bluuebunny/crossref_metadata_2025_split huggingface dataset:
FOUNDATION MODELLING FOR COOLING WATER PUMP MACHINE IN PT PUPUK SRIWIJAYA (PURSI) II-B PROJECTS
Authors: Dewi Ratna , Hastuti Yulia , Mentari Agnes 
Published: October 2016

PT Pupuk Sriwijaya (PUSRI) in Palembang, South Sumatera, Indonesia uses a lot of machines to run the fabric. One of the project is PUSRI II-B, which use cooling water pump machine. The machine will not operate properly if it does not use the appropriate foundation to support static and dynamic loads. The Terzaghi and Meyerhof methods were used in static analysis to measure the settlement in the pile group and soil bearing capacity. The frequency, damping, and vibration amplitude of the vibration that occur in a vertical and horizontal vibration, and the vibration rocking were calculated by using the trial error method for dynamic analysis. Modelling frame foundation machine is the main focus in this research. The result shows that the most effective foundation dimension for cooling water pump machine is frame foundation type with the pile cap dimensions of 9.8 m x 4 m x 1.5 m; column of 0.5 m x 0.5 m x 1 m and slab of 9.8 m x 4 m x 0.3 m, and using the piles with a diameter of 0.35 m, length of 21 m and the spacing between the piles is about 2.45 m. The gravel was compacted to the same level where the pile cap was planned in order to increase the soil shear modulus.
DEPOSITION THICKNESS AND ITS EFFECT ON CRITICAL SHEAR STRESS FOR INCIPIENT MOTION OF SEDIMENTS
Authors: Joo Bong Charles Hin , Putuhena Frederik Josep , Lau Tze Liang , Ab. Ghani Aminuddin 
Published: October 2016

There are evidences in existing literatures suggesting the incipient motion values for any particle size is substantially lower for rigid boundary condition as compared to loose boundary condition. The objective of the current study is to determine the effect of sediment deposition thickness on the critical shear stress for incipient motion. Experimental works for incipient motion were carried out in a rectangular flume with varying sediment deposits thickness. Results showed that the sediment deposits thickness has effect on the critical shear stress at low sediment deposits thickness and the effect will slowly diminish as the sediment deposits thickness increases. Multiple linear regression analysis was performed on the experimental data to develop a new critical shear stress equation. The best regression model has value of 0.69; value of 0.60; value of 0.009 and Mallow’s value of 3.00. The new equation appears to be more consistent as compared to existing incipient motion equations for rigid boundary condition by having 80% of the predicted data falls within the acceptable discrepancy ratio when tested with data from other authors. The new equation can be used to determine critical shear stress values for self-cleansing sewerage design and other related engineering applications
Informing Antibiotic Treatment Decisions: Evaluating Rapid Molecular Diagnostics To Identify Susceptibility and Resistance to Carbapenems against Acinetobacter spp. in PRIMERS III
Authors: Evans Scott R. , Hujer Andrea M. , Jiang Hongyu , Hill Carol B. , Hujer Kristine M. , Mediavilla Jose R. , Manca Claudia , Tran Thuy Tien T. , Domitrovic T. Nicholas , Higgins Paul G. , Seifert Harald , Kreiswirth Barry N. , Patel Robin , Jacobs Michael R. , Chen Liang , Sampath Rangarajan , Hall Thomas , Marzan Christine , Fowler Vance G. , Chambers Henry F. , Bonomo Robert A. 
Published: October 2016

