bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating the role and measures of juvenile growth rate: latitudinal variation in insect life histories
Authors: Meister Hendrik , Esperk Toomas , Välimäki Panu , Tammaru Toomas
Published: May 2017

Latitudinal and elevational trends in body size are found in numerous animal taxa, with various adaptive explanations proposed. It is however debatable whether geographic trends in adult body size are accompanied by corresponding differences in juvenile growth rate (= mass gain per unit time). Respective studies have been complicated by conceptual and methodological problems related to defining and measuring this variable, particularly in organisms with discontinuous growth like arthropods. Using an original method for estimating differential (instantaneous) juvenile growth rates, we compared geographically distant European populations of six insect species in a common garden experiment. We found no among population differences in differential growth rate in any of the species. This result is in concert with concurrent increase in both adult size and developmental time towards the south. While opposite examples exist, we interpret our results as challenging the view that growth rate is a trait that readily responds to environmentally based selective pressures. Our results thus advocate the more classical view of growth rate maximisation within its physiological limits. We discuss the advantages of using differential (rather than integral) measures of growth rate in evolutionary ecological studies and evaluate the reasons for the detected latitudinal trends in life history traits.
Temperature and consumer type dependencies of energy flows in natural communities
Authors: Lang Birgit , Ehnes Roswitha B. , Brose Ulrich , Rall Björn C.
Published: May 2017

With the world continuously warming, a mechanistic understanding of how temperature affects interaction strengths, which are fundamental to food‐web stability, is needed. As interaction strengths are determined by the flows of energy from resources to consumers, we investigated effects of temperature on animal energetics. We used newly compiled datasets on respiration rates and assimilation efficiencies to assess how temperature affects the energy use (respiration rates) and the efficiency of energy gain (assimilation efficiency) for different consumer types. Furthermore, we incorporated our findings in a simulation of temperature effects on maintenance feeding rates (i.e. energy consumption necessary to sustain life). Our analysis revealed a generally positive temperature dependence of assimilation efficiencies across consumer types thus implying a net energy gain with warming. The temperature scaling of respiration rates did not differ between consumer types. Based on these parameters we calculated maintenance feeding rates and compared them to empirically measured (realized) feeding rates. This comparison revealed that detritivores and herbivores have the potential to increase their biomasses under warming as their maintenance feeding rates increase less strongly than their realized feeding rates. For carnivores, however, we found a stronger increase of their maintenance feeding rates compared to their realized feeding rates, which should lead to decreased population sizes under warming. Overall, our results increase the understanding of climate change effects on ecosystems as they suggest profound energetic consequences for natural communities.
Physiological effects of titrated oxygen via nasal high‐flow cannulae in COPD exacerbations: A randomized controlled cross‐over trial
Authors: Pilcher Janine , Eastlake Leonie , Richards Michael , Power Sharon , Cripps Terrianne , Bibby Susan , Braithwaite Irene , Weatherall Mark , Beasley Richard
Published: May 2017

ABSTRACT

Background and objective

Increased arterial carbon dioxide tension (PaCO2
) is an important complication of acute exacerbations of COPD. The effects of nasal high‐flow cannulae (NHF) on PaCO2
in patients with COPD exacerbations, and whether this therapy should be used in this clinical situation, are less certain. We aimed to investigate the effect of NHF on PaCO2
in patients admitted to hospital with a COPD exacerbation.

Methods

We performed a single‐centre randomized controlled cross‐over trial in 24 hospital inpatients with acute exacerbations of COPD receiving oxygen via standard nasal prongs (SNPs). Patients received both supplemental oxygen via NHF (35 L/min) and SNP for 30 min each, with oxygen titrated to maintain the patient's baseline oxygen saturation, measured by pulse oximetry (SpO2
). Interventions were administered in random order with a minimum 15‐min washout between interventions. The primary outcome was difference in transcutaneous carbon dioxide tension (PtCO2
) at 30 min adjusted for time zero.

Results

The difference in PtCO2
adjusted for time zero was lower after 30 min for NHF compared with SNP (−1.4 mm Hg (95% CI: −2.2 to −0.6), P = 0.001). There was no difference in SpO2
at 30 min (−0.02% (95% CI: −0.8 to 0.7), P = 0.96). The reduction in respiratory rate for NHF at 30 min was not statistically significant (−2.0 breaths/min (95% CI: −4.5 to 0.4), P = 0.099).

Conclusion

Short‐term use of NHF results in a small reduction in PtCO2
compared with SNP in patients with acute exacerbations of COPD, but whether this is clinically significant is uncertain.
Multi‐Exposure Pathway Model to Compare Escherichia coli O157 Risks and Interventions
Authors: Chapman B. , Pintar K. , Smith B. A.
Published: May 2017

