bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiscale Simulation of Knudsen-Pump Channel Flows
Authors: Patronis Alexander , Lockerby Duncan A. 
Published: December 2014

This paper describes the development and application of an efficient hybrid continuum-molecular approach for simulating non-isothermal, low-speed, internal rarefied gas flows, and its application to flows in Knudsen compressors. The method is an extension of the hybrid approach presented by Patronis et al. (2013) [J. Comp. Phys., 255, pp 558–571], which is based on the framework originally proposed by Borg et al. (2013) [J. Comp. Phys., 233, pp 400–413] for the simulation of micro/nano flows of high-aspect-ratio.
The efficiency of the multiscale method allows the investigation of alternative Knudsen-compressor configurations to be undertaken. We characterise the effectiveness of the single-stage Knudsen-compressor channel by the pressure differential that can be achieved between two connected reservoirs, for a given temperature difference. Our multiscale simulations indicate that the efficiency of the single-stage Knudsen compressor is robust to modifications of the streamwise temperature variation.
A new quantitative image analysis method for improving breast cancer diagnosis using DCE‐MRI examinations
Authors: Yang Qian , Li Lihua , Zhang Juan , Shao Guoliang , Zheng Bin 
Published: December 2014

Purpose:To investigate the feasibility of applying a new quantitative image analysis method to improve breast cancer diagnosis performance using dynamic contrast enhanced magnetic resonance imaging (DCE‐MRI) by integrating background parenchymal enhancement (BPE) features into the decision making process.Methods:A dataset involving 115 DCE‐MRI examinations was used in this study. Each examination depicts one identified suspicious breast tumor. Among them, 75 cases were verified as malignant and 40 were benign by the biopsy results. A computer‐aided detection scheme was applied to segment breast regions and the suspicious tumor depicted on the sequentially scanned MR images of each case. We then computed 18 kinetic features in which 6 were computed from the segmented breast tumor and 12 were BPE features from the background parenchymal regions (excluding the tumor). Support vector machine (SVM) based statistical learning classifiers were trained and optimized using different combinations of features that were computed either from tumor only or from both tumor and BPE. Each SVM was tested using a leave‐one‐case‐out validation method and assessed using an area under the receiver operating characteristic curve (AUC).Results:When using kinetic features computed from tumors only, the maximum AUC is 0.865 ± 0.035. After fusing with the BPE features, AUC increased to 0.919 ± 0.029. At 90% specificity, the tumor classification sensitivity increased by 13.2%.Conclusions:The proposed quantitative BPE features provide valuable supplementary information to the kinetic features of breast tumors in DCE‐MRI. Their addition to computer‐aided diagnosis methodologies could improve breast cancer diagnosis based on DCE‐MRI examinations.
Impact of CT attenuation correction method on quantitative respiratory‐correlated (4D) PET/CT imaging
Authors: Nyflot Matthew J. , Lee Tzu‐Cheng , Alessio Adam M. , Wollenweber Scott D. , Stearns Charles W. , Bowen Stephen R. , Kinahan Paul E. 
Published: December 2014

