bluuebunny/crossref_metadata_2025 huggingface dataset:
A New Niche for Anoxygenic Phototrophs as Endoliths
Authors: Roush Daniel , Couradeau Estelle , Guida Brandon , Neuer Susanne , Garcia-Pichel Ferran
Published: December 2017

Anoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. Anad hocphylogenetic classification of these sequences enabled us to refine the assignments more stringently. Even then, all locations contained such putative APBs, often reaching a significant proportion of all phototrophic sequences. In fact, in some 20% of samples, their contribution exceeded that of oxygenic phototrophs, previously regarded as the major type of endolithic microbe in carbonates. The communities contained representatives of APBs in theChloroflexales, various proteobacterial groups, andChlorobi. The most abundant phylotypes varied with geography: on Isla de Mona,RoseiflexusandChlorothrix-related phylotypes dominated, whereas those related toErythrobacterwere the most common in Menorca. The presence of active populations of APBs was corroborated through an analysis of photopigments: bacteriochlorophylls were detected in all samples, bacteriochlorophyllcandabeing most abundant. We discuss the potential metabolism and geomicrobial roles of endolithic APBs. Phylogenetic inference suggests that APBs may be playing a role as photoheterotrophs, adding biogeochemical complexity to our understanding of such communities. Given the global extent of coastal carbonate platforms, they likely represent a very large and unexplored habitat for APBs.

IMPORTANCEEndolithic microbial communities from carbonates, which have been explored for over 2 centuries in predominantly naturalistic studies, were thought to be primarily composed of eukaryotic algae and cyanobacteria. Our report represents a paradigm shift in this regard, at least for the marine environment, demonstrating the presence of ubiquitous and abundant populations of APBs in this habitat. It raises questions about the role of these organisms in the geological dynamics of coastal carbonates, including coral reefs.
The Emergency Medical Service Microbiome
Authors: Hudson Andrew J. , Glaister Graeme D. , Wieden Hans-Joachim
Published: December 2017

Emergency medical services (EMS) personnel are an integral component of the health care framework and function to transport patients from various locations to and between care facilities. In addition to physical injury, EMS personnel are expected to be at high risk to acquire and transmit health care-associated infections (HAIs) in the workplace. However, currently, little is known about EMS biosafety risk factors and the epidemiological contribution of EMS to pathogen transmission within and outside the health care sector. Health care facility microbiomes contain diverse bacterial, fungal, and viral pathogens that cause over 1.7 million HAIs each year in the United States alone. While hospital microbiomes have been relatively well studied, there is scant information about EMS infrastructure and equipment microbiomes or the role(s) they play in HAI transmission between health care facilities. We review recent literature investigating the microbiome of ambulances and other EMS service facilities which consistently identify antibiotic-resistant pathogens causing HAIs, including methicillin-resistant
Staphylococcus aureus
(MRSA), vancomycin-resistant
Enterococcus
, and
Klebsiella pneumoniae
. Our review provides evidence that EMS microbiomes are dynamic and important pathogen reservoirs, and it underscores the need for more widespread and in-depth microbiome studies to elucidate patterns of pathogen transmission. We discuss emerging DNA sequencing technologies and other methods that can be applied to characterize and mitigate EMS biosafety risks in the future. Understanding the complex interplay between EMS and hospital microbiomes will provide key insights into pathogen transmission mechanisms and identify strategies to minimize HAIs and community infection.
Genome Sequences of 19 Rhodococcus erythropolis Cluster CA Phages
Authors: Bonilla J. Alfred , Isern Sharon , Findley Ann M. , Klyczek Karen K. , Michael Scott F. , Saha Margaret S. , Buchser William J. , Forsyth Mark H. , Paudel Sudip , Gissendanner Christopher R. , Wiedemeier Allison M. D. , Alonzo Fernanda L. ,   University of Wisconsin–River Falls SEA-PHAGES,   Florida Gulf Coast University SEA-PHAGES,   University of Louisiana–Monroe SEA-PHAGES,   College of William & Mary SEA-PHAGES, Garlena Rebecca A. , Russell Daniel A. , Pope Welkin H. , Cresawn Steven G. , Jacobs-Sera Deborah , Hatfull Graham F.
Published: December 2017

We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using
Rhodococcus erythropolis
as a host. All of the phages are
Siphoviridae
, have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity.
Full-Length Genome Sequence of a Chikungunya Virus Isolate from the 2017 Autochthonous Outbreak, Lazio Region, Italy
Authors: Carletti Fabrizio , Marsella Patrizia , Colavita Francesca , Meschi Silvia , Lalle Eleonora , Bordi Licia , Di Lallo Domenico , Panella Vincenzo , Di Caro Antonino , Nicastri Emanuele , Scognamiglio Paola , Lanini Simone , Vairo Francesco , Capobianchi Maria R. , Ippolito Giuseppe , Castilletti Concetta
Published: December 2017

We report here the genome sequence of a human chikungunya virus isolate from the ongoing autochthonous outbreak in central Italy. The sequence (East-Central-South African lineage, Indian Ocean sublineage), which is similar to recent sequences from Pakistan and India, shows E1 and E2 signatures of strains whose main mosquito vector is
Aedes aegypti
, although
Aedes albopictus
is the vector in Italy.
Complete Genome Sequences of Plasmid-Bearing Campylobacter coli and Campylobacter jejuni Strains Isolated from Retail Chicken Liver
Authors: Marasini Daya , Fakhr Mohamed K.
Published: December 2017