The relative contributions of exposure pathways associated with cattle‐manure‐borne Escherichia coli O157:H7 on public health have yet to be fully characterized. A stochastic, quantitative microbial risk assessment (QMRA) model was developed to describe a hypothetical cattle farm in order to compare the relative importance of five routes of exposure, including aquatic recreation downstream of the farm, consumption of contaminated ground beef processed with limited interventions, consumption of leafy greens, direct animal contact, and the recreational use of a cattle pasture. To accommodate diverse environmental and hydrological pathways, existing QMRAs were integrated with novel and simplistic climate and field‐level submodels. The model indicated that direct animal contact presents the greatest risk of illness per exposure event during the high pathogen shedding period. However, when accounting for the frequency of exposure, using a high‐risk exposure‐receptor profile, consumption of ground beef was associated with the greatest risk of illness. Additionally, the model was used to evaluate the efficacy of hypothetical interventions affecting one or more exposure routes; concurrent evaluation of multiple routes allowed for the assessment of the combined effect of preharvest interventions across exposure pathways—which may have been previously underestimated—as well as the assessment of the effect of additional downstream interventions. This analysis represents a step towards a full evaluation of the risks associated with multiple exposure pathways; future incorporation of variability associated with environmental parameters and human behaviors would allow for a comprehensive assessment of the relative contribution of exposure pathways at the population level.
Direct and Indirect Treatment Effects–Causal Chains and Mediation Analysis with Instrumental Variables
Authors: Frölich Markus , Huber Martin
Published: May 2017

The paper discusses the non-parametric identification of causal direct and indirect effects of a binary treatment based on instrumental variables. We identify the indirect effect, which operates through a mediator (i.e. intermediate variable) that is situated on the causal path between the treatment and the outcome, as well as the unmediated direct effect of the treatment by using distinct instruments for the endogenous treatment and the endogenous mediator. We examine various settings to obtain non-parametric identification of (natural) direct and indirect as well as controlled direct effects for continuous and discrete mediators and continuous and discrete instruments. We also provide a simulation study and two empirical illustrations.
A consistent experimental protocol for the strain rate characterization of thermoplastic fabrics
Authors: Coussa Fabien , Renard Jacques , Joannes Sébastien , Teissedre Jean‐Christophe , Bompoint Rémy , Feld Nicolas
Published: May 2017

This paper introduces an experimental procedure aiming at performing a consistent mechanical characterization of textile composites behavior, under static and dynamic loadings, and particularly their macroscopic strain rate‐dependent mechanisms. The procedure includes the design and validation of a reduced specimen adapted to dynamic testing, which guarantees the consistency of the identified macroscopic properties under a wide range of strain rates. An interrupted high speed tensile apparatus was also developed to investigate the strain rate sensitivity of the nonlinear constitutive behavior from
= 10 − 4 s − 1 to 102 s − 1. The originality of this experimental device lies in its ability to stop high speed loadings before ultimate failure, at adjustable, accurate strain levels. Finally, an extensive characterization campaign was performed. Results reveal a high strain rate dependency of the linear and nonlinear behavior. The procedure therefore generates consistent characterization data that may trustworthily be used for modeling purposes.
Two‐dimensional discrete Fourier transform analysis of karst and coral reef morphologies
Authors: Davis Jerry D. , Chojnacki Joseph D.
Published: May 2017

Fourier transforms have been used in the analysis of landscapes that exhibit the influence of cyclic structures or other morphogenetic controls. Two‐dimensional Fourier transforms have been most successful when modeling features with a high frequency over the sample space. This research focuses on applications of 2D discrete Fourier transforms for karst and spur and groove coral reefs, using ArcGIS geoprocessing tools extended with Python NumPy numerical methods. Ten‐meter digital elevation data from Puerto Rico and Kentucky holokarst landscapes and five‐meter bathymetry from more unidirectional spur and groove coral reefs at Midway Atoll were analyzed. Our method identifies the dominant contributing waves in frequency space, and analyzed power contributions by 5° and 15° azimuth bins. A limiting factor in this analysis is the spatial extent of consistent morphology in the landscape. In contrast to time‐domain Fourier analysis, dominant landform frequencies can thus be of low magnitude, creating an imprecise estimate of wave morphometry and direction since this is derived from the combination of inverted x and y frequency values, and the limited frequency grain inherent in the discrete model degrades precision in the solution. Simulated karst and spur & groove landscapes were used to evaluate the grain of waveform orientation solutions.
Differentiating pulmonary transfusion reactions using recipient and transfusion factors
Authors: Roubinian Nareg H. , Looney Mark R. , Keating Sheila , Kor Daryl J. , Lowell Clifford A. , Gajic Ognjen , Hubmayr Rolf , Gropper Michael , Koenigsberg Monique , Wilson Gregory A. , A. Matthay Michael , Toy Pearl , Murphy Edward L. ,   the TRALI Study Group
Published: May 2017

BACKGROUND

It is increasingly recognized that recipient risk factors play a prominent role in possible transfusion‐related acute lung injury (pTRALI) and transfusion‐associated circulatory overload (TACO). We hypothesized that both transfusion and recipient factors including natriuretic peptides could be used to distinguish TRALI from TACO and pTRALI.

STUDY DESIGN AND METHODS

We performed a post hoc analysis of a case‐control study of pulmonary transfusion reactions conducted at the University of California at San Francisco and Mayo Clinic, Rochester. We evaluated clinical data and brain natriuretic peptides (BNP) levels drawn after transfusion in patients with TRALI (n = 21), pTRALI (n = 26), TACO (n = 22), and controls (n = 24). Logistic regression and receiver operating characteristics curve analyses were used to determine the accuracy of clinical and biomarker predictors in differentiating TRALI from TACO and pTRALI.

RESULTS

We found that pTRALI and TACO were associated with older age, higher fluid balance, and elevated BNP levels relative to those of controls and TRALI. The following variables were useful in distinguishing cases of pTRALI and TACO from TRALI: age more than 70 years, BNP levels more than 1000 pg/mL, 24‐hour fluid balance of more than 3 L, and a lower number of transfused blood components. Using the above variables, our logistic model had a 91% negative predictive value in the differential diagnosis of TRALI.

