bluuebunny/crossref_metadata_2025_split huggingface dataset:
ANALYZING THE FEATURES OF MUGHAL GARDEN DESIGN: CASE OF TAJ MAHAL, AGRA, INDIA
Authors: Azmee Nurshamiela , Mohd Yunos Mohd Yazid , Mydin Md Azree Othuman , Ismail Sumarni , Mohd Ariffin Noor Fazamimah , Mohd Isa Nor Kalsum , Abdul Latiff Zainab 
Published: May 2016

Islamic garden is a place for rest and reflection, and a reminder to paradise. The themes of an Islamic garden are shade and water element. The Islamic Gardens are influenced by the historic Islamic Garden that majority fromSpain,Iran, and MughalIndia. Those are among the recognized gardens design during Islamic Civilization and remain as a legacy of the influential era of Islamic rulers. However the gardens have different culture influences that make each of the gardens are different in their design. This paper is to analyzing the features used in the garden design ofMughalGarden: Taj Mahal,Agra,India.Â Â The study used a content analysis and observation of features used in the design for the garden. The outcome of this study will enhance the understanding and appreciation towards Islamic garden design as an Islamic cultural heritage for the next generation.Â Â
PEDESTRIAN POTENTIAL RISK WHILE CROSSING AT SIGNALIZED INTERSECTIONS
Authors: Hamidun Rizati , Kordi Nurul Elma , Endut Intan Rohani , Ishak Siti Zaharah , Mohd Yusof Mohd Faudzi 
Published: May 2016

Risk of pedestrian while crossing a road section may influence by several factors, including their crossing behaviors which might be difficult to be measured. In this paper, a model using Petri nets is introduced to consider the behavioral factors in measuring pedestrian risk. The crossing scenario of the pedestrian was observed to identify the pedestrian accident event. Sequence of event in pedestrian accident was modeled into Petri Nets elements. The model is designed in the hierarchical structure to consider risk factors related to human behavior, engineering and environment. The analysis of the model provides the numerical value of pedestrian potential risk as they crossed at a signalized intersection. The effect of each factor on the potential risk can be observed through sensitivity analysis. The use of Petri Nets is a novel approach in predicting pedestrian potential risk through the modeling of pedestrian accident process.
REMOVAL OF OIL AND GREASE FROM WASTEWATER USING NATURAL ADSORBENTS
Authors: Abdul Hamid Noor Sa’adah , Che Malek Nur Afirah , Mokhtar Hamizah , Mazlan Wan Suriatty , Mohd Tajuddin Ramlah 
Published: May 2016

There are several pollutants that can harm our environment. Oil and grease are one of the examples of a pollutant that can cause a severe environmental problem. The highest concentration of oil and grease inside the sewer system can cause the sewer to clog that can lead to overflow. It can affect not only to the environment but can also affecting our health. There are various methods of oil and grease removal that one of the examples is by using adsorption method. This method commonly uses activated carbon that is one of the effective adsorbents. Although effective, the cost for activated carbon is expensive thus a study was conducted by using agricultural residues as alternative adsorbents for oil and grease removal. This study objective is to determine the ability of two adsorbents, which are sugarcane bagasse and banana pith as an adsorbent in removing oil and grease from wastewater. It involved the characterization of adsorbent and the performance studies of the adsorbent. The adsorbent was characterized in term of physical and chemical characterization. Dosage and contact time are the parameter used for performance studies, to see the ability of adsorbents in removing oil and grease.
MEASURING THE ECONOMIC BENEFITS FROM THE CONTAMINATED SOIL REMEDIATION POLICY IN KOREA: A CONTINGENT VALUATION STUDY
Authors: Lim Seul-Ye , Yoo Seung-Hoon 
Published: May 2016

Soil contamination caused by economic growth through industrialization and urbanization has been progressed inKorea. Soil polluted with heavy metals and chemicals makes significantly negative effects on human and wildlife health. This paper attempts to measure the economic benefits from the contaminated soil remediation policy using a specific case study ofKorea. To this end, the contingent valuation (CV) method is employed. A CV national survey of randomly selected 500 households was implemented using person-to-person interviewing in May 2105. To elicit the willingness to pay (WTP), we apply one-and-one-half bound dichotomous choice question format to reduce the potential for response bias and spike model to deal with zero willingness to pay (WTP). The mean WTP for the policy is estimated to be KRW 1,357 (USD 1.2) for next ten years per household per year and statistically significant at the 1% level. Expanding the value to the national population gives us KRW 25.4 billion (USD 22.9 million) per year. We can judge that the Korean public places a significant value and be utilized in assessing the total benefits from the policy.
MODELING OF ANAEROBIC CO-DIGESTION OF PIG MANURE AND DOMESTIC ORGANIC WASTE
Authors: Thongnan Rachadaporn , Thongpan Hathaikarn , Rakmak Nirattisai , Siripatana Chairat 
Published: May 2016