Complete genome sequences of
Campylobacter coli
strains WA333, YF2105, BG2108, MG1116, and BP3183 and
Campylobacter jejuni
strain IF1100 isolated from retail chicken liver showed the presence of 1,841,551-, 1,687,232-, 1,695,638-, 1,665,146-, 1,695,360-, and 1,744,171-bp circular chromosomes, respectively. These isolates also contained plasmids ranging in size from 5,209 to 55,122 bp.
Molecular Methods for Detection of Antimicrobial Resistance
Authors: Anjum Muna F. , Zankari Ea , Hasman Henrik
Published: December 2017

The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR. In this article we describe some of the common molecular methods currently used for detection of AMR genes. These include PCR, DNA microarray, whole-genome sequencing and metagenomics, and matrix-assisted laser desorption ionization–time of flight mass spectrometry. The strengths and weaknesses of these methods are discussed, especially in the context of implementing them for routine surveillance activities on a global scale for mitigating the risk posed by AMR worldwide. Based on current popularity and ease of use, PCR and single-isolate whole-genome sequencing seem irreplaceable.
Antimicrobial Resistance inCorynebacteriumspp.,Arcanobacteriumspp., andTrueperella pyogenes
Authors: Feßler Andrea T. , Schwarz Stefan
Published: December 2017

There is currently only limited information on the antimicrobial susceptibility and resistance ofCorynebacteriumspp.,Arcanobacteriumspp., andTrueperella pyogenesfrom animals. The comparability of the data is hampered by the use of different antimicrobial susceptibility testing methods and interpretive criteria. To date, standard broth microdilution methods and clinical breakpoints that are approved by the Clinical and Laboratory Standards Institute and are applicable toCorynebacteriumspp.,Arcanobacteriumspp., andT. pyogenesare available. The lack of species-specific clinical breakpoints for the different animal species reduces the explanatory power of the data. Among the isolates of the three genera, elevated MICs for different classes of antimicrobial agents (e.g., β-lactams, macrolides, lincosamides, tetracyclines, aminoglycosides, phenicols, sulfonamides/diaminopyrimidines, and fluoroquinolones) have been described. The most comprehensive data set is available forT. pyogenes, which also includes information about genes and mutations involved in antimicrobial resistance. InT. pyogenesisolates, the macrolide-lincosamide-streptogramin B resistance geneserm(B) anderm(X) were identified. Tetracycline resistance inT. pyogeneswas based on the resistance genestet(W),tet(Z), andtet(33), whereas the aminoglycoside resistance genesaacC,aadA1,aadA2,aadA5,aadA24, andaadBhave been described inT. pyogenes. So far, only single genes conferring either phenicol resistance (cmlA6), trimethoprim resistance (dfrB2a), or β-lactam resistance (blaP1) are known to occur inT. pyogenesisolates. Various 23S rRNA mutations, including A2058T, A2058G, and G2137C, were identified in macrolide/lincosamide-resistantT. pyogenes.
Workplace violence, psychological stress, sleep quality and subjective health in Chinese doctors: a large cross-sectional study
Authors: Sun Tao , Gao Lei , Li Fujun , Shi Yu , Xie Fengzhe , Wang Jinghui , Wang Shuo , Zhang Shue , Liu Wenhui , Duan Xiaojian , Liu Xinyan , Zhang Zhong , Li Li , Fan Lihua
Published: December 2017

Background

Workplace violence (WPV) against healthcare workers is known as violence in healthcare settings and referring to the violent acts that are directed towards doctors, nurses or other healthcare staff at work or on duty. Moreover, WPV can cause a large number of adverse outcomes. However, there is not enough evidence to test the link between exposure to WPV against doctors, psychological stress, sleep quality and health status in China.

Objectives

This study had three objectives: (1) to identify the incidence rate of WPV against doctors under a new classification, (2) to examine the association between exposure to WPV, psychological stress, sleep quality and subjective health of Chinese doctors and (3) to verify the partial mediating role of psychological stress.

Design

A cross-sectional online survey study.

Setting

The survey was conducted among 1740 doctors in tertiary hospitals, 733 in secondary hospital and 139 in primary hospital across 30 provinces of China.

Participants

A total of 3016 participants were invited. Ultimately, 2617 doctors completed valid questionnaires. The effective response rate was 86.8%.

Results

The results demonstrated that the prevalence rate of exposure to verbal abuse was the highest (76.2%), made difficulties (58.3%), smear reputation (40.8%), mobbing behaviour (40.2%), intimidation behaviour (27.6%), physical violence (24.1%) and sexual harassment (7.8%). Exposure to WPV significantly affected the psychological stress, sleep quality and self-reported health of doctors. Moreover, psychological stress partially mediated the relationship between work-related violence and health damage.