CONCLUSIONS

Models incorporating readily available clinical and biomarker data can be used to differentiate transfusion‐related respiratory complications. Additional studies examining recipient risk factors and the likelihood of TRALI may be useful in decision making regarding donor white blood cell antibody testing.
Homeland Security in a Nutshell
Authors: White Richard
Published: May 2017

As the Department of Homeland Security begins its 2018 Quadrennial Homeland Security Review, it will certainly address the question “what is homeland security?”. This article is meant to provide a concise overview. It begins with a definition and relates it back to the origins of homeland security. It then takes that same definition and projects it onto the DHS mission sets. It then takes a closer look at DHS missions in border and transportation security, counterterrorism, emergency management, countering weapons of mass destruction, critical infrastructure protection, and cybersecurity. It concludes with a unique argument that homeland security may be only a transient concern, and that technological change may offer a brighter future.
Integration of a Pressurized-Air Solar Receiver Array to a Gas Turbine Power Cycle for Solar Tower Applications
Authors: Poživil Peter , Steinfeld Aldo
Published: May 2017

The thermal performance of an array of pressurized-air solar receiver modules integrated to a gas turbine power cycle is analyzed for a simple Brayton cycle (BC), recuperated Brayton cycle (RC), and combined Brayton–Rankine cycle (CC). While the solar receiver's solar-to-heat efficiency decreases at higher operating temperatures and pressures, the opposite is true for the power cycle's heat-to-work efficiency. The optimal operating conditions are achieved with a preheat stage for a solar receiver outlet air temperature of 1300 °C and an air cycle pressure ratio of 9, yielding a peak solar-to-electricity efficiency—defined as the ratio of the net cycle work output divided by the solar radiative power input through the receiver's aperture—of 39.3% for the combined cycle configuration.
Aerodynamic Optimization of a Winglet-Shroud Tip Geometry for a Linear Turbine Cascade
Authors: Zhang Min , Liu Yan , Zhang Tianlong , Zhang Mengchao , He Ying
Published: May 2017

This paper presents a continued study on a previously investigated novel winglet-shroud (WS) (or partial shroud) geometry for a linear turbine cascade. Various widths of double-side winglets (DSW) and different locations of a partial shroud are considered. In addition, both a plain tip and a full shroud tip are applied as the datum cases which were examined experimentally and numerically. Total pressure loss and viscous loss coefficients are comparatively employed to execute a quantitative analysis of aerodynamic performance. The effectiveness of various widths (w) of DSW set at 3%, 5%, 7%, and 9% of the blade pitch (p) is numerically investigated. Skin-friction lines on the tip surface indicate that different DSW cases do not alter flow field features including the separation bubble and reattachment flow within the tip gap region, even for the case with the broadest width (w/p = 9%). However, the pressure side extension of the DSW exhibits the formation of separation bubble, while the suction side platform of the DSW turns the tip leakage vortex (TLV) away from the suction surface (SS). Meanwhile, the horse-shoe vortex (HV) near the casing is not generated even for the case with the smallest width (w/p = 3%). As a result, both the tip leakage and the upper passage vortices are weakened and further dissipated with wider w/p in the DSW cases. Larger width of the DSW geometry is indeed able to improve the aerodynamic performance, but only to a slight degree. With the w/p increasing from 3% to 9%, the mass-averaged total pressure loss coefficient over an exit plane is reduced by only 2.61%. Therefore, considering both the enlarged (or reduced) tip area and the enhanced (or deteriorated) performance compared to the datum cases, a favorable width of w/p = 5% is chosen to design the WS structure. Three locations for the partial shroud (linkage segment) are devised, locating them near the leading edge, in the middle and close to the trailing edge, respectively. Results demonstrate that all three cases of the WS design have advantages over the DSW arrangement in lessening the aerodynamic loss, with the middle linkage segment location producing the optimal effect. This conclusion verifies the feasibility of the previously studied WS configuration.
Symmetry-Based Transformable and Foldable Plate Structures
Authors: Beatini Valentina
Published: May 2017

This paper presents a novel family of modular flat-foldable rigid plate structures composed by assemblies of 4R-linkages. First, in the field of foldable plates, the proposed system is characterized by being not only foldable but also transformable: the slope of one module over the other is capable of changing not only magnitude but also sign. This transformable behavior extends the range of application of foldable plates from simply larger–smaller configurations to substantially different configurations and usages. The transformable curve is obtained by means of symmetry operations on the spherical length of links. For each module, three configurations can be designed. Various examples are illustrated.
Pool Boiling Heat Transfer Characteristics of Inclined pHEMA-Coated Surfaces
Authors: Khalili Sadaghiani Abdolali , Reza Motezakker Ahmad , Volkan Özpınar Alsan , Özaydın İnce Gözde , Koşar Ali
Published: May 2017