The normal practice in Thailand is that the wastes from pig-farms and households are treated separately. Nutrient imbalance as well as other physico-chemical characteristics of each waste cause the anaerobic digestion process to work at suboptimal rates. This work is an attempt to describe the kinetics of anaerobic co-digestion of wastewater mixture from a pig-farm and domestic organic waste to understand the effect of their ratio on the biogas production efficiency in batch digesters which mimic a similar industrial practice. The batch experiments were carried out at three different temperatures (28 oC, 32oC and 35oC ), with and without initial pH adjustment (pH 7), and four levels of total solid (8%,12%,16% and 20% TS). It was found that the best operating condition was 35 oC, 16% TS and the pig-manure-to-domestic-waste ratio of 75:25. The modified Gompertz equation was used to estimate some Monod parameters and biomethane potential. Then modified two-substrate Monod equation was used to estimate the maximum specific biogas production rate (MBPR). It was also used to describe the microbial growth, substrate consumption and biogas production satisfactorily.
Comparison of three ultrasound based elastographic techniques in children and adolescents with chronic diffuse liver diseases.
Authors: Belei Oana , Sporea Ioan , Gradinaru-Tascau Oana , Olariu Laura , Popescu Alina , Simedrea Ioan , Marginean Otilia 
Published: May 2016

Non-invasive techniques for liver fibrosis assessment were developed for adults and recent researches tested their accuracy in children. The only validated elastographic method for non-invasive liver fibrosis evaluation in children is Transient Elastography (TE). The aim of our study was to investigate the feasibility of liver stiffness (LS) measurement in paediatric patients with chronic liver diseases by means of Acoustic Radiation Force Impulse Elastography (ARFI) and 2D-Shear Wave Elastography (2D-SWE), compared to TE as reference method. Material and methods: We enrolled 54 consecutive children and adolescents with different chronic liver diseases. All patients were examined by means of TE, ARFI, and 2D-SWE. All measurements were performed in the right liver lobe, in the same session, in fasting condition. We considered reliable LS elastographic measurements as follows: for TE and ARFI - the median value of ten measurements with a success rate≥60% and an interquartile range<30%, for 2D-SWE - the median value of five measurements. Results: The successful measurement rate for TE was 94.4% (51/54). Taking TE as a reference method, sensitivity of ARFI for detecting fibrosis F1 was 71.42%, for F2-77.77%, for F3-62.5% and for F4-71.42%. Sensitivity of 2D-SWE for detecting F1 was 92.85%, for F2-83.33%, for F3-87.5% and for F4-85.71%. We found significant correlations between TE and 2D-SWE on the entire lot (Kappa correlation factor=0.843, p=0.001). Analyzing the subgroup with SR=60%-70%, we did not find significant correlation between TE and ARFI (Kappa correlation factor=0.172, p=0.452). Assessing the subgroup with SR>70%, we found a significant correlation between TE and ARFI (Kappa correlation factor=0.761, p=0.001). Conclusions: Overall, 2D-SWE correlate better with TE compared to ARFI in children. Excluding patients with less satisfactory technical parameters, we obtained significant correlations between all three methods. Both SWE and ARFI are non-invasive techniques feasible of performing on paediatric patients along with TE.
Technical Note: Enhancing the surface dose using a weak longitudinal magnetic field
Authors: Carlone Marco , Tadic Tony , Keller Harald , Rezaee Mohammad , Jaffray David 
Published: May 2016

Purpose:The surface dose in radiotherapy is subject to the physical properties of the radiation beam and collimator. The purpose of this work is to investigate the manipulation of surface dose using magnetic fields produced with a resistive magnet. Better understanding of the feasibility and mechanisms of altered surface dose could have important clinical applications where the surface dose must be increased for therapeutic goals, or reduced to enhance the therapeutic benefit.Methods:A resistive magnet capable of generating a peak magnetic field up to 0.24 T was integrated with a cobalt treatment unit. The magnetic fringe field of the magnet was small due to the self‐shielding built within the magnet. The magnetic field at the beam collimation jaws of the cobalt irradiator was less than 10 G. The surface dose and depth dose were measured for varying magnetic field strengths.Results:The resistive magnet was able to alter the dose in the buildup region of the 60Co depth dose significantly, and the magnitude of dose enhancement was directly related to the strength of the longitudinal magnetic field. Peak magnetic fields as low as 0.08 T were able to affect the surface dose. At a peak field of 0.24 T, the authors measured a surface dose enhancement of 2.8‐fold.Conclusions:Surface dose enhancement using resistive magnets is feasible. Further experimental study is needed to understand the origin of the scattered electrons that contribute to the increase in surface dose.
Immunoassay Analysis of Kanamycin in Serum Using the Tobramycin Kit
Authors: Dijkstra J. A. , Voerman A. J. , Greijdanus B. , Touw D. J. , Alffenaar J. W. C. 
Published: May 2016