Conclusion

In China, most doctors have encountered various WPV from patients and their relatives. The prevalence of three new types of WPV have been investigated in our study, which have been rarely mentioned in past research. A safer work environment for Chinese healthcare workers needs to be provided to minimise health threats, which is a top priority for both government and society.
Benefits of probiotics in preterm neonates in low-income and medium-income countries: a systematic review of randomised controlled trials
Authors: Deshpande Girish , Jape Gayatri , Rao Shripada , Patole Sanjay
Published: December 2017

Objective

Although there is an overall reduction in underfive mortality rate, the progress in reducing neonatal mortality rate has been very slow. Over the last 20 years, preterm births have steadily increased in low-income and medium-income countries (LMICs) particularly in sub-Saharan Africa and South Asia. Preterm birth is associated with increased mortality and morbidity, particularly in LMICs. Based on systematic reviews of randomised controlled trials (RCTs), many neonatal units in high-income countries have adopted probiotics as standard of care for preterm neonates. We aimed to systematically review the safety and efficacy of probiotics in reducing mortality and morbidity in preterm neonates in LMICs.

Design

Systematic review and meta-analysis of RCTs.

Data sources

Medline, Embase, Cochrane Central Register of Controlled Trials, Cumulative Index of Nursing and Allied Health Literature and E-abstracts from Pediatric Academic Society meetings and other paediatric and neonatal conference proceedings were searched in January 2017.

Eligibility criteria

RCTs comparing probiotics versus placebo/no probiotic in preterm neonates (gestation<37 weeks) conducted in LMICs.

Results

Total 23 (n=4783) RCTs from 4 continents and 10 LMICs were eligible for inclusion in the meta-analysis using fixed effect model. The risk of necrotising enterocolitis (NEC greater than or equal to stage II) (risk ratio (RR) 0.46 (95% CI 0.34 to 0.61), P<0.00001, numbers needed to treat (NNT) 25 (95% CI 20 to 50)), late-onset sepsis (LOS) (RR 0.80 (95% CI 0.71 to 0.91), P=0.0009, NNT 25 (95% CI 17 to 100)) and all-cause mortality (RR 0.73 (95% CI 0.59 to 0.90), P=0.003, NNT 50 (95% CI 25 to 100)) were significantly lower in probiotic supplemented neonates. The results were significant on random effects model analysis and after excluding studies with high risk of bias. No significant adverse effects were reported.

Conclusion

Probiotics have significant potential to reduce mortality and morbidity (eg, NEC, LOS) in preterm neonates in LMICs.
Evaluation of cognitive load and emotional states during multidisciplinary critical care simulation sessions
Authors: Pawar Swapnil , Jacques Theresa , Deshpande Kush , Pusapati Raju , Meguerdichian Michael J
Published: December 2017

Background

The simulation in critical care setting involves a heterogeneous group of participants with varied background and experience. Measuring the impacts of simulation on emotional state and cognitive load in this setting is not often performed. The feasibility of such measurement in the critical care setting needs further exploration.

Methods

Medical and nursing staff with varying levels of experience from a tertiary intensive care unit participated in a standardised clinical simulation scenario. The emotional state of each participant was assessed before and after completion of the scenario using a validated eight-item scale containing bipolar oppositional descriptors of emotion. The cognitive load of each participant was assessed after the completion of the scenario using a validated subjective rating tool.

Results

A total of 103 medical and nursing staff participated in the study. The participants felt more relaxed (−0.28±1.15 vs 0.14±1, P<0.005; d=0.39), excited (0.25±0.89 vs 0.55±0.92, P<0.005, d=0.35) and alert (0.85±0.87 vs 1.28±0.73, P<0.00001, d=0.54) following simulation. There was no difference in the mean scores for the remaining five items. The mean cognitive load for all participants was 6.67±1.41. There was no significant difference in the cognitive loads among medical staff versus nursing staff (6.61±2.3 vs 6.62±1.7; P>0.05).

Conclusion

A well-designed complex high fidelity critical care simulation scenario can be evaluated to identify the relative cognitive load of the participants’ experience and their emotional state. The movement of learners emotionally from a more negative state to a positive state suggests that simulation can be an effective tool for improved knowledge transfer and offers more opportunity for dynamic thinking.
How are junior doctors managing patients with self-limiting illnesses at their first presentation? A video vignette study
Authors: D’Souza Eugene , Krejany Catherine , Meng Rosie , Jiwa Moyez
Published: December 2017

Purpose

To conduct a video vignette survey of medical students and doctors investigating test ordering for patients presenting with self-limiting or minor illness.

Methods

Participants were shown six video vignettes of common self-limiting illnesses and invited to devise investigation and management plans for the patients’ current presentation. The number of tests ordered was compared with those recommended by an expert panel. A Theory of Planned Behaviour Questionnaire explored participants’ beliefs and attitudes about ordering tests in the context of self-limiting illness.

Results

Participants (n=61) were recruited from across Australia. All participants ordered at least one test that was not recommended by the experts in most cases. Presentations that focused mainly on symptoms (eg, in cases with bowel habit disturbance and fatigue) resulted in more tests being ordered. A test not recommended by experts was ordered on 54.9% of occasions. With regard to attitudes to test ordering, junior doctors were strongly influenced by social norms. The number of questionable tests ordered in this survey of 366 consultations has a projected cost of $17 000.