New requirements for heat exchangers offered pool boiling heat transfer on structured and coated surfaces as one of the promising methods for effective heat removal. In this study, pool boiling experiments were conducted on polyhydroxyethylmethacrylate (pHEMA)-coated surfaces to investigate the effect of surface orientation on bubble dynamics and nucleate boiling heat transfer. pHEMA coatings with thicknesses of 50, 100, and 200 nm were deposited using the initiated chemical deposition (iCVD) method. De-ionized water was used as the working fluid. Experiments were performed on horizontal and inclined surfaces (inclination angles of 10 deg, 30 deg, 50 deg, and 70 deg) under the constant heat flux (ranging from 10 to 80 kW/m2) boundary condition. Obtained results were compared to their plain surface counterparts, and heat transfer enhancements were observed. Accordingly, it was observed that the bubble departure phenomenon was affected by heat flux and wall superheat on bare silicon surfaces, while the supply path of vapor altered the bubble departure process on pHEMA-coated surfaces. Furthermore, the surface orientation played a major role on bubble dynamics and could be considered as a mechanism for fast vapor removal from surfaces. Bubble coalescence and liquid replenishment on coated surfaces had a promising effect on heat transfer coefficient enhancement on coated surfaces. For horizontal surfaces, a maximum enhancement of 25% relative to the bare surface was achieved, while the maximum enhancement was 105% for the inclined coated surface under the optimum condition. iCVD was proven to be a practical method for coating surfaces for boiling heat transfer applications due to the obtained promising results.
Applicability of Net-Section Collapse Load Approach to Multiple-Cracked Pipe Assessment: Numerical Study
Authors: Lee Myeong-Woo , Lee So-Dam , Kim Yun-Jae
Published: May 2017

In this paper, applicability of net-section collapse load approach to circumferential multiple-cracked pipe assessment is investigated using finite element (FE) damage analysis. The FE damage analysis based on the stress-modified fracture strain model is validated against limited fracture test data of two circumferential surface-cracked pipes. Then, the systematic parametric study is performed using the FE damage analysis for symmetrical and asymmetrical surface-cracked pipes. It is found that predictions using the net-section collapse load approach tend to be more accurate with increasing the distance between two symmetrical cracks. For asymmetrical cracks, it is found that the deeper crack plays a more important role and that the existing net-section collapse load expression can be potentially nonconservative. Idealization to symmetrical cracks based on the deeper crack is proposed.
Characterization of Bulk and Thin Film Fracture in Electronic Packaging
Authors: Subramanian Vijay , Yazzie Kyle , Alazar Tsgereda , Penmecha Bharat , Liu Pilin , Bai Yiqun , Malatkar Pramod
Published: May 2017

As semiconductor packaging technologies continue to scale, it drives the use of existing and new materials in thin layer form factors. Increasing packaging complexity implies that materials in thin layers are subject to nontrivial loading conditions, which may exceed the toughness of the material, leading to cracks. It is important to ensure that the reliability of these low-cost materials is at par or better than currently used materials. This in turn leads to significant efforts in the area of material characterization at the lab level to speed up the development process. Methods for testing and characterizing fracture-induced failures in various material systems in electronic packaging are investigated in this paper. The learnings from different test methods are compared and discussed here. More specifically, different fracture characterization techniques on (a) freestanding “thin” solder-resist films and (b) filled “bulk” epoxy materials such as underfills and epoxy mold compounds are investigated. For thin films, learnings from different test methods for measuring fracture toughness, namely, uniaxial tension (with and without an edge precrack) and membrane penetration tests, are discussed. Reasonably good agreement is found between the various thin film toughness test methods; however, ease of sample preparation, fixture, and adaptability to environmental testing will be discussed. In the case of filled epoxy resin systems, the single-edge-notched bending (SENB) technique is utilized to obtain the fracture toughness of underfills and mold compounds with filler materials. Learnings on different methods of creating precracks in SENB samples are also investigated and presented.
Dynamic wall slip behavior of yield stress fluids under large amplitude oscillatory shear
Authors: Yang Kai , Yu Wei
Published: May 2017

Wall slip occurs under large amplitude oscillation shear (LAOS) for yield stress fluids. In this work, we investigated how the boundary conditions affect the nonlinear behavior under LAOS and proposed a simple methodology based on the geometric average of Lissajous curves to study the dynamic wall slip behavior under oscillatory shear. The results show that the stress-mean strain curve is a good candidate to define material's functions since it is almost not influenced by the wall slip effect. Meanwhile, the stress-mean strain rate curves from smooth plates and rough plates can be used to determine the wall slip velocity. It is found that the intercycle maximum slip strain rate follows the generalized Navier's law, while the intracycle slip behavior can be well described by a Maxwell-like dynamic slip model, which helps to determine the slip relaxation time. It is also found that the slip Deborah number is independent of the angular frequency and is a monotonically decreasing function of the reduced stress. Moreover, the slip Deborah number depends on the reduced stress through a power law, and there is an evident transition of the power law exponent at the yield stress.
Miocene flooding events of western Amazonia
Authors: Jaramillo Carlos , Romero Ingrid , D’Apolito Carlos , Bayona German , Duarte Edward , Louwye Stephen , Escobar Jaime , Luque Javier , Carrillo-Briceño Jorge D. , Zapata Vladimir , Mora Alejandro , Schouten Stefan , Zavada Michael , Harrington Guy , Ortiz John , Wesselingh Frank P.
Published: May 2017

Two distinct and short-lived flooding events of shallow marine waters covered western Amazonia during the Miocene.
Fibulin-4 is essential for maintaining arterial wall integrity in conduit but not muscular arteries
Authors: Halabi Carmen M. , Broekelmann Thomas J. , Lin Michelle , Lee Vivian S. , Chu Mon-Li , Mecham Robert P.
Published: May 2017

