin resistance and antimalarial drug resistance status in
P. falciparum
using data and parasites from three previous efficacy studies in this region. These efficacy studies of dihydroartemisinin-piperaquine combination and artesunate monotherapy of uncomplicated falciparum malaria in 248
P. falciparum
patients showed an overall 28-day adequate clinical and parasitological response of >95% and day 3 parasite-positive rates of 6.3 to 23.1%. Comparison of the 57 K13 sequences (24 and 33 from day 3 parasite-positive and -negative cases, respectively) identified nine point mutations in 38 (66.7%) samples, of which F446I (49.1%) and an N-terminal NN insertion (86.0%) were predominant. K13 propeller mutations collectively, the F446I mutation alone, and the NN insertion all were significantly associated with day 3 parasite positivity. Increased ring-stage survival determined using the ring-stage survival assay (RSA) was highly associated with the K13 mutant genotype. Day 3 parasite-positive isolates had ∼10 times higher ring survival rates than day 3 parasite-negative isolates. Divergent K13 mutations suggested independent evolution of artemisinin resistance. Taken together, this study confirmed multidrug resistance and emergence of artemisinin resistance in
P. falciparum
at the China-Myanmar border. RSA and K13 mutations are useful phenotypic and molecular markers for monitoring artemisinin resistance.
Greater Ciprofloxacin Tolerance as a Possible Selectable Phenotype Underlying the Pandemic Spread of the
H
30 Subclone of Escherichia coli Sequence Type 131
Authors: Johnson James R. , Porter Stephen B. , Thuras Paul , Johnson Timothy J. , Price Lance B. , Tchesnokova Veronika , Sokurenko Evgeni V. 
Published: September 2015

ABSTRACT

Minimum bactericidal concentrations (MBCs) for ciprofloxacin were significantly higher among 41 members of the
H
30 subclone within
Escherichia coli
sequence type 131 than among 48 other fluoroquinolone-resistant
E. coli
isolates. This MBC difference, which was not explained by ciprofloxacin MICs,
gyrA
,
parC
, and
parE
mutations, the presence of
aac
(
6
′)-
Ib-cr
, or organic solvent tolerance (a surrogate for efflux pump activity), conceivably could have promoted the pandemic emergence of the
H
30 sequence type 131 subclone.
Functions of a GyrBA Fusion Protein and Its Interaction with QnrB and Quinolones
Authors: Chen Chunhui , Villet Regis , Jacoby George A. , Hooper David C. 
Published: September 2015

ABSTRACT

In order to study the interactions between
Escherichia coli
DNA gyrase and the gyrase interacting protein QnrB
in vivo
, we constructed a
gyrB-gyrA
fusion and validated its ability to correct the temperature-sensitive growth of
gyrA
and
gyrB
mutants. Like wild-type
gyrA
, the
gyrB-gyrA
fusion complemented a quinolone-resistant
gyrA
mutant to increase susceptibility. It functioned as an active type II topoisomerase, catalyzed negative supercoiling of DNA, was inhibited by quinolone, and was protected by QnrB.
In Vivo
Curative and Protective Potential of Orally Administered 5-Aminolevulinic Acid plus Ferrous Ion against Malaria
Authors: Suzuki Shigeo , Hikosaka Kenji , Balogun Emmanuel O. , Komatsuya Keisuke , Niikura Mamoru , Kobayashi Fumie , Takahashi Kiwamu , Tanaka Tohru , Nakajima Motowo , Kita Kiyoshi 
Published: September 2015