ABSTRACT
Kanamycin is one of the aminoglycosides used in the treatment of multidrug-resistant tuberculosis. Blood concentrations of kanamycin are predictive for the treatment efficacy and the occurrence of side effects, and dose adjustments can be needed to optimize therapy. However, an immunoassay method for the quantification of kanamycin is not commercially available. We modified the existing tobramycin immunoassay to analyze kanamycin. This modified method was tested in a concentration range of 0.3 to 80.0 mg/liter for inaccuracy and imprecision. In addition, the analytical results of the immunoassay method were compared to those obtained by a liquid chromatography-tandem mass spectrometry (LC-MS/MS) analytical method using Passing and Bablok regression. Within-day imprecision varied from 2.3 to 13.3%, and between-day imprecision ranged from 0.0 to 11.3%. The inaccuracy ranged from −5.2 to 7.6%. No significant cross-reactivity with other antimicrobials and antiviral agents was observed. The results of the modified immunoassay method were comparable with the LC-MS/MS analytical outcome. This new immunoassay method enables laboratories to perform therapeutic drug monitoring of kanamycin without the need for complex and expensive LC-MS/MS equipment.
Iron Limitation Triggers Early Egress by the Intracellular Bacterial Pathogen Legionella pneumophila
Authors: O'Connor Tamara J. , Zheng Huaixin , VanRheenen Susan M. , Ghosh Soma , Cianciotto Nicholas P. , Isberg Ralph R. 
Published: May 2016

ABSTRACT

Legionella pneumophila
is an intracellular bacterial pathogen that replicates in alveolar macrophages, causing a severe form of pneumonia. Intracellular growth of the bacterium depends on its ability to sequester iron from the host cell. In the
L. pneumophila
strain 130b, one mechanism used to acquire this essential nutrient is the siderophore legiobactin. Iron-bound legiobactin is imported by the transport protein LbtU. Here, we describe the role of LbtP, a paralog of LbtU, in iron acquisition in the
L. pneumophila
strain Philadelphia-1. Similar to LbtU, LbtP is a siderophore transport protein and is required for robust growth under iron-limiting conditions. Despite their similar functions, however, LbtU and LbtP do not contribute equally to iron acquisition. The Philadelphia-1 strain lacking LbtP is more sensitive to iron deprivation
in vitro
. Moreover, LbtP is important for
L. pneumophila
growth within macrophages while LbtU is dispensable. These results demonstrate that LbtP plays a dominant role over LbtU in iron acquisition. In contrast, loss of both LbtP and LbtU does not impair
L. pneumophila
growth in the amoebal host
Acanthamoeba castellanii
, demonstrating a host-specific requirement for the activities of these two transporters in iron acquisition. The growth defect of the Δ
lbtP
mutant in macrophages is not due to alterations in growth kinetics. Instead, the absence of LbtP limits
L. pneumophila
replication and causes bacteria to prematurely exit the host cell. These results demonstrate the existence of a preprogrammed exit strategy in response to iron limitation that allows
L. pneumophila
to abandon the host cell when nutrients are exhausted.
Amyloid Structures as Biofilm Matrix Scaffolds
Authors: Taglialegna Agustina , Lasa Iñigo , Valle Jaione 
Published: May 2016

ABSTRACT
Recent insights into bacterial biofilm matrix structures have induced a paradigm shift toward the recognition of amyloid fibers as common building block structures that confer stability to the exopolysaccharide matrix. Here we describe the functional amyloid systems related to biofilm matrix formation in both Gram-negative and Gram-positive bacteria and recent knowledge regarding the interaction of amyloids with other biofilm matrix components such as extracellular DNA (eDNA) and the host immune system. In addition, we summarize the efforts to identify compounds that target amyloid fibers for therapeutic purposes and recent developments that take advantage of the amyloid structure to engineer amyloid fibers of bacterial biofilm matrices for biotechnological applications.
Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea
Authors: Fu Xian , Liu Rui , Sanchez Iona , Silva-Sanchez Cecilia , Hepowit Nathaniel L. , Cao Shiyun , Chen Sixue , Maupin-Furlow Julie 
Published: May 2016