Characterization of a cutis laxa mouse model reveals distinct requirements for elastic fiber formation along the arterial tree.
Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells
Authors: Takahashi Yuta , Wu Jun , Suzuki Keiichiro , Martinez-Redondo Paloma , Li Mo , Liao Hsin-Kai , Wu Min-Zu , Hernández-Benítez Reyna , Hishida Tomoaki , Shokhirev Maxim Nikolaievich , Esteban Concepcion Rodriguez , Sancho-Martinez Ignacio , Belmonte Juan Carlos Izpisua
Published: May 2017

Stable epigenetic modifications can be introduced into stem cells via precise and targeted manipulation of DNA methylation.
Noise pollution is pervasive in U.S. protected areas
Authors: Buxton Rachel T. , McKenna Megan F. , Mennitt Daniel , Fristrup Kurt , Crooks Kevin , Angeloni Lisa , Wittemyer George
Published: May 2017

Human-produced noise infiltrates natural protected areas.
Negative selection in humans and fruit flies involves synergistic epistasis
Authors: Sohail Mashaal , Vakhrusheva Olga A. , Sul Jae Hoon , Pulit Sara L. , Francioli Laurent C. ,   Genome of the Netherlands Consortium,   Alzheimer’s Disease Neuroimaging Initiative, van den Berg Leonard H. , Veldink Jan H. , de Bakker Paul I. W. , Bazykin Georgii A. , Kondrashov Alexey S. , Sunyaev Shamil R. , Menelaou Androniki , van Dijk Freerk , Palamara Pier Francesco , Elbers Clara C. , Neerincx Pieter B.T. , Ye Kai , Guryev Victor , Kloosterman Wigard P. , Deelen Patrick , Abdellaoui Abdel , van Leeuwen Elisabeth M. , van Oven Mannis , Vermaat Martijn , Li Mingkun , Laros Jeroen F.J. , Karssen Lennart C. , Kanterakis Alexandros , Amin Najaf , Hottenga Jouke Jan , Lameijer Eric-Wubbo , Kattenberg Mathijs , Dijkstra Martijn , Byelas Heorhiy , van Setten Jessica , van Schaik Barbera D.C. , Bot Jan , Nijman Isac J. , Renkens Ivo , Marschall Tobias , Schnhuth Alexander , Hehir-Kwa Jayne Y. , Handsaker Robert E , Polak Paz , Vuzman Dana , Hormozdiari Fereydoun , van Enckevort David , Mei Hailiang , Koval Vyacheslav , Moed Matthijs H. , Joeri van der Velde K. , Rivadeneira Fernando , Estrada Karol , Medina-Gomez Carolina , Isaacs Aaron , McCarroll Steven A. , Beekman Marian , de Craen Anton J.M. , Suchiman H. Eka D. , Hofman Albert , Oostra Ben , Uitterlinden Andr G. , Willemsen Gonneke ,   LifeLines Cohort Study, Platteel Mathieu , Pitts Steven J. , Potluri Shobha , Sundar Purnima , Cox David R. , den Dunnen Johan T. , Stoneking Mark , de Knijff Peter , Kayser Manfred , Li Qibin , Li Yingrui , Du Yuanping , Chen Ruoyan , Cao Hongzhi , Li Ning , Cao Sujie , Wang Jun , Bovenberg Jasper A. , Pe’er Itsik , Slagboom P. Eline , van Duijn Cornelia M. , Boomsma Dorret I. , van Ommen Gert-Jan B , Swertz Morris A. , Wijmenga Cisca
Published: May 2017

Ongoing selection against rare protein-disrupting mutations depends on an individual’s relative decline in fitness with each additional mutation.
Unmask temporal trade-offs in climate policy debates
Authors: Ocko Ilissa B. , Hamburg Steven P. , Jacob Daniel J. , Keith David W. , Keohane Nathaniel O. , Oppenheimer Michael , Roy-Mayhew Joseph D. , Schrag Daniel P. , Pacala Stephen W.
Published: May 2017

Both 20- and 100-year time scales should always be reported
Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages
Authors: Ip W. K. Eddie , Hoshi Namiko , Shouval Dror S. , Snapper Scott , Medzhitov Ruslan
Published: May 2017

An interleukin controls a metabolic switch in macrophages that inhibits a signaling pathway, thereby suppressing intestinal inflammation.
Comment on “Density functional theory is straying from the path toward the exact functional”
Authors: Kepp Kasper P.
Published: May 2017

Medvedev
et al
. (Reports, 6 January 2017, p. 49) argue that recent density functionals stray from the path toward exactness. This conclusion rests on very compact 1s
2
and 1s
2
2s
2
systems favored by the Hartree-Fock picture. Comparison to actual energies for the same systems indicates that the “straying” is not chemically relevant and is at best specific to the studied dense systems.
Transcription factors read epigenetics
Authors: Hughes Timothy R. , Lambert Samuel A.
Published: May 2017

Many homeodomain transcription factors can bind methylated DNA
Evaluation of Aptima Zika Virus Assay
Authors: Ren Ping , Ortiz Daniel A. , Terzian Ana C. B. , Colombo Tatiana E. , Nogueira Mauricio L. , Vasilakis Nikos , Loeffelholz Michael J.
Published: May 2017

