bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equity in water supply in intermittent water distribution networks
Authors: Gottipati Prasad V. K. S. V. , Nanduri Umamahesh V. 
Published: December 2013

AbstractEquity in water supply is one of the major problems faced in intermittent water distribution systems. A new index ‘uniformity coefficient’ is introduced to measure the equity in distribution of water within the network, which may be useful for performance evaluation of water distribution networks (WDNs). An iterative head‐driven analysis technique is developed to compute the uniformity coefficient of a network. The effect of various design parameters of WDN on the uniform coefficient is studied. The results indicate that equity in water supply is significantly affected by the location of the tank and layout of the network. The equity in water supply can be improved in an existing network by staggered supply.
Point-of-Care System for Detection of Mycobacterium tuberculosis and Rifampin Resistance in Sputum Samples
Authors: Castan Pablo , de Pablo Alicia , Fernández-Romero Natalia , Rubio José Miguel , Cobb Benjamin D. , Mingorance Jesús , Toro Carlos 
Published: December 2013

ABSTRACT

Early detection of
Mycobacterium tuberculosis
complex (MTBC) and markers conveying drug resistance can have a beneficial impact on preventive public health actions. We describe here a new molecular point-of-care (POC) system, the Genedrive, which is based on simple sample preparation combined with PCR to detect MTBC and simultaneously detect mutation markers in the
rpoB
gene directly from raw sputum sample. Hybridization probes were used to detect the presence of the key mutations in codons 516, 526, and 531 of the
rpoB
gene. The sensitivities for MTBC and
rpoB
detection from sputum samples were assessed using model samples spiked with known numbers of bacteria prepared from liquid cultures of
M. tuberculosis
. The overall sensitivities were 90.8% (95% confidence interval [CI], 81, 96.5) for MTBC detection and 72.3% (95% CI, 59.8, 82.7) for
rpoB
detection. For samples containing ≥1,000 CFU/ml, the sensitivities were 100% for MTBC and 85.7% for
rpoB
detection, while for samples containing ≤100 CFU/ml, the sensitivities were 86.4% and 65.9% for MTBC and
rpoB
detection, respectively. The specificity was shown to be 100% (95% CI, 83.2, 100) for MTBC and
rpoB
. The clinical sputum samples were processed using the same protocol and showed good concordance with the data generated from the model. Tuberculosis-infected subjects with smear samples assessed as scanty or negative were detectable by the Genedrive system. In these paucibacillary patients, the performance of the Genedrive system was comparable to that of the GeneXpert assay. The characteristics of the Genedrive platform make it particularly useful for detecting MTBC and rifampin resistance in low-resource settings and for reducing the burden of tuberculosis disease.
Crustal evolution, intra-cratonic architecture and the metallogeny of an Archaean craton
Authors: Mole D. R. , Fiorentini M. L. , Cassidy K. F. , Kirkland C. L. , Thebaud N. , McCuaig T. C. , Doublier M. P. , Duuring P. , Romano S. S. , Maas R. , Belousova E. A. , Barnes S. J. , Miller J. 
Published: December 2013

Abstract
The generation of the Earth's continental crust modified the composition of the mantle and provided a stable, buoyant reservoir capable of capturing mantle material and ultimately preserving ore deposits. Within the continental crust, lithospheric architecture and associated cratonic margins are a first-order control on camp-scale mineralization. Here we show that the evolving crustal architecture of the Archaean Yilgarn Craton, Western Australia, played a key role in controlling the localization of camp-scale gold, iron and nickel mineralized systems. The age and source characteristics of Archaean lithosphere are heterogeneous in both space and time and are recorded by the varying Nd isotopic signature of crustal rocks. Spatial and temporal variations in isotopic character document the evolution of an intra-cratonic architecture through time, and in doing so map transient lithospheric discontinuities where gold, nickel and iron mineral systems were concentrated. Komatiite-hosted nickel deposits cluster into camps localized within young, juvenile crust at the isotopic margin with older lithosphere; orogenic gold systems are typically localized along major structures within juvenile crust; and banded iron formation (BIF)-hosted iron deposits are localized at the edge of, and within, older lithospheric blocks. Furthermore, this work shows that crustal evolution plays an important role in the development and localization of favourable sources of nickel, gold and iron by controlling the occurrence of thick BIFs, ultramafic lavas and fertile (juvenile) crust, respectively. Fundamentally, this study demonstrates that the lithospheric architecture of a craton can be effectively imaged by isotopic techniques and used to identify regions prospective for camp-scale mineralization.
Logical relations for a logical framework
Authors: Rabe Florian , Sojakova Kristina 
Published: December 2013