Purpose:Respiratory‐correlated positron emission tomography (PET/CT) 4D PET/CT is used to mitigate errors from respiratory motion; however, the optimal CT attenuation correction (CTAC) method for 4D PET/CT is unknown. The authors performed a phantom study to evaluate the quantitative performance of CTAC methods for 4D PET/CT in the ground truth setting.Methods:A programmable respiratory motion phantom with a custom movable insert designed to emulate a lung lesion and lung tissue was used for this study. The insert was driven by one of five waveforms: two sinusoidal waveforms or three patient‐specific respiratory waveforms. 3DPET and 4DPET images of the phantom under motion were acquired and reconstructed with six CTAC methods: helical breath‐hold (3DHEL), helical free‐breathing (3DMOT), 4D phase‐averaged (4DAVG), 4D maximum intensity projection (4DMIP), 4D phase‐matched (4DMATCH), and 4D end‐exhale (4DEXH) CTAC. Recovery of SUVmax, SUVmean, SUVpeak, and segmented tumor volume was evaluated as RCmax, RCmean, RCpeak, and RCvol, representing percent difference relative to the static ground truth case. Paired Wilcoxon tests and Kruskal–Wallis ANOVA were used to test for significant differences.Results:For 4DPET imaging, the maximum intensity projection CTAC produced significantly more accurate recovery coefficients than all other CTAC methods (p < 0.0001 over all metrics). Over all motion waveforms, ratios of 4DMIP CTAC recovery were 0.2 ± 5.4, −1.8 ± 6.5, −3.2 ± 5.0, and 3.0 ± 5.9 for RCmax, RCpeak, RCmean, and RCvol. In comparison, recovery coefficients for phase‐matched CTAC were −8.4 ± 5.3, −10.5 ± 6.2, −7.6 ± 5.0, and −13.0 ± 7.7 for RCmax, RCpeak, RCmean, and RCvol. When testing differences between phases over all CTAC methods and waveforms, end‐exhale phases were significantly more accurate (p = 0.005). However, these differences were driven by the patient‐specific respiratory waveforms; when testing patient and sinusoidal waveforms separately, patient waveforms were significantly different between phases (p < 0.0001) while the sinusoidal waveforms were not significantly different (p = 0.98). When considering only the subset of 4DMATCH images that corresponded to the end‐exhale image phase, 4DEXH, mean and interquartile range were similar to 4DMATCH but variability was considerably reduced.Conclusions:Comparative advantages in accuracy and precision of SUV metrics and segmented volumes were demonstrated with the use of the maximum intensity projection and end‐exhale CT attenuation correction. While respiratory phase‐matched CTAC should in theory provide optimal corrections, image artifacts and differences in implementation of 4DCT and 4DPET sorting can degrade the benefit of this approach. These results may be useful to guide the implementation, analysis, and development of respiratory‐correlated thoracic PET/CT in the radiation oncology and diagnostic settings.
Leptin Receptor Mutation Results in Defective Neutrophil Recruitment to the Colon during Entamoeba histolytica Infection
Authors: Naylor Caitlin , Burgess Stacey , Madan Rajat , Buonomo Erica , Razzaq Khadija , Ralston Katherine , Petri William A. 
Published: December 2014

ABSTRACTAmebiasis is an enteric infection caused byEntamoeba histolytica, with symptoms ranging in severity from asymptomatic colonization to dysentery. Humans with the Q223R leptin receptor mutation have increased susceptibility to amebiasis, but the mechanism has been unclear. Using a mouse model expressing the mutation, we tested the impact of the Q223R mutation on the innate immune response toE. histolyticainfection. The 223R mutation resulted in delayed clearance of amebae from the cecum, as had been previously observed. We found that neutrophil influx to the site of the infection was reduced 12 h after infection in 223R mice. Depletion of neutrophils with anti-Ly6G monoclonal antibody increased susceptibility of wild-type mice to infection, supporting the importance of neutrophils in innate defense. Leptin expression was increased in the cecum byE. histolyticainfection, suggesting that leptin could serve as a homing signal for neutrophils to the gut. Interestingly, neutrophils from mice with the 223R mutation had diminished chemotaxis toward leptin. This impaired chemotaxis likely explained the reduced gut infiltration of neutrophils. The newly recognized effect of the leptin receptor Q223R mutation on neutrophil chemotaxis and the impact of this mutation on multiple infectious diseases suggest a broader impact of this mutation on susceptibility to disease.IMPORTANCEThe Q223R leptin receptor mutation results in increased susceptibility of children and adults toE. histolytica, one of the leading causes of diarrhea morbidity and mortality in children of the developing world. Here we show that the mutation results in reduced neutrophil infiltration to the site of infection. This decreased infiltration is likely due to the mutation’s impact on neutrophil chemotaxis toward leptin, an inflammatory agent upregulated in the cecum after infection. The significance of this work thus extends beyond understandingE. histolyticasusceptibility by also providing insight into the potential impact of leptin on neutrophil function in other states of altered leptin signaling, which include both malnutrition and obesity.
Sirtuins Are Evolutionarily Conserved Viral Restriction Factors
Authors: Koyuncu Emre , Budayeva Hanna G. , Miteva Yana V. , Ricci Dante P. , Silhavy Thomas J. , Shenk Thomas , Cristea Ileana M. 
Published: December 2014