The Zika virus (ZIKV) epidemic in the Americas poses a public health emergency that requires a swift response. Accurate and reliable ZIKV diagnostic tests serve as an important tool for limiting the spread of ZIKV infections. The Aptima Zika virus assay (Hologic, Marlborough, MA) performed on the automated Panther system is a rapid and high-throughput method for detecting ZIKV RNA using transcription-mediated amplification (TMA) technology. We evaluated the performance characteristics of the Aptima Zika virus assay on clinical serum and urine specimens (
n
= 124) from two different patient populations and samples spiked with ZIKV from three different lineages (
n
= 10). Compared to the real-time reverse transcription-PCR (rRT-PCR) reference method, the Aptima ZIKV assay detected ZIKV RNA with a diagnostic accuracy of 94.8% (95% confidence interval [CI], 89.4 to 97.6), a sensitivity of 94.7% (95% CI, 73.5 to 99.9), and a specificity of 94.8% (95% CI, 88.9 to 97.8). Similar results were obtained regardless of whether a serum or urine source was used. The limits of detection of the assay at a 95% detection probability were 11.5 genome copy equivalents (GCE)/ml (95% fiducial limits, 7.9 to 20.2) in serum and 17.9 GCE/ml (95% fiducial limits, 13.1 to 27.5) in urine. The Aptima Zika virus assay results were highly reproducible (99%), and no cross-reactivity was seen during the testing of a panel of 95 specimens with potentially interfering substances, such as clinically relevant bacteria, fungi, and viruses, including other flaviviruses. The excellent performance characteristics and the convenience of a fully automated testing system make the Aptima ZIKV assay an attractive choice for clinical laboratories detecting ZIKV RNA from serum and urine.
Rubicon Modulates Antiviral Type I Interferon (IFN) Signaling by Targeting IFN Regulatory Factor 3 Dimerization
Authors: Kim Jae-Hoon , Kim Tae-Hwan , Lee Hyun-Cheol , Nikapitiya Chamilani , Uddin Md Bashir , Park Min-Eun , Pathinayake Prabuddha , Lee Eun Seo , Chathuranga Kiramage , Herath Thilina U. B. , Chathuranga W. A. Gayan , Lee Jong-Soo
Published: May 2017

Rubicon is part of a Beclin-1-Vps34-containing autophagy complex. Rubicon induces antimicrobial responses upon Toll-like receptor (TLR) stimulation and functions as a feedback inhibitor to prevent unbalanced proinflammatory responses depending on dectin-1 signaling. However, the role played by Rubicon during antiviral immune responses, particularly the type I interferon (IFN) responses, remains largely unknown. Here, we report that Rubicon acts as a negative regulator for virus-triggered IFN signaling. Knockdown of Rubicon promoted type I interferon signaling and inhibited virus replication, while overexpression of Rubicon had the opposite effect. Rubicon specifically interacts with the interferon regulatory factor (IRF) association domain (IAD) of IRF3, and this interaction leads to inhibition of the dimerization of IRF3, which negatively regulates IFN-mediated antiviral response. Thus, our findings suggest the novel additional role of Rubicon as a negative regulator that inhibits the IFN signaling and cellular antiviral responses, providing a novel cellular mechanism of IRF3 inhibition.

IMPORTANCE
The type I IFN system is a critical innate immune response that protects organisms against virus infection. However, type I IFN signaling must be tightly regulated to avoid excessive production of IFNs. Hence, negative regulatory mechanisms for type I IFN signaling are important, and to date, several related molecules have been identified. Here, we show that Rubicon is a major negative regulator of type I IFN signaling, and unlike previous reports of cellular molecules that inhibit IRF3 activation via proteasomal degradation or dephosphorylation of IRF3, we show that Rubicon interacts with IRF3 and that ultimately this interaction leads to inhibition of the dimerization of IRF3. Thus, we identified a novel negative regulator of type I IFN signaling pathways and a novel cellular mechanism of IRF3 inhibition. The results of this study will increase our understanding of the role of negative-feedback mechanisms that regulate type I IFN signaling and maintain immune homeostasis.
Suppressor Analysis of the Fusogenic Lambda Spanins
Authors: Cahill Jesse , Rajaure Manoj , Holt Ashley , Moreland Russell , O'Leary Chandler , Kulkarni Aneesha , Sloan Jordan , Young Ry
Published: May 2017

The final step of lysis in phage λ infections of
Escherichia coli
is mediated by the spanins Rz and Rz1. These proteins form a complex that bridges the cell envelope and that has been proposed to cause fusion of the inner and outer membranes. Accordingly, mutations that block spanin function are found within coiled-coil domains and the proline-rich region, motifs essential in other fusion systems. To gain insight into spanin function, pseudorevertant alleles that restored plaque formation for lysis-defective mutants of
Rz
and
Rz1
were selected. Most second-site suppressors clustered within a coiled-coil domain of Rz near the outer leaflet of the cytoplasmic membrane and were not allele specific. Suppressors largely encoded polar insertions within the hydrophobic core of the coiled-coil interface. Such suppressor changes resulted in decreased proteolytic stability of the Rz double mutants
in vivo
. Unlike the wild type, in which lysis occurs while the cells retain a rod shape, revertant alleles with second-site suppressor mutations supported lysis events that were preceded by spherical cell formation. This suggests that destabilization of the membrane-proximal coiled coil restores function for defective spanin alleles by increasing the conformational freedom of the complex at the cost of its normal, all-or-nothing functionality.