ABSTRACT
The molecular mechanisms of targeted proteolysis in archaea are poorly understood, yet they may have deep evolutionary roots shared with the ubiquitin-proteasome system of eukaryotic cells. Here, we demonstrate in archaea that TBP2, a TATA-binding protein (TBP) modified by ubiquitin-like isopeptide bonds, is phosphorylated and targeted for degradation by proteasomes. Rapid turnover of TBP2 required the functions of UbaA (the E1/MoeB/ThiF homolog of archaea), AAA ATPases (Cdc48/p97 and Rpt types), a type 2 JAB1/MPN/MOV34 metalloenzyme (JAMM/MPN+) homolog (JAMM2), and 20S proteasomes. The ubiquitin-like protein modifier small archaeal modifier protein 2 (SAMP2) stimulated the degradation of TBP2, but SAMP2 itself was not degraded. Analysis of the TBP2 fractions that were not modified by ubiquitin-like linkages revealed that TBP2 had multiple N termini, including Met1-Ser2, Ser2, and Met1-Ser2(p) [where (p) represents phosphorylation]. The evidence suggested that the Met1-Ser2(p) form accumulated in cells that were unable to degrade TBP2. We propose a model in archaea in which the attachment of ubiquitin-like tags can target proteins for degradation by proteasomes and be controlled by N-terminal degrons. In support of a proteolytic mechanism that is energy dependent and recycles the ubiquitin-like protein tags, we find that a network of AAA ATPases and a JAMM/MPN+ metalloprotease are required, in addition to 20S proteasomes, for controlled intracellular proteolysis.

IMPORTANCE
This study advances the fundamental knowledge of signal-guided proteolysis in archaea and sheds light on components that are related to the ubiquitin-proteasome system of eukaryotes. In archaea, the ubiquitin-like proteasome system is found to require function of an E1/MoeB/ThiF homolog, a type 2 JAMM/MPN+ metalloprotease, and a network of AAA ATPases for the targeted destruction of proteins. We provide evidence that the attachment of the ubiquitin-like protein is controlled by an N-terminal degron and stimulates proteasome-mediated proteolysis.
Baseline Biomarkers for Outcome of Melanoma Patients Treated with Pembrolizumab
Authors: Weide Benjamin , Martens Alexander , Hassel Jessica C. , Berking Carola , Postow Michael A. , Bisschop Kees , Simeone Ester , Mangana Johanna , Schilling Bastian , Di Giacomo Anna Maria , Brenner Nicole , Kähler Katharina , Heinzerling Lucie , Gutzmer Ralf , Bender Armin , Gebhardt Christoffer , Romano Emanuela , Meier Friedegund , Martus Peter , Maio Michele , Blank Christian , Schadendorf Dirk , Dummer Reinhard , Ascierto Paolo A. , Hospers Geke , Garbe Claus , Wolchok Jedd D. 
Published: May 2016

AbstractPurpose: Biomarkers for outcome after immune-checkpoint blockade are strongly needed as these may influence individual treatment selection or sequence. We aimed to identify baseline factors associated with overall survival (OS) after pembrolizumab treatment in melanoma patients.Experimental Design: Serum lactate dehydrogenase (LDH), routine blood count parameters, and clinical characteristics were investigated in 616 patients. Endpoints were OS and best overall response following pembrolizumab treatment. Kaplan–Meier analysis and Cox regression were applied for survival analysis.Results: Relative eosinophil count (REC) ≥1.5%, relative lymphocyte count (RLC) ≥17.5%, ≤2.5-fold elevation of LDH, and the absence of metastasis other than soft-tissue/lung were associated with favorable OS in the discovery (n = 177) and the confirmation (n = 182) cohort and had independent positive impact (all P &lt; 0.001). Their independent role was subsequently confirmed in the validation cohort (n = 257; all P &lt; 0.01). The number of favorable factors was strongly associated with prognosis. One-year OS probabilities of 83.9% versus 14.7% and response rates of 58.3% versus 3.3% were observed in patients with four of four compared to those with none of four favorable baseline factors present, respectively.Conclusions: High REC and RLC, low LDH, and absence of metastasis other than soft-tissue/lung are independent baseline characteristics associated with favorable OS of patients with melanoma treated with pembrolizumab. Presence of four favorable factors in combination identifies a subgroup with excellent prognosis. In contrast, patients with no favorable factors present have a poor prognosis, despite pembrolizumab, and additional treatment advances are still needed. A potential predictive impact needs to be further investigated. Clin Cancer Res; 22(22); 5487–96. ©2016 AACR.
Use of Liquid Biopsies in Clinical Oncology: Pilot Experience in 168 Patients
Authors: Schwaederle Maria , Husain Hatim , Fanta Paul T. , Piccioni David E. , Kesari Santosh , Schwab Richard B. , Patel Sandip P. , Harismendy Olivier , Ikeda Megumi , Parker Barbara A. , Kurzrock Razelle 
Published: May 2016