Conclusions

This study suggests that there is some evidence of questionable test ordering by these participants with significant implications for costs to the health system. Further research is needed to explore the extent and reasons for test ordering by junior doctors across a range of clinical settings.
Synovial tissue macrophages: friend or foe?
Authors: Kurowska-Stolarska Mariola , Alivernini Stefano
Published: December 2017

Healthy synovial tissue includes a lining layer of synovial fibroblasts and macrophages. The influx of leucocytes during active rheumatoid arthritis (RA) includes monocytes that differentiate locally into proinflammatory macrophages, and these produce pathogenic tumour necrosis factor. During sustained remission, the synovial tissue macrophage numbers recede to normal. The constitutive presence of tissue macrophages in the lining layer of the synovial membrane in healthy donors and in patients with RA during remission suggests that this macrophage population may have a role in maintaining and reinstating synovial tissue homeostasis respectively. Recent appreciation of the different origins and functions of tissue-resident compared with monocyte-derived macrophages has improved the understanding of their relative involvement in organ homeostasis in mouse models of disease. In this review, informed by mouse models and human data, we describe the presence of different functional subpopulations of human synovial tissue macrophages and discuss their distinct contribution to joint homeostasis and chronic inflammation in RA.
The influence of adiposity and acute exercise on circulating hepatokines in normal-weight and overweight/obese men
Authors: Sargeant Jack A. , Aithal Guruprasad P. , Takamura Toshinari , Misu Hirofumi , Takayama Hiroaki , Douglas Jessica A. , Turner Mark C. , Stensel David J. , Nimmo Myra A. , Webb David R. , Yates Thomas , King James A.
Published: December 2017

Hepatokines are liver-secreted proteins with potential to influence glucose regulation and other metabolic parameters. This study investigated differences in adiposity status on 5 novel hepatokines and characterised their response to acute moderate-intensity exercise in groups of normal-weight and overweight/obese men. Twenty-two men were recruited into normal-weight and overweight/obese groups (body mass index: 18.5 to 24.9 and 25.0 to 34.9 kg·m−2). Each completed 2 experimental trials, exercise and control. During exercise trials, participants performed 60 min of moderate-intensity treadmill exercise (∼60% peak oxygen uptake) and then rested for 6 h. Participants rested throughout control trials. Circulating fibroblast growth factor-21 (FGF21), follistatin, leukocyte cell-derived chemotaxin 2 (LECT2), fetuin-A, and selenoprotein-P (SeP) were measured throughout. Fasted (resting) FGF21 and LECT2 were higher in overweight/obese individuals (129% and 55%; P ≤ 0.01) and correlated with indices of adiposity and insulin resistance; whereas circulating follistatin was lower in overweight/obese individuals throughout trial days (17%, P < 0.05). In both groups, circulating concentrations of FGF21 and follistatin were transiently elevated after exercise for up to 6 h (P ≤ 0.02). Circulating fetuin-A and SeP were no different between groups (P ≥ 0.19) and, along with LECT2, were unaffected by exercise (P ≥ 0.06). These findings show that increased adiposity is associated with a modified hepatokine profile, which may represent a novel mechanism linking excess adiposity to metabolic health. Furthermore, acute perturbations in circulating FGF21 and follistatin after exercise may contribute to the health benefits of an active lifestyle.
Centrifuge modeling of geotechnical mitigation measures for shallow foundations subjected to reverse faulting
Authors: Ashtiani Mehdi , Ghalandarzadeh Abbas , Mahdavi Mehdi , Hedayati Majid
Published: December 2017

Surface fault ruptures are particularly damaging to buildings, lifelines, and bridges located across or adjacent to active faults. These structures should be designed in consideration of surface fault rupture hazards or strategies should be adopted to protect the structures from fault-induced damage. Geotechnical mitigation strategies such as diversion of the fault rupture away from the structure and diffusion of the rupture over a wide zone are possible strategies. The effectiveness of these geotechnical mitigation measures for reverse faulting on shallow embedded foundations was investigated using a series of centrifuge tests. These measures included excavation of a vertical trench adjacent to the foundation and installation of geogrid layers beneath the foundation. The trench was shown to be effective for a range of foundation positions depending on the magnitude of the fault offset, dip angle of the fault, depth of the trench, embedment depth of the foundation, and the number of trenches used. The geogrid layers prevented a distinct fault rupture from reaching the surface and spread fault displacement over a wider zone, but were unable to mitigate the surface fault rupture hazard for shallow embedded foundations.
Phylogeography and climate-associated morphological variation in the endemic white oakQuercus deserticola(Fagaceae) along the Trans-Mexican Volcanic Belt
Authors: Rodríguez-Gómez Flor , Oyama Ken , Ochoa-Orozco Magaly , Mendoza-Cuenca Luis , Gaytán-Legaria Ricardo , González-Rodríguez Antonio
Published: December 2017