ABSTRACT

The widespread dissemination of carbapenem-resistant
Acinetobacter
spp. has created significant therapeutic challenges. At present, rapid molecular diagnostics (RMDs) that can identify this phenotype are not commercially available. Two RMD platforms, PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS) and molecular beacons (MB), for detecting genes conferring resistance/susceptibility to carbapenems in
Acinetobacter
spp. were evaluated. An archived collection of 200 clinical
Acinetobacter
sp. isolates was tested. Predictive values for susceptibility and resistance were estimated as a function of susceptibility prevalence and were based on the absence or presence of beta-lactamase (
bla
) NDM, VIM, IMP, KPC, and OXA carbapenemase genes (e.g.,
bla
OXA-23
,
bla
OXA-24/40
, and
bla
OXA-58
found in this study) against the reference standard of MIC determinations. According to the interpretation of MICs, 49% (
n
= 98) of the isolates were carbapenem resistant (as defined by either resistance or intermediate resistance to imipenem). The susceptibility sensitivities (95% confidence interval [CI]) for imipenem were 82% (74%, 89%) and 92% (85%, 97%) for PCR/ESI-MS and MB, respectively. Resistance sensitivities (95% CI) for imipenem were 95% (88%, 98%) and 88% (80%, 94%) for PCR/ESI-MS and MB, respectively. PRIMERS III establishes that RMDs can discriminate between carbapenem resistance and susceptibility in
Acinetobacter
spp. In the context of a known prevalence of resistance, SPVs and RPVs can inform clinicians regarding the best choice for empiric antimicrobial therapy against this multidrug-resistant pathogen.
Replication-Deficient Particles: New Insights into the Next Generation of Bluetongue Virus Vaccines
Authors: Celma Cristina C. , Stewart Meredith , Wernike Kerstin , Eschbaumer Michael , Gonzalez-Molleda Lorenzo , Breard Emmanuel , Schulz Claudia , Hoffmann Bernd , Haegeman Andy , De Clercq Kris , Zientara Stephan , van Rijn Piet A. , Beer Martin , Roy Polly 
Published: October 2016

ABSTRACT
Bluetongue virus (BTV) is endemic in many parts of the world, often causing severe hemorrhagic disease in livestock. To date, at least 27 different serotypes have been recognized. Vaccination against all serotypes is necessary to protect susceptible animals and to prevent onward spread of the virus by insect vectors. In our previous studies, we generated replication-deficient (disabled infectious single-cycle [DISC]) virus strains for a number of serotypes and reported preliminary data on their protective efficacy in animals. In this report, to advance the DISC vaccines to the marketplace, we investigated different parameters of these DISC vaccines. First, we demonstrated the genetic stabilities of these vaccine strains and also the complementing cell line. Subsequently, the optimal storage conditions of vaccines, including additives, temperature, and desiccation, were determined and their protective efficacies in animals confirmed. Furthermore, to test if mixtures of different vaccine strains could be tolerated, we tested cocktails of DISC vaccines in combinations of three or six different serotypes in sheep and cattle, the two natural hosts of BTV. Groups of sheep vaccinated with a cocktail of six different vaccines were completely protected from challenge with individual virulent serotypes, both in early challenge and after 5 months of challenge without any clinical disease. There was no interference in protection between the different vaccines. Protection was also achieved in cattle with a mixture of three vaccine strains, albeit at a lesser level than in sheep. Our data support and validate the suitability of these virus strains as the next-generation vaccines for BTV.

IMPORTANCE
Bluetongue (BT) is a debilitating and in many cases lethal disease that affects ruminants of economic importance. Classical vaccines that afford protection against bluetongue virus, the etiological agent, are not free from secondary and undesirable effects. A surge in new approaches to produce highly attenuated, safer vaccines was evident after the development of the BTV reverse-genetics system that allows the introduction of targeted mutations in the virus genome. We targeted an essential gene to develop disabled virus strains as vaccine candidates. The results presented in this report further substantiate our previous evidence and support the suitability of these virus strains as the next-generation BTV vaccines.
Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression
Authors: Mars Ruben A. T. , Nicolas Pierre , Denham Emma L. , van Dijl Jan Maarten 
Published: October 2016

SUMMARY

Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include
trans
-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as
Escherichia coli
and
Salmonella
. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium
Bacillus subtilis
. A recent study identified 1,583 putative regulatory RNAs in
B. subtilis
, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in
B. subtilis
, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in
B. subtilis
mostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in
B. subtilis
. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in
B. subtilis
.
Factors associated with the difficulty in hospital acceptance at the scene by emergency medical service personnel: a population-based study in Osaka City, Japan
Authors: Katayama Yusuke , Kitamura Tetsuhisa , Kiyohara Kosuke , Iwami Taku , Kawamura Takashi , Hayashida Sumito , Yoshiya Kazuhisa , Ogura Hiroshi , Shimazu Takeshi 
Published: October 2016