Abstract
Purpose: There is a growing interest in using circulating tumor DNA (ctDNA) testing in patients with cancer.
Experimental Design: A total of 168 patients with diverse cancers were analyzed. Patients had digital next-generation sequencing (54 cancer-related gene panel including amplifications in ERBB2, EGFR, and MET) performed on their plasma. Type of genomic alterations, potential actionability, concordance with tissue testing, and patient outcome were examined.
Results: Fifty-eight percent of patients (98/168) had ≥1 ctDNA alteration(s). Of the 98 patients with alterations, 71.4% had ≥ 1 alteration potentially actionable by an FDA-approved drug. The median time interval between the tissue biopsy and the blood draw was 2.7 months for patients with ≥ 1 alteration in common compared with 14.4 months (P = 0.006) for the patients in whom no common alterations were identified in the tissue and plasma. Overall concordance rates for tissue and ctDNA were 70.3% for TP53 and EGFR, 88.1% for PIK3CA, and 93.1% for ERBB2 alterations. There was a significant correlation between the cases with ≥ 1 alteration with ctDNA ≥ 5% and shorter survival (median = 4.03 months vs. not reached at median follow-up of 6.1 months; P &lt; 0.001). Finally, 5 of the 12 evaluable patients (42%) matched to a treatment targeting an alteration(s) detected in their ctDNA test achieved stable disease ≥ 6 months/partial remission compared with 2 of 28 patients (7.1%) for the unmatched patients, P = 0.02.
Conclusions: Our initial study demonstrates that ctDNA tests provide information complementary to that in tissue biopsies and may be useful in determining prognosis and treatment. Clin Cancer Res; 22(22); 5497–505. ©2016 AACR.
Dual mTORC1/2 Inhibition as a Novel Strategy for the Resensitization and Treatment of Platinum-Resistant Ovarian Cancer
Authors: Musa Fernanda , Alard Amandine , David-West Gizelka , Curtin John P. , Blank Stephanie V. , Schneider Robert J. 
Published: May 2016

AbstractThere is considerable interest in the clinical development of inhibitors of mTOR complexes mTORC1 and 2. Because mTORC1 and its downstream mRNA translation effectors may protect against genotoxic DNA damage, we investigated the inhibition of mTORC1 and mTORC1/2 in the ability to reverse platinum resistance in tissue culture and in animal tumor models of serous ovarian cancer. Cell survival, tumor growth, PI3K–AKT–mTOR pathway signaling, DNA damage and repair response (DDR) gene expression, and translational control were all investigated. We show that platinum-resistant OVCAR-3 ovarian cancer cells are resensitized to low levels of carboplatin in culture by mTOR inhibition, demonstrating reduced survival after treatment with either mTORC1 inhibitor everolimus or mTORC1/2 inhibitor PP242. Platinum resistance is shown to be associated with activating phosphorylation of AKT and CHK1, inactivating phosphorylation of 4E-BP1, the negative regulator of eIF4E, which promotes increased cap-dependent mRNA translation and increased levels of CHK1 and BRCA1 proteins. Animals with platinum-resistant OVCAR-3 tumors treated with carboplatin plus mTORC1/2 inhibition had significantly longer median survival and strikingly reduced metastasis compared with animals treated with carboplatin plus everolimus, which inhibits only mTORC1. Reduced tumor growth, metastasis, and increased survival by mTORC1/2 inhibition with carboplatin treatment was associated with reduced AKT-activating phosphorylation and increased 4E-BP1 hypophosphorylation (activation). We conclude that mTORC1/2 inhibition is superior to mTORC1 inhibition in reversing platinum resistance in tumors and strongly impairs AKT activation, DNA repair responses, and translation, promoting improved survival in the background of platinum resistance. Mol Cancer Ther; 15(7); 1557–67. ©2016 AACR.