Logical relations are a central concept used to study various higher-order type theories and occur frequently in the proofs of a wide variety of meta-theorems. Besides extending the logical relation principle to more general languages, an important research question has been how to represent and thus verify logical relation arguments in logical frameworks.
We formulate a theory of logical relations for Dependent Type Theory (DTT) with β η-equality which guarantees that any valid logical relation satisfies the Basic Lemma. Our definition is syntactic and reflective in the sense that a relation at a type is represented as a DTT type family but also permits expressing certain semantic definitions. We use the Edinburgh Logical Framework (LF) incarnation of DTT and implement our notion of logical relations in the type-checker Twelf. This enables us to formalize and mechanically decide the validity of logical relation arguments. Furthermore, our implementation includes a module system so that logical relations can be built modularly. We validate our approach by formalizing and verifying several syntactic and semantic meta-theorems in Twelf. Moreover, we show how object languages encoded in DTT can inherit a notion of logical relation from the logical framework.
CUL4A Induces Epithelial–Mesenchymal Transition and Promotes Cancer Metastasis by Regulating ZEB1 Expression
Authors: Wang Yunshan , Wen Mingxin , Kwon Yongwon , Xu Yangyang , Liu Yueyong , Zhang Pengju , He Xiuquan , Wang Qin , Huang Yurong , Jen Kuang-Yu , LaBarge Mark A. , You Liang , Kogan Scott C. , Gray Joe W. , Mao Jian-Hua , Wei Guangwei 
Published: December 2013

Abstract
The ubiquitin ligase CUL4A has been implicated in tumorigenesis, but its contributions to progression and metastasis have not been evaluated. Here, we show that CUL4A is elevated in breast cancer as well as in ovarian, gastric, and colorectal tumors in which its expression level correlates positively with distant metastasis. CUL4A overexpression in normal or malignant human mammary epithelial cells increased their neoplastic properties in vitro and in vivo, markedly increasing epithelial–mesenchymal transition (EMT) and the metastatic capacity of malignant cells. In contrast, silencing CUL4A in aggressive breast cancer cells inhibited these processes. Mechanistically, we found that CUL4A modulated histone H3K4me3 at the promoter of the EMT regulatory gene ZEB1 in a manner associated with its transcription. ZEB1 silencing blocked CUL4A-driven proliferation, EMT, tumorigenesis, and metastasis. Furthermore, in human breast cancers, ZEB1 expression correlated positively with CUL4A expression and distant metastasis. Taken together, our findings reveal a pivotal role of CUL4A in regulating the metastatic behavior of breast cancer cells. Cancer Res; 74(2); 520–31. ©2013 AACR.
Cell-Autonomous and Non–Cell-Autonomous Mechanisms of Transformation by Amplified FGFR1 in Lung Cancer
Authors: Malchers Florian , Dietlein Felix , Schöttle Jakob , Lu Xin , Nogova Lucia , Albus Kerstin , Fernandez-Cuesta Lynnette , Heuckmann Johannes M. , Gautschi Oliver , Diebold Joachim , Plenker Dennis , Gardizi Masyar , Scheffler Matthias , Bos Marc , Seidel Danila , Leenders Frauke , Richters André , Peifer Martin , Florin Alexandra , Mainkar Prathama S. , Karre Nagaraju , Chandrasekhar Srivari , George Julie , Silling Steffi , Rauh Daniel , Zander Thomas , Ullrich Roland T. , Reinhardt H. Christian , Ringeisen Francois , Büttner Reinhard , Heukamp Lukas C. , Wolf Jürgen , Thomas Roman K. 
Published: December 2013