ABSTRACTThe seven human sirtuins are a family of ubiquitously expressed and evolutionarily conserved NAD+-dependent deacylases/mono-ADP ribosyltransferases that regulate numerous cellular and organismal functions, including metabolism, cell cycle, and longevity. Here, we report the discovery that all seven sirtuins have broad-range antiviral properties. We demonstrate that small interfering RNA (siRNA)-mediated knockdown of individual sirtuins and drug-mediated inhibition of sirtuin enzymatic activity increase the production of virus progeny in infected human cells. This impact on virus growth is observed for both DNA and RNA viruses. Importantly, sirtuin-activating drugs inhibit the replication of diverse viruses, as we demonstrate for human cytomegalovirus, a slowly replicating DNA virus, and influenza A (H1N1) virus, an RNA virus that multiplies rapidly. Furthermore, sirtuin defense functions are evolutionarily conserved, since CobB, the sirtuin homologue inEscherichia coli, protects against bacteriophages. Altogether, our findings establish sirtuins as broad-spectrum and evolutionarily conserved components of the immune defense system, providing a framework for elucidating a new set of host cell defense mechanisms and developing sirtuin modulators with antiviral activity.IMPORTANCEWe live in a sea of viruses, some of which are human pathogens. These pathogenic viruses exhibit numerous differences: DNA or RNA genomes, enveloped or naked virions, nuclear or cytoplasmic replication, diverse disease symptoms, etc. Most antiviral drugs target specific viral proteins. Consequently, they often work for only one virus, and their efficacy can be compromised by the rapid evolution of resistant variants. There is a need for the identification of host proteins with broad-spectrum antiviral functions, which provide effective targets for therapeutic treatments that limit the evolution of viral resistance. Here, we report that sirtuins present such an opportunity for the development of broad-spectrum antiviral treatments, since our findings highlight these enzymes as ancient defense factors that protect against a variety of viral pathogens.
A national survey of the diagnosis and management of suspected ventilator-associated pneumonia
Authors: Browne Emma , Hellyer Thomas P , Baudouin Simon V , Conway Morris Andrew , Linnett Vanessa , McAuley Danny F , Perkins Gavin D , Simpson A John 
Published: December 2014

BackgroundVentilator-associated pneumonia (VAP) affects up to 20% of patients admitted to intensive care units (ICU). It is associated with increased morbidity, mortality and healthcare costs. Despite published guidelines, variability in diagnosis and management exists, the extent of which remains unclear. We sought to characterise consultant opinions surrounding diagnostic and management practice for VAP in the UK.MethodsAn online survey was sent to all consultant members of the UK Intensive Care Society (n=∼1500). Data were collected regarding respondents’ individual practice in the investigation and management of suspected VAP including use of diagnostic criteria, microbiological sampling, chest X-ray (CXR), bronchoscopy and antibiotic treatments.Results339 (23%) responses were received from a broadly representative spectrum of ICU consultants. All respondents indicated that microbiological confirmation should be sought, the majority (57.8%) stating they would take an endotracheal aspirate prior to starting empirical antibiotics. Microbiology reporting services were described as qualitative only by 29.7%. Only 17% of respondents had access to routine reporting of CXRs by a radiologist. Little consensus exists regarding technique for bronchoalveolar lavage (BAL) with the reported volume of saline used ranging from 5 to 500 mL. 24.5% of consultants felt inadequately trained in bronchoscopy.ConclusionsThere is wide variability in the approach to diagnosis and management of VAP among UK consultants. Such variability challenges the reliability of the diagnosis of VAP and its reported incidence as a performance indicator in healthcare systems. The data presented suggest increased radiological and microbiological support, and standardisation of BAL technique, might improve this situation.
Compensatory Smoking from Gradual and Immediate Reduction in Cigarette Nicotine Content
Authors: Hatsukami Dorothy K. , Donny Eric C. , Koopmeiners Joseph S. , Benowitz Neal L. 
Published: December 2014