ObjectivesTo investigate the association between the difficulty in hospital acceptance at the scene by emergency medical service (EMS) personnel and prehospital demographic factors and reasons for EMS calls.DesignA retrospective, observational study.SettingOsaka City, Japan.ParticipantsA total of 100 649 patients transported to medical institutions by EMS from January 2013 to December 2013.Primary outcome measurementsThe definition of difficulty in hospital acceptance at the scene was EMS personnel making ≥5 phone calls to medical institutions until a decision to transport was determined. Multivariable analysis was used to assess the relationship between difficulty in hospital acceptance and prehospital factors and reasons for EMS calls.ResultsMultivariable analysis showed the elderly, foreigners, loss of consciousness, holiday/weekend, and night-time to be positively associated with difficulty in hospital acceptance at the scene. As reasons for EMS calls, gas poisoning (adjusted OR 3.281, 95% CI 1.201 to 8.965), trauma by assault (adjusted OR 2.662, 95% CI 2.390 to 2.966), self-induced drug abuse/gas poisoning (adjusted OR 4.527, 95% CI 3.921 to 5.228) and self-induced trauma (adjusted OR 1.708, 95% CI 1.369 to 2.130) were positively associated with the difficulty in hospital acceptance at the scene.ConclusionsAmbulance records in Osaka City showed that certain prehospital factors such as night-time were positively associated with difficulty in hospital acceptance at the scene, and reasons for EMS calls, such as self-induced drug abuse/gas poisoning, were also positive predictors for difficulty in hospital acceptance at the scene.
Multicentre validation of a microRNA-based assay for diagnosing indeterminate thyroid nodules utilising fine needle aspirate smears
Authors: Lithwick-Yanai Gila , Dromi Nir , Shtabsky Alexander , Morgenstern Sara , Strenov Yulia , Feinmesser Meora , Kravtsov Vladimir , Leon Marino E , Hajdúch Marián , Ali Syed Z , VandenBussche Christopher J , Zhang Xinmin , Leider-Trejo Leonor , Zubkov Asia , Vorobyov Sergey , Kushnir Michal , Goren Yaron , Tabak Sarit , Kadosh Etti , Benjamin Hila , Schnitzer-Perlman Temima , Marmor Hagai , Motin Maria , Lebanony Danit , Kredo-Russo Sharon , Mitchell Heather , Noller Melissa , Smith Alexis , Dattner Olivia , Ashkenazi Karin , Sanden Mats , Berlin Kenneth A , Bar Dganit , Meiri Eti 
Published: October 2016

AimsThe distinction between benign and malignant thyroid nodules has important therapeutic implications. Our objective was to develop an assay that could classify indeterminate thyroid nodules as benign or suspicious, using routinely prepared fine needle aspirate (FNA) cytology smears.MethodsA training set of 375 FNA smears was used to develop the microRNA-based assay, which was validated using a blinded, multicentre, retrospective cohort of 201 smears. Final diagnosis of the validation samples was determined based on corresponding surgical specimens, reviewed by the contributing institute pathologist and two independent pathologists. Validation samples were from adult patients (≥18 years) with nodule size >0.5 cm, and a final diagnosis confirmed by at least one of the two blinded, independent pathologists. The developed assay, RosettaGX Reveal, differentiates benign from malignant thyroid nodules, using quantitative RT-PCR.ResultsTest performance on the 189 samples that passed quality control: negative predictive value: 91% (95% CI 84% to 96%); sensitivity: 85% (CI 74% to 93%); specificity: 72% (CI 63% to 79%). Performance for cases in which all three reviewing pathologists were in agreement regarding the final diagnosis (n=150): negative predictive value: 99% (CI 94% to 100%); sensitivity: 98% (CI 87% to 100%); specificity: 78% (CI 69% to 85%).ConclusionsA novel assay utilising microRNA expression in cytology smears was developed. The assay distinguishes benign from malignant thyroid nodules using a single FNA stained smear, and does not require fresh tissue or special collection and shipment conditions. This assay offers a valuable tool for the preoperative classification of thyroid samples with indeterminate cytology.
Innovation Intermediaries in Technological Alliances
Authors: Weng Calvin S. 
Published: October 2016