IMPORTANCE
Caudovirales
encode cell envelope-spanning proteins called spanins, which are thought to fuse the inner and outer membranes during phage lysis. Recent genetic analysis identified the functional domains of the lambda spanins, which are similar to class I viral fusion proteins. While the pre- and postfusion structures of model fusion systems have been well characterized, the intermediate structure(s) formed during the fusion reaction remains elusive. Genetic analysis would be expected to identify functional connections between intermediates. Since most membrane fusion systems are not genetically tractable, only few such investigations have been reported. Here, we report a suppressor analysis of lambda spanin function. To our knowledge this is the first suppression analysis of a class I-like complex and also the first such analysis of a prokaryote membrane fusion system.
Human Sera Collected between 1979 and 2010 Possess Blocking-Antibody Titers to Pandemic GII.4 Noroviruses Isolated over Three Decades
Authors: Sharma Sumit , Carlsson Beatrice , Czakó Rita , Vene Sirkka , Haglund Mats , Ludvigsson Johnny , Larson Göran , Hammarström Lennart , Sosnovtsev Stanislav V. , Atmar Robert L. , Green Kim Y. , Estes Mary K. , Svensson Lennart
Published: May 2017

The emergence of pandemic GII.4 norovirus (NoV) strains has been proposed to occur due to changes in receptor usage and thereby to lead to immune evasion. To address this hypothesis, we measured the ability of human sera collected between 1979 and 2010 to block glycan binding of four pandemic GII.4 noroviruses isolated in the last 4 decades. In total, 268 sera were investigated for 50% blocking titer (BT
50
) values of virus-like particles (VLPs) against pig gastric mucin (PGM) using 4 VLPs that represent different GII.4 norovirus variants identified between 1987 and 2012. Pre- and postpandemic sera (sera collected before and after isolation of the reference NoV strain) efficiently prevented binding of VLP strains MD145 (1987), Grimsby (1995), and Houston (2002), but not the Sydney (2012) strain, to PGM. No statistically significant difference in virus-blocking titers was observed between pre- and postpandemic sera. Moreover, paired sera showed that blocking titers of ≥160 were maintained over a 6-year period against MD145, Grimsby, and Houston VLPs. Significantly higher serum blocking titers (geometric mean titer [GMT], 1,704) were found among IgA-deficient individuals than among healthy blood donors (GMT, 90.9) (
P
< 0.0001). The observation that prepandemic sera possess robust blocking capacity for viruses identified decades later suggests a common attachment factor, at least until 2002. Our results indicate that serum IgG possesses antibody-blocking capacity and that blocking titers can be maintained for at least 6 years against 3 decades of pandemic GII.4 NoV.

IMPORTANCE
Human noroviruses (NoVs) are the major cause of acute gastroenteritis worldwide. Histo-blood group antigens (HBGAs) in saliva and gut recognize NoV and are the proposed ligands that facilitate infection. Polymorphisms in HBGA genes, and in particular a nonsense mutation in
FUT2
(G428A), result in resistance to global dominating GII.4 NoV. The emergence of new pandemic GII.4 strains occurs at intervals of several years and is proposed to be attributable to epochal evolution, including amino acid changes and immune evasion. However, it remains unclear whether exposure to a previous pandemic strain stimulates immunity to a pandemic strain identified decades later. We found that prepandemic sera possess robust virus-blocking capacity against viruses identified several decades later. We also show that serum lacking IgA antibodies is sufficient to block NoV VLP binding to HBGAs. This is essential, considering that 1 in every 600 Caucasian children is IgA deficient.
RNA Interference Restricts Rift Valley Fever Virus in Multiple Insect Systems
Authors: Dietrich Isabelle , Jansen Stephanie , Fall Gamou , Lorenzen Stephan , Rudolf Martin , Huber Katrin , Heitmann Anna , Schicht Sabine , Ndiaye El Hadji , Watson Mick , Castelli Ilaria , Brennan Benjamin , Elliott Richard M. , Diallo Mawlouth , Sall Amadou A. , Failloux Anna-Bella , Schnettler Esther , Kohl Alain , Becker Stefanie C.
Published: May 2017

Rift Valley fever virus (RVFV;
Phlebovirus
,
Bunyaviridae
) is an emerging zoonotic mosquito-borne pathogen of high relevance for human and animal health. Successful strategies of intervention in RVFV transmission by its mosquito vectors and the prevention of human and veterinary disease rely on a better understanding of the mechanisms that govern RVFV-vector interactions. Despite its medical importance, little is known about the factors that govern RVFV replication, dissemination, and transmission in the invertebrate host. Here we studied the role of the antiviral RNA interference immune pathways in the defense against RVFV in natural vector mosquitoes and mosquito cells and draw comparisons to the model insect
Drosophila melanogaster
. We found that RVFV infection induces both the exogenous small interfering RNA (siRNA) and piRNA pathways, which contribute to the control of viral replication in insects. Furthermore, we demonstrate the production of virus-derived piRNAs in
Culex quinquefasciatus
mosquitoes. Understanding these pathways and the targets within them offers the potential of the development of novel RVFV control measures in vector-based strategies.
0.2% chlorhexidine acetate as skin disinfectant prevents skin lesions in extremely preterm infants: a preliminary report
Authors: Janssen Lisanne M A , Tostmann Alma , Hopman Joost , Liem Kian D
Published: May 2017

Objective

The skin disinfectant ‘0.5% chlorhexidine gluconate in 70% alcohol’ (0.5% CHG-70% alc) may cause skin lesions in extremely preterm infants (gestational age <26 weeks). In April 2013, 0.2% chlorhexidine gluconate solution in acetate (0.2% CHG-acetate) was introduced as skin disinfectant for extremely preterm infants in our neonatal intensive care units. We aimed to compare the incidence of skin lesions and central line-associated bloodstream infection (CLABSI) among extremely preterm infants when using 0.5% CHG-70% alc and 0.2% CHG-acetate.