ABSTRACT

5-Aminolevulinic acid (ALA) is a naturally occurring amino acid present in diverse organisms and a precursor of heme biosynthesis. ALA is commercially available as a component of cosmetics, dietary supplements, and pharmaceuticals for cancer diagnosis and therapy. Recent reports demonstrated that the combination of ALA and ferrous ion (Fe
2+
) inhibits the
in vitro
growth of the human malaria parasite
Plasmodium falciparum
. To further explore the potential application of ALA and ferrous ion as a combined antimalarial drug for treatment of human malaria, we conducted an
in vivo
efficacy evaluation. Female C57BL/6J mice were infected with the lethal strain of rodent malaria parasite
Plasmodium yoelii
17XL and orally administered ALA plus sodium ferrous citrate (ALA/SFC) as a once-daily treatment. Parasitemia was monitored in the infected mice, and elimination of the parasites was confirmed using diagnostic PCR. Treatment of
P. yoelii
17XL-infected mice with ALA/SFC provided curative efficacy in 60% of the mice treated with ALA/SFC at 600/300 mg/kg of body weight; no mice survived when treated with vehicle alone. Interestingly, the cured mice were protected from homologous rechallenge, even when reinfection was attempted more than 230 days after the initial recovery, indicating long-lasting resistance to reinfection with the same parasite. Moreover, parasite-specific antibodies against reported vaccine candidate antigens were found and persisted in the sera of the cured mice. These findings provide clear evidence that ALA/SFC is effective in an experimental animal model of malaria and may facilitate the development of a new class of antimalarial drug.
Arsenic Trioxide Negatively Affects Echinococcus granulosus
Authors: Wang Bo , Jiang Yufeng , Wang Zhuo , Li Fangfang , Xing Guoqiang , Peng Xinyu , Zhang Shijie , Lv Hailong 
Published: September 2015

ABSTRACT

Spillage of cyst contents during surgery is the major cause of recurrences of hydatidosis, also called cystic echinococcosis (CE). Currently, many scolicidal agents are used for inactivation of the cyst contents. However, due to complications in the use of those agents, new and more-effective treatment options are urgently needed. The aim of this study was to investigate the
in vitro
efficacy of arsenic trioxide (ATO) against
Echinococcus granulosus
protoscolices. Protoscolices of
E. granulosus
were incubated
in vitro
with 2, 4, 6, and 8 μmol/liter ATO; viability of protoscolices was assessed daily by microscopic observation of movements and 0.1% eosin staining. A small sample from each culture was processed for scanning and transmission electron microscopy. ATO demonstrated a potent ability to kill protoscolices, suggesting that ATO may represent a new strategy in treating hydatid cyst echinococcosis. However, the
in vivo
efficacy and possible side effects of ATO need to be explored.
EepR Mediates Secreted-Protein Production, Desiccation Survival, and Proliferation in a Corneal Infection Model
Authors: Brothers Kimberly M. , Stella Nicholas A. , Romanowski Eric G. , Kowalski Regis P. , Shanks Robert M. Q. 
Published: September 2015

ABSTRACT

Serratia marcescens
is a soil- and water-derived bacterium that secretes several host-directed factors and causes hospital infections and community-acquired ocular infections. The putative two-component regulatory system composed of EepR and EepS regulates hemolysis and swarming motility through transcriptional control of the
swrW
gene and pigment production through control of the
pigA
-
pigN
operon. Here, we identify and characterize a role for EepR in regulation of exoenzyme production, stress survival, cytotoxicity to human epithelial cells, and virulence. Genetic analysis supports the model that EepR is in a common pathway with the widely conserved cyclic-AMP receptor protein that regulates protease production. Together, these data introduce a novel regulator of host-pathogen interactions and secreted-protein production.
Role of the Tet38 Efflux Pump in Staphylococcus aureus Internalization and Survival in Epithelial Cells
Authors: Truong-Bolduc Q. C. , Bolduc G. R. , Medeiros H. , Vyas J. M. , Wang Y. , Hooper D. C. 
Published: September 2015