Technological alliances play an important role in generating innovations but face the challenge of effective matchmaking when finding suitable partners in “open innovation” among networks of innovating firms. Intermediaries refer to those external mechanisms/institutions that can appropriately support companies in their innovation-related activities. They are frequently used to build a bridge between different competency constraints among companies. The purpose of this paper was to try to understand the role of a firm’s alliances within the context of open innovation. What do innovation intermediaries of collaborative partners contribute? Using the “Strategic Alliance Database” established by the National Science Council (NSC) in Taiwan as a basis, this study empirically explored the brokerage roles in the alliance that intermediaries take on to facilitate technological innovation and an innovation process. By using the technique of two-mode network analysis for social network analysis, this research focused on the question of how a technological alliance creates a platform for firms to execute matchmaking for new and/or relevant partners. The results presented here reveal that brokerage roles can be used to develop collaborations. The strategic position of the intermediary can activate different resources from the ones embedded in an alliance network.
Alox5 Blockade Eradicates JAK2V617F-Induced Polycythemia Vera in Mice
Authors: Chen Yaoyu , Shan Yi , Lu Min , DeSouza Ngoc , Guo Zhiru , Hoffman Ronald , Liang Aibin , Li Shaoguang 
Published: October 2016

Abstract
Myeloproliferative neoplasms such as polycythemia vera (PV), which are associated with the JAK mutation V617F, remain incurable despite progress in the use of JAK2 inhibitors for treatment of some of these diseases. In this study, we employed mice that undergo JAK2V617F-induced PV as a tool to explore new candidate targets for therapy. Our investigations focused on the lipid metabolic enzyme arachidonate 5-lipoxygenase (Alox5), which we found to be strongly upregulated by JAK2V617F in hematopoietic cells in vitro and in vivo. Notably, genetic deletion of Alox5 or its inhibition in mice with a bioactive small-molecule inhibitor was sufficient to attenuate PV development. This therapeutic effect was associated with induction of a blockade in cell-cycle progression and also with apoptosis in PV cells. Genetic loss exerted an inhibitory effect on PV-initiating cells. Similarly, Alox5 inhibition was sufficient to suppress colony formation in human JAK2V617F-expressing CD34+ cells. Mechanistic investigations showed that Alox5 inhibition reduced AKT activation and decreased β-catenin expression in JAK2V617F-expressing cells. Together, our results define Alox5 as a key genetic effector of JAK2V617F in driving PV, and they identify this enzyme as a candidate therapeutic target to treat this refractory myeloproliferative neoplasm. Cancer Res; 77(1); 164–74. ©2016 AACR.
Mutational Landscape and Gene Expression Patterns in Adult Acute Myeloid Leukemias with Monosomy 7 as a Sole Abnormality
Authors: Eisfeld Ann-Kathrin , Kohlschmidt Jessica , Mrózek Krzysztof , Volinia Stefano , Blachly James S. , Nicolet Deedra , Oakes Christopher , Kroll Karl , Orwick Shelley , Carroll Andrew J. , Stone Richard M. , Byrd John C. , de la Chapelle Albert , Bloomfield Clara D. 
Published: October 2016

AbstractMonosomy of chromosome 7 is the most frequent autosomal monosomy in acute myeloid leukemia (AML), where it associates with poor clinical outcomes. However, molecular features associated with this sole monosomy subtype (-7 AML), which may give insights into the basis for its poor prognosis, have not been characterized. In this study, we analyzed 36 cases of -7 AML for mutations in 81 leukemia/cancer-associated genes using a customized targeted next-generation sequencing panel (Miseq). Global gene and miRNA expression profiles were also determined using paired RNA and small RNA sequencing data. Notably, gene mutations were detected in all the major AML-associated functional groups, which include activated signaling, chromatin remodeling, cohesin complex, methylation, NPM1, spliceosome, transcription factors, and tumor suppressors. Gene mutations in the chromatin remodeling groups were relatively more frequent in patients &lt;60 years of age, who also had less mutations in the methylation and spliceosome groups compared with patients ≥60 years of age. Novel recurrent mutational events in AML were identified in the SMARCA2 gene. In patients ≥60 years of age, the presence of spliceosome mutations associated with a lower complete remission rate (P = 0.03). RNA sequencing revealed distinct gene and miRNA expression patterns between the sole -7 and non -7 AML cases, with reduced expression, as expected, of many genes and miRNAs mapped to chromosome 7, and overexpression of ID1, MECOM, and PTPRM, among others. Overall, our findings illuminate a number of molecular features of the underlying aggressive pathobiology in -7 AML patients. Cancer Res; 77(1); 207–18. ©2016 AACR.
Gemcitabine Mechanism of Action Confounds Early Assessment of Treatment Response by 3′-Deoxy-3′-[18F]Fluorothymidine in Preclinical Models of Lung Cancer
Authors: Schelhaas Sonja , Held Annelena , Wachsmuth Lydia , Hermann Sven , Honess Davina J. , Heinzmann Kathrin , Smith Donna-Michelle , Griffiths John R. , Faber Cornelius , Jacobs Andreas H. 
Published: October 2016