Abstract
Reducing the addictiveness of cigarettes by reducing their nicotine content can potentially have a profound impact on public health. Two different approaches to nicotine reduction have been proposed: gradual and immediate. To determine if either of these approaches results in significant compensatory smoking behavior, which might lead to safety concerns, we performed a secondary analysis of data from studies that have utilized these two approaches. The number of cigarettes smoked per day, carbon monoxide exposure, and cotinine levels in plasma or urine were assessed while participants smoked reduced nicotine content cigarettes and compared with when they smoked their usual brand cigarettes. The results showed that in general, these two approaches led to minimal compensatory smoking and reduced levels of cotinine over the course of the experimental period, suggesting that neither of these approaches poses a major safety concern. Cancer Epidemiol Biomarkers Prev; 24(2); 472–6. ©2014 AACR.
Tobacco and Alcohol in Relation to Male Breast Cancer: An Analysis of the Male Breast Cancer Pooling Project Consortium
Authors: Cook Michael B. , Guénel Pascal , Gapstur Susan M. , van den Brandt Piet A. , Michels Karin B. , Casagrande John T. , Cooke Rosie , Van Den Eeden Stephen K. , Ewertz Marianne , Falk Roni T. , Gaudet Mia M. , Gkiokas George , Habel Laurel A. , Hsing Ann W. , Johnson Kenneth , Kolonel Laurence N. , La Vecchia Carlo , Lynge Elsebeth , Lubin Jay H. , McCormack Valerie A. , Negri Eva , Olsson Håkan , Parisi Dominick , Petridou Eleni Th. , Riboli Elio , Sesso Howard D. , Swerdlow Anthony , Thomas David B. , Willett Walter C. , Brinton Louise A. 
Published: December 2014

AbstractBackground: The etiology of male breast cancer is poorly understood, partly due to its relative rarity. Although tobacco and alcohol exposures are known carcinogens, their association with male breast cancer risk remains ill-defined.Methods: The Male Breast Cancer Pooling Project consortium provided 2,378 cases and 51,959 controls for analysis from 10 case–control and 10 cohort studies. Individual participant data were harmonized and pooled. Unconditional logistic regression was used to estimate study design–specific (case–control/cohort) ORs and 95% confidence intervals (CI), which were then combined using fixed-effects meta-analysis.Results: Cigarette smoking status, smoking pack-years, duration, intensity, and age at initiation were not associated with male breast cancer risk. Relations with cigar and pipe smoking, tobacco chewing, and snuff use were also null. Recent alcohol consumption and average grams of alcohol consumed per day were also not associated with risk; only one subanalysis of very high recent alcohol consumption (&gt;60 g/day) was tentatively associated with male breast cancer (ORunexposed referent = 1.29; 95% CI, 0.97–1.71; OR&gt;0–&lt;7 g/day referent = 1.36; 95% CI, 1.04–1.77). Specific alcoholic beverage types were not associated with male breast cancer. Relations were not altered when stratified by age or body mass index.Conclusions: In this analysis of the Male Breast Cancer Pooling Project, we found little evidence that tobacco and alcohol exposures were associated with risk of male breast cancer.Impact: Tobacco and alcohol do not appear to be carcinogenic for male breast cancer. Future studies should aim to assess these exposures in relation to subtypes of male breast cancer. Cancer Epidemiol Biomarkers Prev; 24(3); 520–31. ©2014 AACR.
Prevalence of hepatitis C virus infection among pregnant women in a rural district in Egypt
Authors: Khamis Hossam Hassan , Farghaly Azza Galal , Shatat Hanan Zakaria , El-Ghitany Engy Mohamed 
Published: December 2014

Background Egypt has the highest prevalence of hepatitis C virus (HCV) infection in the world. Screening of HCV during pregnancy is not as routinely done in Egypt compared with many other countries, although pregnancy is an important period where screening of HCV infection is important owing to low immunity, the possibility of vertical transmission and possible horizontal transmission to the baby or other household contacts at a later stage. Aim To determine the seroprevalence of HCV antibodies (HCV-Ab) and risk factors associated with infection among pregnant women in Egypt. Patients and Method A total of 360 pregnant women visiting the healthcare units for routine antenatal care were tested using third generation ELISA test for detection of HCV-Ab. Polymerase chain reaction (PCR) was done for seropositive cases. Results A total of 6.1% (22/360) of pregnant women were HCV seropositive; of them only 45% (9/20) had viraemia. Risk factors were their age, the age of their husband and the presence of chronic liver disease in the husband. Conclusion The prevalence of HCV infection in pregnant women in Egypt appears to be lower than previously reported. The detected risk factors are old age of the pregnant women and their husbands, and chronic liver disease in the husbands. None of the other known risk factors was found to be significantly associated with HCV infection in pregnant women.
The value of post-operative radiographs in clinical management of AO type A distal radius fractures
Authors: Huffaker S. , Earp B. E. , Blazar P. E. 
Published: December 2014