Mexico is a center of diversification for the genus Quercus, with an important number of taxa occurring along the Trans-Mexican Volcanic Belt (TMVB). However, the impact of the interaction between historical and current climatic variation and geological heterogeneity in the TMVB on the genetic and phenotypic diversification within oak species has been scarcely investigated. We used chloroplast DNA microsatellites and a geometric morphometrics analysis of leaf shape to understand differentiation between populations of Quercus deserticola Trel., which inhabits dry highlands along the TMVB. Ecological niche modeling for present-day conditions and projections into past scenarios were performed to evaluate the influence of environmental variables on the evolutionary history of the species. Results showed high genetic diversity (hS= 0.774) and high genetic structure (RST= 0.75) and the morphological subdivision of populations into two clusters, corresponding to the west/south and east/north sectors of the Q. deserticola geographic distribution. Ecological niche modeling indicated that the potential distribution of the species has remained similar from the late Pleistocene to the present. Seemingly, the phylogeographic structure of the species has been shaped by low seed-mediated gene flow and mostly local migration patterns. In turn, leaf shape is responding to climate differences either through phenotypic plasticity or local adaptation.
A FIRST LEVEL APPROXIMATION MODEL OF THE DYNAMIC ELASTICITY OF A PARTIALLY BIORESORBABLE COMPOSITE INTERNAL FIXATION SYSTEM
Authors: COATES CAMERON , COATES-CLARK CAMILLE , CRAWFORD ZACHARY , COPELAND ZACHARY
Published: December 2017

The objective of this work is to develop a first level approximation hybrid model that predicts the rate of reduction of the elastic modulus for a composite internal fixation plate. The first level model combines a modified composite theory in which the bioresorbable constituent moduli and volume fractions are time-dependent, with predictions from a Finite Element (FE) model, but ignores viscoelastic effects. The FE model is used to predict relationships between geometrical constraints (material interfaces), while a theoretical combined elastic modulus is determined using the Reuss model. The composite internal fixation device design comprises Poly-L-lactide and Hydroxyapatite (HA/PLLA) and Titanium. The geometrical relationships established by the FE static model are combined with the theoretical mathematical model in order to predict the rate of decrease of the elastic modulus of the composite device. The first level model predicts that the composite plate modulus decreases at a rate that appropriately compensates for the increasing modulus of the healing bone during fracture healing. This suggests that the proposed composite fixation plate has a strong potential for improved fracture healing through the reduction of stress shielding while the fracture heals, and the elimination of stress shielding after fracture healing.
Some Novel Numerical Applications of Cosserat Continua
Authors: Fantuzzi Nicholas , Leonetti Lorenzo , Trovalusci Patrizia , Tornabene Francesco
Published: December 2017

Cosserat continua demonstrated to have peculiar mechanical properties, with respect to classic Cauchy continua, because they are able to more accurately describe heterogeneous materials, as particle composites and masonry-like material, taking into account size effects. Many studies have been devoted to their numerical implementation. In this paper, some reference benchmarks, referred to an isotropic heterogeneous sample, are shown by comparing the solutions provided by strong and weak formulations. The strong formulation finite element method (SFEM), implemented in MATLAB®, is compared to the finite element method (FEM), given by COMSOL® Multiphysics, and the advantages of the two approaches are highlighted and discussed.
Accurate Multi-Physics Numerical Analysis of Particle Preconcentration Based on Ion Concentration Polarization
Authors: Li Zirui , Liu Wei , Gong Lingyan , Zhu Yudan , Gu Yuantong , Han Jongyoon
Published: December 2017

This paper studies the mechanism of preconcentration of charged particles in a straight microchannel embedded with permselective membranes by numerically solving the coupled transport equations of ions, charged particles and solvent fluid without any simplifying assumptions. It is demonstrated that trapping and preconcentration of charged particles are determined by the interplay between drag force from the electroosmotic fluid flow and the electrophoretic force applied through the electric field. Several insightful characteristics are revealed, including the diverse dynamics of co-ions and counter ions, replacement of co-ions by focused particles, lowered ion concentrations in particle-enriched zone, and enhanced electroosmotic pumping effect, etc. Conditions for particles that can be concentrated are identified in terms of charges, sizes and electrophoretic mobilities of particles and co-ions. Dependences of enrichment factor on cross-membrane voltage, initial particle concentration and buffer ion concentrations are analyzed and the underlying reasons are elaborated. Finally, post priori condition for the validity of decoupled simulation model is given based on the charges carried by focused particles and buffer co-ions. These results provide an important guidance in the design and optimization of nanofluidic preconcentration and other related devices.
Free Vibration Analysis of Pipes Conveying Fluid Based on Linear and Nonlinear Complex Modes Approach
Authors: Liang Feng , Yang Xiao-Dong , Qian Ying-Jing , Zhang Wei
Published: December 2017

In this paper, linear and nonlinear complex modes are used to analyze the free vibration of pipes conveying fluid involving the gyroscopic properties of the system. The natural frequencies, complex mode functions and time domain responses of the admissible mode functions based on discretized model are obtained using the invariant manifold method and compared with those of the continuous model. A good agreement has been achieved if the admissible mode functions for the static beams are adopted. The energy contributions of different admissible modes to the modal motions are also studied which explores the gyroscopic coupling variation among the admissible modes for different fluid velocities. Nonlinear complex modes are constructed for the nonlinear case and the morphology of the modal motions is demonstrated for different initial energy to show the contribution of the nonlinear terms. ‘Traveling waves’ are found for the transverse vibrations of the pipes conveying fluid due to the gyroscopic effects, contrary to the “standing waves” found for the pipes without moving fluid.
Engineering Hydrogel Microenvironments to Recapitulate the Stem Cell Niche
Authors: Madl Christopher M. , Heilshorn Sarah C.
Published: December 2017