Abstract
The 8p12 locus (containing the FGFR1 tyrosine kinase gene) is frequently amplified in squamous cell lung cancer. However, it is currently unknown which of the 8p12-amplified tumors are also sensitive to fibroblast growth factor receptor (FGFR) inhibition. We found that, in contrast with other recurrent amplifications, the 8p12 region included multiple centers of amplification, suggesting marked genomic heterogeneity. FGFR1-amplified tumor cells were dependent on FGFR ligands in vitro and in vivo. Furthermore, ectopic expression of FGFR1 was oncogenic, which was enhanced by expression of MYC. We found that MYC was coexpressed in 40% of FGFR1-amplified tumors. Tumor cells coexpressing MYC were more sensitive to FGFR inhibition, suggesting that patients with FGFR1-amplified and MYC-overexpressing tumors may benefit from FGFR inhibitor therapy. Thus, both cell-autonomous and non–cell-autonomous mechanisms of transformation modulate FGFR dependency in FGFR1-amplified lung cancer, which may have implications for patient selection for treatment with FGFR inhibitors.
Significance: Amplification of FGFR1 is one of the most frequent candidate targets in lung cancer. Here, we show that multiple factors affect the tumorigenic potential of FGFR1, thus providing clinical hypotheses for refinement of patient selection. Cancer Discov; 4(2); 246–57. ©2013 AACR.
See related commentary by Lockwood and Politi, p. 152
This article is highlighted in the In This Issue feature, p. 131
Dynamic Permeability and Quantitative Susceptibility
Authors: Mikati Abdul Ghani , Tan Huan , Shenkar Robert , Li Luying , Zhang Lingjiao , Guo Xiaodong , Larsson Henrik B.W. , Shi Changbin , Liu Tian , Wang Yi , Shah Akash , Edelman Robert R. , Christoforidis Gregory , Awad Issam 
Published: December 2013

Background and Purpose—
Hyperpermeability and iron deposition are 2 central pathophysiological phenomena in human cerebral cavernous malformation (CCM) disease. Here, we used 2 novel MRI techniques to establish a relationship between these phenomena.

Methods—
Subjects with CCM disease (4 sporadic and 17 familial) underwent MRI imaging using the dynamic contrast-enhanced quantitative perfusion and quantitative susceptibility mapping techniques that measure hemodynamic factors of vessel leak and iron deposition, respectively, previously demonstrated in CCM disease. Regions of interest encompassing the CCM lesions were analyzed using these techniques.

Results—

Susceptibility measured by quantitative susceptibility mapping was positively correlated with permeability of lesions measured using dynamic contrast-enhanced quantitative perfusion (
r
=0.49;
P
≤0.0001). The correlation was not affected by factors, including lesion volume, contrast agent, and the use of statin medication. Susceptibility was correlated with lesional blood volume (
r
=0.4;
P
=0.0001) but not with lesional blood flow.

Conclusions—
The correlation between quantitative susceptibility mapping and dynamic contrast-enhanced quantitative perfusion suggests that the phenomena of permeability and iron deposition are related in CCM; hence, more leaky lesions also manifest a more cumulative iron burden. These techniques might be used as biomarkers to monitor the course of this disease and the effect of therapy.
The Madden–Julian Oscillation’s Impacts on Worldwide Tropical Cyclone Activity
Authors: Klotzbach Philip J. 
Published: December 2013

Abstract
The 30–60-day Madden–Julian oscillation (MJO) has been documented in previous research to impact tropical cyclone (TC) activity for various tropical cyclone basins around the globe. The MJO modulates large-scale convective activity throughout the tropics, and concomitantly modulates other fields known to impact tropical cyclone activity such as vertical wind shear, midlevel moisture, vertical motion, and sea level pressure. The Atlantic basin typically shows the smallest modulations in most large-scale fields of any tropical cyclone basins; however, it still experiences significant modulations in tropical cyclone activity. The convectively enhanced phases of the MJO and the phases immediately following them are typically associated with above-average tropical cyclone frequency for each of the global TC basins, while the convectively suppressed phases of the MJO are typically associated with below-average tropical cyclone frequency. The number of rapid intensification periods are also shown to increase when the convectively enhanced phase of the MJO is impacting a particular tropical cyclone basin.
Improvement of in-hospital telemetry monitoring in coronary care units: An intervention study for achieving optimal electrode placement and attachment, hygiene and delivery of critical information to patients
Authors: Pettersen Trond R , Fålun Nina , Norekvål Tone M 
Published: December 2013