The value of post-operative radiographs following stabilization of Arbeitsgemeinschaft für Osteosynthesefragen (AO) type A distal radius fractures with volar locking plates is unclear. We examined the value of post-operative radiographs of type A fractures treated with volar locking plates. A retrospective review was performed on all AO type A distal radius fractures treated with volar locking plates between 2007 and 2010 at two institutions. A total of 158 patients receiving 446 sets of post-operative radiographs were included. Reviewing all clinic, emergency, and operative notes, we found that 94% of radiographs were performed as routine follow-up, with no set of post-operative radiographs demonstrating findings of hardware/fracture site complications. All cases requiring further workup or interventions were heralded by patient complaints. Routine post-operative radiographs following volar locking plates for extra-articular distal radius fractures did not demonstrably alter clinical decision making; this is an area where a reduction in resource utilization would not seem to alter clinical quality care, but further studies with larger populations are needed to establish the incidence of radiographic problems prior to symptom occurrence. Level of Evidence: Diagnostic III
Visualization of bone marrow monocyte mobilization using Cx3cr1gfp/+Flt3L−/− reporter mouse by multiphoton intravital microscopy
Authors: Evrard Maximilien , Chong Shu Zhen , Devi Sapna , Chew Weng Keong , Lee Bernett , Poidinger Michael , Ginhoux Florent , Tan Suet Mien , Ng Lai Guan 
Published: December 2014

Abstract
Monocytes are innate immune cells that play critical roles in inflammation and immune defense. A better comprehension of how monocytes are mobilized and recruited is fundamental to understand their biologic role in disease and steady state. The BM represents a major “checkpoint” for monocyte homeostasis, as it is the primary site for their production and release. Our study determined that the Cx3cr1gfp/+ mouse strain is currently the most ideal model for the visualization of monocyte behavior in the BM by multiphoton intravital microscopy. However, we observed that DCs are also labeled with high levels of GFP and thus, interfere with the accuracy of monocyte tracking in vivo. Hence, we generated a Cx3cr1gfp/+Flt3L−/− reporter mouse and showed that whereas monocyte numbers were not affected, DC numbers were reduced significantly, as DCs but not monocytes depend on Flt3 signaling for their development. We thus verified that mobilization of monocytes from the BM in Cx3cr1gfp/+Flt3L−/− mice is intact in response to LPS. Collectively, our study demonstrates that the Cx3cr1gfp/+Flt3L−/− reporter mouse model represents a powerful tool to visualize monocyte activities in BM and illustrates the potential of a Cx3cr1gfp/+-based, multifunctionality fluorescence reporter approach to dissect monocyte function in vivo.
Subdivisions of the adult zebrafish pallium based on molecular marker analysis
Authors: Ganz Julia , Kroehne Volker , Freudenreich Dorian , Machate Anja , Geffarth Michaela , Braasch Ingo , Kaslin Jan , Brand Michael 
Published: December 2014

Background: The telencephalon shows a remarkable structural diversity among vertebrates. In particular, the everted telencephalon of ray-finned fishes has a markedly different morphology compared to the evaginated telencephalon of all other vertebrates. This difference in development has hampered the comparison between different areas of the pallium of ray-finned fishes and the pallial nuclei of all other vertebrates. Various models of homology between pallial subdivisions in ray-finned fishes and the pallial nuclei in tetrapods have been proposed based on connectional, neurochemical, gene expression and functional data. However, no consensus has been reached so far. In recent years, the analysis of conserved developmental marker genes has assisted the identification of homologies for different parts of the telencephalon among several tetrapod species.Results: We have investigated the gene expression pattern of conserved marker genes in the adult zebrafish (Danio rerio)pallium to identify pallial subdivisions and their homology to pallial nuclei in tetrapods. Combinatorial expression analysis ofascl1a,eomesa,emx1,emx2,emx3, and Prox1 identifies four main divisions in the adult zebrafish pallium. Within these subdivisions, we propose that Dm is homologous to the pallial amygdala in tetrapods and that the dorsal subdivision of Dl is homologous to part of the hippocampal formation in mouse. We have complemented this analysis be examining the gene expression ofemx1,emx2andemx3in the zebrafish larval brain.Conclusions: Based on our gene expression data, we propose a new model of subdivisions in the adult zebrafish pallium and their putative homologies to pallial nuclei in tetrapods. Pallial nuclei control sensory, motor, and cognitive functions, like memory, learning and emotion. The identification of pallial subdivisions in the adult zebrafish and their homologies to pallial nuclei in tetrapods will contribute to the use of the zebrafish system as a model for neurobiological research and human neurodegenerative diseases.