Stem cells are a powerful resource for many applications including regenerative medicine, patient-specific disease modeling, and toxicology screening. However, eliciting the desired behavior from stem cells, such as expansion in a naïve state or differentiation into a particular mature lineage, remains challenging. Drawing inspiration from the native stem cell niche, hydrogel platforms have been developed to regulate stem cell fate by controlling microenvironmental parameters including matrix mechanics, degradability, cell-adhesive ligand presentation, local microstructure, and cell–cell interactions. We survey techniques for modulating hydrogel properties and review the effects of microenvironmental parameters on maintaining stemness and controlling differentiation for a variety of stem cell types. Looking forward, we envision future hydrogel designs spanning a spectrum of complexity, ranging from simple, fully defined materials for industrial expansion of stem cells to complex, biomimetic systems for organotypic cell culture models.
Harnessing Protease Activity to Improve Cancer Care
Authors: Dudani Jaideep S. , Warren Andrew D. , Bhatia Sangeeta N.
Published: December 2017

Proteolysis plays critical roles in normal and pathologic physiology; these enzymes are intricately involved in cancer progression and spread. Our understanding of protease function has advanced from nonspecific degrading enzymes to a modern appreciation of their diverse roles in posttranslational modification and signaling in a complex microenvironment. This new understanding has led to next-generation diagnostics and therapeutics that exploit protease activity in cancer. For diagnostics, protease activity may be measured as a biomarker of cancer, with wide-ranging utility from early detection to monitoring therapeutic response. Therapeutically, while broad inhibition of protease activity proved disappointing, new approaches that more specifically modulate proteases in concert with secondary targets might enable potent combination therapies. In addition, clinical evaluation is underway for tools that leverage protease activity to activate therapeutics, ranging from imaging agents that monitor surgical margins to immunotherapies with improved specificity. Technologies that interact with, measure, or modulate proteases are poised to improve cancer management on diagnostic and therapeutic fronts to realize the promise of precision medicine.
Transparent Social Inquiry: Implications for Political Science
Authors: Elman Colin , Kapiszewski Diana , Lupia Arthur
Published: December 2017

Political scientists use diverse methods to study important topics. The findings they reach and conclusions they draw can have significant social implications and are sometimes controversial. As a result, audiences can be skeptical about the rigor and relevance of the knowledge claims that political scientists produce. For these reasons, being a political scientist means facing myriad questions about how we know what we claim to know. Transparency can help political scientists address these questions. An emerging literature and set of practices suggest that sharing more data and providing more information about our analytic and interpretive choices can help others understand the rigor and relevance of our claims. At the same time, increasing transparency can be costly and has been contentious. This review describes opportunities created by, and difficulties posed by, attempts to increase transparency. We conclude that, despite the challenges, consensus about the value and practice of transparency is emerging within and across political science's diverse and dynamic research communities.
Principal Components, Sufficient Dimension Reduction, and Envelopes
Authors: Cook R. Dennis
Published: December 2017

We review probabilistic principal components, principal fitted components, sufficient dimension reduction, and envelopes, arguing that at their core they are all based on variations of the conditional independence argument that Fisher used to develop his fundamental concept of sufficiency. We emphasize the foundations of the methods. Methodological details, derivations, and examples are included when they convey the flavor and implications of basic concepts. In addition to the main topics, this review covers extensions of probabilistic principal components, the central subspace and central mean subspace, sliced inverse regression, sliced average variance estimation, dimension reduction for covariance matrices, and response and predictor envelopes.
On p-Values and Bayes Factors
Authors: Held Leonhard , Ott Manuela
Published: December 2017

The p-value quantifies the discrepancy between the data and a null hypothesis of interest, usually the assumption of no difference or no effect. A Bayesian approach allows the calibration of p-values by transforming them to direct measures of the evidence against the null hypothesis, so-called Bayes factors. We review the available literature in this area and consider two-sided significance tests for a point null hypothesis in more detail. We distinguish simple from local alternative hypotheses and contrast traditional Bayes factors based on the data with Bayes factors based on p-values or test statistics. A well-known finding is that the minimum Bayes factor, the smallest possible Bayes factor within a certain class of alternative hypotheses, provides less evidence against the null hypothesis than the corresponding p-value might suggest. It is less known that the relationship between p-values and minimum Bayes factors also depends on the sample size and on the dimension of the parameter of interest. We illustrate the transformation of p-values to minimum Bayes factors with two examples from clinical research.
Toward Integrative Bayesian Analysis in Molecular Biology
Authors: Ickstadt Katja , Schäfer Martin , Zucknick Manuela
Published: December 2017

In the postgenome era, multiple types of molecular data for the same set of samples are often available and should be analyzed jointly in an integrative analysis in order to maximize the information gain. Bayesian methods are particularly well suited for integrating different biological data sources. In this article, we cover crucial tasks and corresponding methods with a focus on integrative analyses. We emphasize gene prioritization, model-based cluster approaches for subgroup identification, regression modeling, and prediction, as well as structure learning using network models. Our review introduces prior concepts for sparsity and variable selection and concludes with some aspects on validation and computation.
Causal Structure Learning
Authors: Heinze-Deml Christina , Maathuis Marloes H. , Meinshausen Nicolai
Published: December 2017