Background: In-hospital telemetry monitoring is important for diagnosis and treatment of patients at risk of developing life-threatening arrhythmias. It is widely used in critical and non-critical care wards. Nurses are responsible for correct electrode placement, thus ensuring optimal quality of the monitoring. The aims of this study were to determine whether a complex educational intervention improves (a) optimal electrode placement, (b) hygiene, and (c) delivery of critical information to patients (reason for monitoring, limitations in cellular phone use, and not to leave the ward without informing a member of staff). Methods: A prospective interventional study design was used, with data collection occurring over two six-week periods: before implementation of the intervention ( n=201) and after the intervention ( n=165). Standard abstraction forms were used to obtain data on patients’ clinical characteristics, and 10 variables related to electrode placement and attachment, hygiene and delivery of critical information. Results: At pre-intervention registration, 26% of the electrodes were misplaced. Twelve per cent of the patients received information about limiting their cellular phone use while monitored, 70% were informed of the purpose of monitoring, and 71% used a protective cover for their unit. Post-intervention, outcome measures for the three variables improved significantly: use of protective cover ( p<0.001), information about the purpose of monitoring ( p=0.005) and information about limitations in cellular phone use ( p=0.003). Nonetheless, 23% of the electrodes were still misplaced. Conclusion: The study highlights the need for better, continued education for in-hospital telemetry monitoring in coronary care units, and other units that monitor patients with telemetry.
Evaluating the protective efficacy of a trivalent vaccine containing Akabane virus, Aino virus and Chuzan virus against Schmallenberg virus infection
Authors: Hechinger Silke , Wernike Kerstin , Beer Martin 
Published: December 2013

Abstract
Schmallenberg virus (SBV), an arthropod borne pathogen, spread rapidly throughout the majority of Europe since 2011. It can cause a febrile disease, milk drop, diarrhea, and fetal malformation in ruminants. SBV, a member of the Simbu serogroup within the genus Orthobunyavirus, is closely related to Akabane virus (AKAV) and Aino virus (AINOV) among others. In the present study, 4 Holstein-Friesian calves were immunized twice four weeks apart with a multivalent, inactivated vaccine against AKAV and AINOV. Another 4 calves were kept as unvaccinated controls. All animals were clinically, serologically and virologically examined before and after challenge infection with SBV. AKAV- and AINOV-specific neutralizing antibodies were detected one week before challenge infection, while SBV-specific antibodies were detectable only thereafter. SBV genome was detected in all vaccinated animals and 3 out of 4 controls in serum samples taken after challenge infection. In conclusion, the investigated vaccine was not able to prevent an SBV-infection. Thus, vaccines for other related Simbu serogroup viruses can not substitute SBV-specific vaccines as an instrument for disease control.
Viral quasispecies inference from 454 pyrosequencing
Authors: Poh Wan-Ting , Xia Eryu , Chin-inmanu Kwanrutai , Wong Lai-Ping , Cheng Anthony Youzhi , Malasit Prida , Suriyaphol Prapat , Teo Yik-Ying , Ong Rick Twee-Hee 
Published: December 2013

Abstract

Background
Many potentially life-threatening infectious viruses are highly mutable in nature. Characterizing the fittest variants within a quasispecies from infected patients is expected to allow unprecedented opportunities to investigate the relationship between quasispecies diversity and disease epidemiology. The advent of next-generation sequencing technologies has allowed the study of virus diversity with high-throughput sequencing, although these methods come with higher rates of errors which can artificially increase diversity.

Results
Here we introduce a novel computational approach that incorporates base quality scores from next-generation sequencers for reconstructing viral genome sequences that simultaneously infers the number of variants within a quasispecies that are present. Comparisons on simulated and clinical data on dengue virus suggest that the novel approach provides a more accurate inference of the underlying number of variants within the quasispecies, which is vital for clinical efforts in mapping the within-host viral diversity. Sequence alignments generated by our approach are also found to exhibit lower rates of error.