ABSTRACT

We previously identified the protein Tet38 as a chromosomally encoded efflux pump of
Staphylococcus aureus
that confers resistance to tetracycline and certain unsaturated fatty acids. Tet38 also contributes to mouse skin colonization. In this study, we discovered a novel regulator of
tet38
, named tetracycline regulator 21 (TetR21), that bound specifically to the
tet38
promoter and repressed pump expression. A Δ
tetR21
mutant showed a 5-fold increase in
tet38
transcripts and an 8-fold increase in resistance to tetracycline and fatty acids. The global regulator MgrA bound to the
tetR21
promoter and indirectly repressed the expression of
tet38
. To further assess the full role of Tet38 in
S. aureus
adaptability, we tested its effect on host cell invasion using A549 (lung) and HMEC-1 (heart) cell lines. We used
S. aureus
RN6390, its Δ
tet38
, Δ
tetR21
, and Δ
mgrA
mutants, and a Δ
tet38 ΔtetR21
double mutant. After 2 h of contact, the Δ
tet38
mutant was internalized in 6-fold-lower numbers than RN6390 in A549 and HMEC-1 cells, and the Δ
tetR21
mutant was internalized in 2-fold-higher numbers than RN6390. A slight increase of 1.5-fold in internalization was found for the Δ
mgrA
mutant. The growth patterns of RN6390 and the Δ
mgrA
and Δ
tetR21
mutants within A549 cells were similar, while no growth was observed for the Δ
tet38
mutant. These data indicate that the Tet38 efflux pump is regulated by TetR21 and contributes to the ability of
S. aureus
to internalize and replicate within epithelial cells.
The Caulobacter crescentus Homolog of DnaA (HdaA) Also Regulates the Proteolysis of the Replication Initiator Protein DnaA
Authors: Wargachuk Richard , Marczynski Gregory T. 
Published: September 2015

ABSTRACT

It is not known how diverse bacteria regulate chromosome replication. Based on
Escherichia coli
studies, DnaA initiates replication and the homolog of DnaA (Hda) inactivates DnaA using the RIDA (
r
egulatory
i
nactivation of
D
na
A
) mechanism that thereby prevents extra chromosome replication cycles. RIDA may be widespread, because the distantly related
Caulobacter crescentus
homolog HdaA also prevents extra chromosome replication (J. Collier and L. Shapiro, J Bacteriol 191:5706–5715, 2009,
http://dx.doi.org/10.1128/JB.00525-09
). To further study the HdaA/RIDA mechanism, we created a
C. crescentus
strain that shuts off
hdaA
transcription and rapidly clears HdaA protein. We confirm that HdaA prevents extra replication, since cells lacking HdaA accumulate extra chromosome DNA. DnaA binds nucleotides ATP and ADP, and our results are consistent with the established
E. coli
mechanism whereby Hda converts active DnaA-ATP to inactive DnaA-ADP. However, unlike
E. coli
DnaA,
C. crescentus
DnaA is also regulated by selective proteolysis.
C. crescentus
cells lacking HdaA reduce DnaA proteolysis in logarithmically growing cells, thereby implicating HdaA in this selective DnaA turnover mechanism. Also, wild-type
C. crescentus
cells remove all DnaA protein when they enter stationary phase. However, cells lacking HdaA retain stable DnaA protein even when they stop growing in nutrient-depleted medium that induces complete DnaA proteolysis in wild-type cells. Additional experiments argue for a distinct HdaA-dependent mechanism that selectively removes DnaA prior to stationary phase. Related freshwater
Caulobacter
species also remove DnaA during entry to stationary phase, implying a wider role for HdaA as a novel component of programed proteolysis.

IMPORTANCE
Bacteria must regulate chromosome replication, and yet the mechanisms are not completely understood and not fully exploited for antibiotic development. Based on
Escherichia coli
studies, DnaA initiates replication, and the homolog of DnaA (Hda) inactivates DnaA to prevent extra replication. The distantly related
Caulobacter crescentus
homolog HdaA also regulates chromosome replication. Here we unexpectedly discovered that unlike the
E. coli
Hda, the
C. crescentus
HdaA also regulates DnaA proteolysis. Furthermore, this HdaA proteolysis acts in logarithmically growing and in stationary-phase cells and therefore in two very different physiological states. We argue that HdaA acts to help time chromosome replications in logarithmically growing cells and that it is an unexpected component of the programed entry into stationary phase.