Graphical models can represent a multivariate distribution in a convenient and accessible form as a graph. Causal models can be viewed as a special class of graphical models that represent not only the distribution of the observed system but also the distributions under external interventions. They hence enable predictions under hypothetical interventions, which is important for decision making. The challenging task of learning causal models from data always relies on some underlying assumptions. We discuss several recently proposed structure learning algorithms and their assumptions, and we compare their empirical performance under various scenarios.
Dental Caries and Developmental Defects of Enamel in the Primary Dentition of Preterm Infants: Case-Control Observational Study
Authors: Schüler Ina Manuela , Haberstroh Stefanie , Dawczynski Kristin , Lehmann Thomas , Heinrich-Weltzien Roswitha
Published: December 2017

Aim: Assessment of dental health in the primary dentition of preterm infants (PTI) including investigation of mother- and infant-related risk factors in a case-control study design. Material and Methods: One hundred twenty-eight infants aged 3-4 years were included. Sixty-four PTI (27 males) were randomly selected from the preterm registry of the Jena University Hospital. As a control group served 64 full-term infants (FTI) recruited from the Department of Paediatric Dentistry, matched for age and sex. Dental examinations were provided by one dentist under standard clinical conditions. Caries was scored using the International Caries Detection and Assessment System (ICDAS II) and the DMFT, gingival health using the Periodontal Screening Index, and developmental defects of enamel using the DDE index. Mother- and infant-related factors were collected via a questionnaire and from medical records. Results: The caries prevalence was 50.0% (ICDAS II >0) in PTI and 12.5% (ICDAS II >0) in FTI. The caries experience was higher in PTI (DMFT 1.0 ± 3.1) than in FTI (DMFT 0.3 ± 1.0). PTI had a higher risk of caries (OR 7.0), initial lesions (OR 6.2), DDE (OR 7.5), and gingivitis (OR 6.5) than FTI. The highest risk occurred in PTI with an extremely low birth weight (<1,000 g). A higher risk of DDE was present when mothers suffered from illness during pregnancy (OR 3.9). A higher risk of caries was revealed in infants with respiratory syndrome (OR 6.2) or when their mothers had a lower socioeconomic status (OR 6.3). Conclusions: PTI had less healthy teeth than FTI and are at a higher risk for DDE, caries, and gingivitis. The poorer dental health in PTI is associated with a low birth weight, a low socioeconomic status, and mothers' illness during pregnancy.
The Asia Pacific Consensus Statement on Laparoscopic Liver Resection for Hepatocellular Carcinoma: A Report from the 7th Asia-Pacific Primary Liver Cancer Expert Meeting Held in Hong Kong
Authors: Cheung Tan To , Han Ho-Seong , She Wong Hoi , Chen Kuo-Hsin , Chow Pierce K.H. , Yoong Boon Koon , Lee Kit Fai , Kubo Shoji , Tang Chung Ngai , Wakabayashi Go
Published: December 2017

Background: Laparoscopic liver resection has been gaining momentum, and it has become an accepted practice after the two international consensus conferences where experts worked up guidelines to standardize this approach and improve its safety. However, most laparoscopic hepatectomies were performed in patients with liver metastases. The concurrent presence of liver cirrhosis with hepatocellular carcinoma (HCC) poses a great challenge to clinicians trying to establish a routine use of laparoscopic liver resection for HCC. Summary: The first Asia Pacific consensus meeting on laparoscopic liver resection for HCC was held in July 2016 in Hong Kong. A group of expert liver surgeons with experience in both open and laparoscopic hepatectomy for HCC convened to formulate recommendations on the role and perspective of laparoscopic liver resection for primary liver cancer. The recommendations consolidate the most recent evidence pertaining to laparoscopic hepatectomy together with the latest thinking of practicing clinicians involved in laparoscopic hepatectomy, and give detailed guidance on how to deploy the treatment effectively for patients in need. Key Message: The panel of experts gathered evidence and produced recommendations providing guidance on the safe practice of laparoscopic hepatectomy for patients with HCC and cirrhosis. The inherent advantage of the laparoscopic approach may result in less blood loss if the procedure is performed in experienced centers. The laparoscopic approach to minor hepatectomy, particularly left lateral sectionectomy, is a preferred practice for HCC at experienced centers. Laparoscopic major liver resection for HCC remains a technically challenging operation, and it should be carried out in centers of excellence. There is emerging evidence that laparoscopic liver resection produces a better oncological outcome for HCC when compared with radiofrequency ablation, particularly when the lesions are peripherally located. Augmented features in laparoscopic liver resection, including indocyanine green fluorescence, 3D laparoscopy, and robot, will become important tools of surgical treatment in the near future. A combination of all of these features will enhance the experience of the surgeons, which may translate into better surgical outcomes. This is the first consensus workforce on laparoscopic liver resection for HCC, which is a unique condition that occurs in the Asia Pacific region.
Negative Symptoms and Avoidance of Social Interaction: A Study of Non-Verbal Behaviour
Authors: Worswick Elizabeth , Dimic Sara , Wildgrube Christiane , Priebe Stefan
Published: December 2017