Conclusions
The ability to infer the viral quasispecies colony that is present within a human host provides the potential for a more accurate classification of the viral phenotype. Understanding the genomics of viruses will be relevant not just to studying how to control or even eradicate these viral infectious diseases, but also in learning about the innate protection in the human host against the viruses.
Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
Authors: Getsin Ilya , Nalbandian Gina H , Yee Daniel C , Vastermark Ake , Paparoditis Philipp CG , Reddy Vamsee S , Saier Milton H 
Published: December 2013

Abstract

Background
Two of the largest fully sequenced prokaryotic genomes are those of the actinobacterium, Streptomyces coelicolor (Sco), and the δ-proteobacterium, Myxococcus xanthus (Mxa), both differentiating, sporulating, antibiotic producing, soil microbes. Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa.

Results
Surprisingly, Sco has 93% more identifiable transport proteins than Mxa. This is because Sco has amplified several specific types of its transport protein genes, while Mxa has done so to a much lesser extent. Amplification is substrate- and family-specific. For example, Sco but not Mxa has amplified its voltage-gated ion channels but not its aquaporins and mechano-sensitive channels. Sco but not Mxa has also amplified drug efflux pumps of the DHA2 Family of the Major Facilitator Superfamily (MFS) (49 versus 6), amino acid transporters of the APC Family (17 versus 2), ABC-type sugar transport proteins (85 versus 6), and organic anion transporters of several families. Sco has not amplified most other types of transporters. Mxa has selectively amplified one family of macrolid exporters relative to Sco (16 versus 1), consistent with the observation that Mxa makes more macrolids than does Sco.

Conclusions
Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently. A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives. The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.
High-frequency stimulation of the subthalamic nucleus modifies the expression of vesicular glutamate transporters in basal ganglia in a rat model of Parkinson’s disease
Authors: Favier Mathieu , Carcenac Carole , Drui Guillaume , Boulet Sabrina , El Mestikawy Salah , Savasta Marc 
Published: December 2013

AbstractBackgroundIt has been suggested that glutamatergic system hyperactivity may be related to the pathogenesis of Parkinson’s disease (PD). Vesicular glutamate transporters (VGLUT1-3) import glutamate into synaptic vesicles and are key anatomical and functional markers of glutamatergic excitatory transmission. Both VGLUT1 and VGLUT2 have been identified as definitive markers of glutamatergic neurons, but VGLUT 3 is also expressed by non glutamatergic neurons. VGLUT1 and VGLUT2 are thought to be expressed in a complementary manner in the cortex and the thalamus (VL/VM), in glutamatergic neurons involved in different physiological functions. Chronic high-frequency stimulation (HFS) of the subthalamic nucleus (STN) is the neurosurgical therapy of choice for the management of motor deficits in patients with advanced PD. STN-HFS is highly effective, but its mechanisms of action remain unclear. This study examines the effect of STN-HFS on VGLUT1-3 expression in different brain nuclei involved in motor circuits, namely the basal ganglia (BG) network, in normal and 6-hydroxydopamine (6-OHDA) lesioned rats.ResultsHere we report that: 1) Dopamine(DA)-depletion did not affect VGLUT1 and VGLUT3 expression but significantly decreased that of VGLUT2 in almost all BG structures studied; 2) STN-HFS did not change VGLUT1-3 expression in the different brain areas of normal rats while, on the contrary, it systematically induced a significant increase of their expression in DA-depleted rats and 3) STN-HFS reversed the decrease in VGLUT2 expression induced by the DA-depletion.ConclusionsThese results show for the first time a comparative analysis of changes of expression for the three VGLUTs induced by STN-HFS in the BG network of normal and hemiparkinsonian rats. They provide evidence for the involvement of VGLUT2 in the modulation of BG cicuits and in particular that of thalamostriatal and thalamocortical pathways suggesting their key role in its therapeutic effects for alleviating PD motor symptoms.