Design

Retrospective pre-post comparison cohort study.

Patients

All electronic patient records of extremely preterm infants born between January 2011–March 2013 (‘0.5% CHG-70% alc’ cohort) and April 2013–October 2015 (‘0.2% CHG-acetate’ cohort) were reviewed.

Main outcome measures

The incidence of skin lesions and CLABSI. Skin lesions were defined as the presence of erythema, blisters, excoriation, oedema or induration. CLABSI was defined according to the definition of the US Centers for Disease Control and Prevention.

Results

The incidence of skin lesions was 22% (95% CI 11% to 37%) in the ‘0.5% CHG-70% alc’ cohort (n=41) and 5% (95% CI 1% to 15%; p=0.02) in the ‘0.2% CHG-acetate’ cohort (n=41). The incidence of CLABSI was the same in both groups (28%; 95% CI 14% to 46% in ‘0.5% CHG-70% alc’ vs 27%; 95% CI 14% to 44% in ‘0.2% CHG-acetate’; p=0.98).

Conclusions

Using 0.2% CHG-acetate as skin disinfectant in extremely preterm infants resulted in statistically significant reduction of skin lesions, without increasing the risk of CLABSI as compared with 0.5% CHG-70% alc.
Skin diseases affecting the nasal planum and footpads of dogs
Authors: Hardy Jon
Published: May 2017

Skin diseases that affect the nasal planum and footpads of dogs are generally quite rare but, when they do occur, the two sites are often affected together and, due to their visible location, can cause considerable concern and distress for owners. Diseases range from benign cosmetic conditions to serious and life‐threatening disorders, so early recognition of a problem and an accurate diagnosis are important. This article reviews the important conditions that affect the nasal planum and footpads of dogs, giving details of their clinical signs and possible treatments.
Taking a full lunch break
Authors: Fawcett Anne , Brailey Juliana
Published: May 2017

THIS series gives readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved.

In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Taking a full lunch break’, was submitted and is discussed by Anne Fawcett and Juliana Brailey. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue.

The series is being coordinated by Steven McCulloch, a practising vet with a PhD in the ethics of veterinary policy. It aims to provide a framework that will help practitioners find solutions when facing similar dilemmas.
Comments on the dilemma in the April issue: Euthanasing treatable patients
Authors: McCulloch Steven
Published: May 2017

In the dilemma discussed in the April issue of In Practice, a recently employed veterinary surgeon is informed by their employer that the practice has a policy of only euthanasing patients who are terminally ill and suffering; it will not kill healthy or treatable patients. While the veterinary surgeon believes the policy is sincerely held, they wonder if it is fair. Does the practice's policy infringe on the veterinary surgeon's moral choice, and should he challenge it? (IP, April 2017, vol 39, pp 190‐191). Simon Coghlan suggested that the veterinary surgeon was entitled to discuss their moral concerns with the employer. This discussion may foster mutual understanding, and even improve the policy and details of its implementation. He also suggested that the employer should have informed the veterinary surgeon before they began work at the practice, to show greater respect for the veterinary surgeon's moral autonomy.
Dealing with possible criminal cases: witness work
Authors: Yeates James
Published: May 2017

Vets play an important role in providing evidence to courts on cases of animal cruelty and abuse. In this article, the second in a series on being involved in potential criminal animal welfare cases, James Yeates discusses the important aspects for vets to consider when acting as veterinary witnesses, either by providing factual testimony or expert opinion to courts, for cases of animal cruelty.
Patterns of genomic diversification reflect differences in life history and reproductive biology between figs (Ficus) and the stone oaks (Lithocarpus)
Authors: Kua Chai-Shian , Cannon Charles H.
Published: May 2017

One of the remarkable aspects of the tremendous biodiversity found in tropical forests is the wide range of evolutionary strategies that have produced this diversity, indicating many paths to diversification. We compare two diverse groups of trees with profoundly different biologies to discover whether these differences are reflected in their genomes. Ficus (Moraceae), with its complex co-evolutionary relationship with obligate pollinating wasps, produces copious tiny seeds that are widely dispersed. Lithocarpus (Fagaceae), with generalized insect pollination, produces large seeds that are poorly dispersed. We hypothesize that these different reproductive biologies and life history strategies should have a profound impact on the basic properties of genomic divergence within each genus. Using shallow whole genome sequencing for six species of Ficus, seven species of Lithocarpus, and three outgroups, we examined overall genomic diversity, how it is shared among the species within each genus, and the fraction of this shared diversity that agrees with the major phylogenetic pattern. A substantially larger fraction of the genome is shared among species of Lithocarpus, a considerable amount of this shared diversity was incongruent with the general background history of the genomes, and each fig species possessed a substantially larger fraction of unique diversity than Lithocarpus.
Design of LPV fault-tolerant controller for pitch system of wind turbine
Authors: Wu Dinghui , Zhang Xiaolin
Published: May 2017

To address failures of wind turbine pitch-angle sensors, traditional wind turbine linear parameter varying (LPV) model is transformed into a double-layer convex polyhedron LPV model. On the basis of this model, when the plurality of the sensor undergoes failure and details of the failure are inconvenient to obtain, each sub-controller is designed using distributed thought and gain scheduling method. The final controller is obtained using all of the sub-controllers by a convex combination. The design method corrects the errors of the linear model, improves the linear degree of the system, and solves the problem of multiple pitch angle faults to ensure stable operation of the wind turbine.