Background: Non-verbal behaviour is fundamental to social interaction. Patients with schizophrenia display an expressivity deficit of non-verbal behaviour, exhibiting behaviour that differs from both healthy subjects and patients with different psychiatric diagnoses. The present study aimed to explore the association between non-verbal behaviour and symptom domains, overcoming methodological shortcomings of previous studies. Sampling and Methods: Standardised interviews with 63 outpatients diagnosed with schizophrenia were videotaped. Symptoms were assessed using the Clinical Assessment Interview for Negative Symptoms (CAINS), the Positive and Negative Syndrome Scale (PANSS) and the Calgary Depression Scale. Independent raters later analysed the videos for non-verbal behaviour, using a modified version of the Ethological Coding System for Interviews (ECSI). Results: Patients with a higher level of negative symptoms displayed significantly fewer prosocial (e.g., nodding and smiling), gesture, and displacement behaviours (e.g., fumbling), but significantly more flight behaviours (e.g., looking away, freezing). No gender differences were found, and these associations held true when adjusted for antipsychotic medication dosage. Conclusions: Negative symptoms are associated with both a lower level of actively engaging non-verbal behaviour and an increased active avoidance of social contact. Future research should aim to identify the mechanisms behind flight behaviour, with implications for the development of treatments to improve social functioning.
Transmanubrial Approach for Removing a Head and Neck Tumor Located at the Upper Lateral Mediastinum
Authors: Masuda Muneyuki , Rikimaru Fumihide , Toh Satoshi , Higaki Yuichiro
Published: December 2017

Background: When a head and neck tumor invades the upper lateral mediastinum, the transmanubrial approach (TMA), in which the sternoclavicular joint is temporary mobilized and replaced back to the physiological position, appears to be an excellent method. However, there have been only a few reports about the application of this approach to head and neck tumors. Materials and Methods: We recently adopted this technique for the removal of 2 head and neck tumors that required handling of the subclavian and innominate veins around the venus angle. Results: We could safely remove the tumors under good surgical view and obtained excellent cosmetic and functional results. Conclusions: TMA is a useful technique for the removal of head and neck tumors, which invade the upper lateral mediastinum. More frequent applications of this method are encouraged in combination with head and neck tumor surgery.
Heminephrectomy in Adults: A Systematic Review with Cumulative Analysis
Authors: Clement Keiran , Hendry Jane , Keeley Francis X.  , Aboumarzouk Omar M.
Published: December 2017

Introduction: Duplex collecting system of the kidney is a relatively common abnormality, with the majority of symptomatic cases discovered in childhood. Treatment is commonly a heminephrectomy of the affected moiety. We aimed to conduct a systematic review of the literature to provide the best available evidence for heminephrectomy for duplex kidneys in the adult population. Materials and Methods: A literature search was conducted in September 2017 with no limitations being placed on language, region, date or publication type. Data were represented numerically and analysed cumulatively. Results: Seven retrospective studies with 66 patients were included. Of which, 56/66 operations were performed laparoscopically, 5/66 were robot-assisted and 5/66 were open procedures. Complete resolution of symptoms was reported in 53/55 (96.4%) of patients in five studies providing outcome data. Of the 6 studies reporting complications, there were a total of 9 complications (9/62, 14.5%), however 5 of these were found to be in one study alone. Conclusions: This review emphasises the scarcity of evidence for heminephrectomy in adults. Nonetheless, it has been shown that this operation may be effective in alleviating patients’ symptoms in addition to being safe in experienced hands.
Renal Resistive Index as a Novel Indicator for Renal Complications in High-Fat Diet-Fed Mice
Authors: Xu Hairong , Ma Zejun , Lu Shan , Li Rui , Lyu Liangkun , Ding Lexi , Lu Qiulun
Published: December 2017

Background/Aims: The renal resistive index (RI) is a novel candidate as a renal injury prognostic indicator, but it remains unclear how renal RI levels correspond to renal injury in diabetic nephropathy. Methods: To examine this issue, we compared 8-week-old male C57BL/6 mice fed with high-fat diet (HFD) versus chow diet (CHD) for 16 weeks. At 8 and 12 weeks, the glomerular filtration rate (GFR), urinary albumin-to-creatinine ratio (UACR), and inflammatory factors (IL-1β, IL-6, TNFα, and MCP-1) were measured, along with the increase in renal RI. Results: Our study suggests RI values positively correlate with GFR for the first 12 weeks of HFD feeding. In contrast, the GFR of 16-week HFD feeding is lower than that of 12-week HFD feeding, whereas RI levels are significantly increased. Additionally, our study suggests RI values accurately indicate the renal fibrosis and renal injury in HFD-fed mice treated with lovastatin. Conclusion: This study seems to confirm the utility of a noninvasive and repeatable ultrasound parameter to rapidly evaluate renal fibrosis in a HFD-induced type 2 diabetic mouse model in vivo. This highly sensitive and comparable renal RI measurement could monitor the whole procedure of disease development in real-time. RI measurement of the renal artery is capable of differentiating responses to standard therapy with lovastatin in HFD-fed mice from the CHD group.