Abstract
3′-Deoxy-3′-[18F]fluorothymidine positron emission tomography ([18F]FLT-PET) and diffusion-weighted MRI (DW-MRI) are promising approaches to monitor tumor therapy response. Here, we employed these two imaging modalities to evaluate the response of lung carcinoma xenografts in mice after gemcitabine therapy. Caliper measurements revealed that H1975 xenografts responded to gemcitabine treatment, whereas A549 growth was not affected. In both tumor models, uptake of [18F]FLT was significantly reduced 6 hours after drug administration. On the basis of the gemcitabine concentration and [18F]FLT excretion measured, this was presumably related to a direct competition of gemcitabine with the radiotracer for cellular uptake. On day 1 after therapy, [18F]FLT uptake was increased in both models, which was correlated with thymidine kinase 1 (TK1) expression. Two and 3 days after drug administration, [18F]FLT uptake as well as TK1 and Ki67 expression were unchanged. A reduction in [18F]FLT in the responsive H1975 xenografts could only be noted on day 5 of therapy. Changes in ADCmean in A549 xenografts 1 or 2 days after gemcitabine did not seem to be of therapy-related biological relevance as they were not related to cell death (assessed by caspase-3 IHC and cellular density) or tumor therapy response. Taken together, in these models, early changes of [18F]FLT uptake in tumors reflected mechanisms, such as competing gemcitabine uptake or gemcitabine-induced thymidylate synthase inhibition, and only reflected growth-inhibitory effects at a later time point. Hence, the time point for [18F]FLT-PET imaging of tumor response to gemcitabine is of crucial importance. Cancer Res; 76(24); 7096–105. ©2016 AACR.
The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development
Authors: Liu Shuang , Mitra Ramkrishna , Zhao Ming-Ming , Fan Wenhong , Eischen Christine M. , Yin Feng , Zhao Zhongming 
Published: October 2016

AbstractLong noncoding RNA (lncRNA) may contribute to the initiation and progression of tumor. In this study, we first systematically compared lncRNA and mRNA expression between glioblastoma and paired normal brain tissues using microarray data. We found 27 lncRNA and 82 mRNA significantly upregulated in glioblastoma, as well as 198 lncRNA and 285 mRNA significantly downregulated in glioblastoma. We identified 138 coexpressed lncRNA–mRNA pairs from these differentially expressed lncRNA and genes. Subsequent pathway analysis of the lncRNA-paired genes indicated that EphrinB–EPHB, p75-mediated signaling, TNFα/NF-κB, and ErbB2/ErbB3 signaling pathways might be altered in glioblastoma. Specifically, lncRNA RAMP2-AS1 had significant decrease of expression in glioblastoma tissues and showed coexpressional relationship with NOTCH3, an important tumor promoter in many neoplastic diseases. Our follow up experiment indicated that (i) an overexpression of RAMP2-AS1 reduced glioblastoma cell proliferation in vitro and also reduced glioblastoma xenograft tumors in vivo; (ii) NOTCH3 and RAMP2-AS1 coexpression rescued the inhibitory action of RAMP2-AS1 in glioblastoma cells; and (iii) RNA pull-down assay revealed a direct interaction of RAMP2-AS1 with DHC10, which may consequently inhibit, as we hypothesize, the expression of NOTCH3 and its downstream signaling molecule HES1 in glioblastoma. Taken together, our data revealed that lncRNA expression profile in glioblastoma tissue was significantly altered; and RAMP2-AS1 might play a tumor suppressive role in glioblastoma through an indirect inhibition of NOTCH3. Our results provided some insights into understanding the key roles of lncRNA–mRNA coregulation in human glioblastoma and the mechanisms responsible for glioblastoma progression and pathogenesis. Mol Cancer Ther; 15(12); 2977–86. ©2016 AACR.