bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of a semi‐empirical dispersion correction for modeling water clusters
Authors: De Silva Nuwan , Adreance Matthew A. , Gordon Mark S.
Published: October 2018

The Grimme‐D3 semi‐empirical dispersion energy correction has been implemented for the original effective fragment potential for water (EFP1), and for systems that contain water molecules described by both correlatedab initioquantum mechanical (QM) molecules and EFP1. Binding energies obtained with these EFP1‐D and QM/EFP1‐D methods were tested using 27 benchmark species, including neutral, protonated, deprotonated, and auto‐ionized water clusters and nine solute–water binary complexes. The EFP1‐D and QM/EFP1‐D binding energies are compared with those obtained using fully QM methods: second‐order perturbation theory, and coupled cluster theory, CCSD(T), at the complete basis set (CBS) limit. The results show that the EFP1‐D and QM/EFP1‐D binding energies are in good agreement with CCSD(T)/CBS binding energies with a mean absolute error of 5.9 kcal/mol for water clusters and 0.8 kcal/mol for solute–water binary complexes. © 2018 Wiley Periodicals, Inc.
First Principles Calculations Toward Understanding SERS of 2,2′‐Bipyridyl Adsorbed on Au, Ag, and Au–Ag Nanoalloy
Authors: Takenaka Masato , Hashimoto Yoshikazu , Iwasa Takeshi , Taketsugu Tetsuya , Seniutinas Gediminas , Balčytis Armandas , Juodkazis Saulius , Nishijima Yoshiaki
Published: October 2018

First principles electrodyanmics and quantum chemical simulations are performed to gain insights into the underlying mechanisms of the surface enhanced Raman spectra of 22BPY adsorbed on pure Au and Ag as well as on Au–Ag alloy nanodiscs. Experimental SERS spectra from Au and Ag nanodiscs show similar peaks, whereas those from Au–Ag alloy reveal new spectral features. The physical enhancement factors due to surface nano‐texture were considered by numerical FDTD simulations of light intensity distribution for the nano‐textured Au, Ag, and Au–Ag alloy and compared with experimental results. For the chemical insights of the enhancement, the DFT calculations with the dispersion interaction were performed using Au20, Ag20, and Au10Ag10 clusters of a pyramidal structure for SERS modeling. Binding of 22BPY to the clusters was simulated by considering possible arrangements of vertex and planar physical as well as chemical adsorption models. The DFT results indicate that 22BPY prefers a coplanar adsorption on a (111) face with trans‐conformation having close energy difference to cis‐conformation. Binding to pure Au cluster is stronger than to pure Ag or Au–Ag alloy clusters and adsorption onto the alloy surface can deform the surface. The computed Raman spectra are compared with experimental data and assignments for pure Au and Ag models are well matching, indicating the need of dispersion interaction to reproduce strong Raman signal at around 800 cm–1. This work provides insight into 3D character of SERS on nanorough surfaces due to different binding energies and bond length of nanoalloys. © 2018 Wiley Periodicals, Inc.
Addressing an instability in unrestricted density functional theory direct dynamics simulations
Authors: Malpathak Shreyas , Ma Xinyou , Hase William L.
Published: October 2018

In Density Functional Theory (DFT) direct dynamics simulations with Unrestricted Hartree Fock (UHF) theory, triplet instability often emerges when numerically integrating a classical trajectory. A broken symmetry initial guess for the wave function is often used to obtain the unrestricted DFT potential energy surface (PES), but this is found to be often insufficient for direct dynamics simulations. An algorithm is described for obtaining smooth transitions between the open‐shell and the closed‐shell regions of the unrestricted PES, and thus stable trajectories, for direct dynamics simulations of dioxetane and its •OCH2‐CH2O• singlet diradical. © 2018 Wiley Periodicals, Inc.
Provider perspectives on a novel moral injury treatment for veterans: Initial assessment of acceptability and feasibility of the Impact of Killing treatment materials
Authors: Burkman Kristine , Purcell Natalie , Maguen Shira
Published: October 2018

Objective

We assessed whether treatment providers specializing in evidence‐based treatment for posttraumatic stress disorder found the Impact of Killing (IOK), a novel treatment for moral injury among combat veterans, acceptable, and feasible.

Methods

Ten providers from a large veterans administration (VA) medical center were provided with materials from IOK. We audio‐recorded a semistructured interview with each provider where we elicited open‐ended feedback as well as asked five structured questions about the relative advantage, compatibility, complexity/simplicity, trialability, and observability of IOK.

Results

All providers found IOK feasible, acceptable, and something they could incorporate into their existing practice. Providers reported that the spiritual and moral concerns addressed in IOK were novel, and that self‐forgiveness and making amends were critical components promoting healing from moral injury not emphasized in other treatments.

Conclusions

Among trauma providers, IOK was found acceptable and feasible, offering a novel approach to addressing moral injury among combat veterans.
Family environment moderates the relation of sluggish cognitive tempo to attention‐deficit/hyperactivity disorder inattention and depression
Authors: Fredrick Joseph W. , Luebbe Aaron M. , Mancini Kathryn J. , Burns G. Leonard , Epstein Jeffery N. , Garner Annie A. , Jarrett Matthew A. , Becker Stephen P.
Published: October 2018

Objectives

The current study investigated whether a maladaptive family environment would moderate the strength of the relations of sluggish cognitive tempo (SCT) to attention‐deficit/hyperactivity disorder inattention (ADHD‐IN) and to depressive symptoms in a large sample of college students.

Methods

Participants (n = 3,172), between the ages of 18–29 (M ± SDage = 19.24 ± 1.52; 69.8% women; 80.4% White) and enrolled in five universities in the United States completed self‐report measures of symptomatology, interparental conflict, and family expressiveness of emotions.

Results

A negative emotional climate strengthened relations of SCT with ADHD‐IN and depressive symptoms. Moreover, the lack of a positive emotional climate strengthened the co‐occurrence of SCT with depressive symptoms, though not with ADHD‐IN.

Conclusions

The current study is the first to demonstrate that the family environment moderates the association between SCT and co‐occurring symptomatology in young adults.
American Psychological Association practice guidelines for psychopharmacology: Ethical practice considerations for psychologists involving psychotropic use with children and adolescents
Authors: Goldberg Susan G. , Wagner Kathryn
Published: October 2018

Objectives

This study discusses the implications of the American Psychological Association’s 2011 Practice Guidelines for Pharmacology as they apply to psychologists working with juvenile clients. Special considerations apply due to concerns about the developmental side effects that occur when psychotropic medications are prescribed to children and adolescents.

Methods or Design

This study provides recommendations for implementing each of the Practice Guidelines. Constructive criticism of the Practice Guidelines is also discussed with the aim of improving service delivery.

Results

This study provides specific recommendations for psychologists regarding obtaining adequate knowledge about psychopharmacology to inform clients or consult with physicians. Suggestions are made for continuing education requirements for psychologists who work with juveniles.

Conclusions

Recommendations are made for psychologists working with juveniles to increase their knowledge of psychotropic medications for a more ethical and informed voice regarding the prescribing of such medications.
I heard it through the grapevine: Where and what parents learn about youth mental health treatments
Authors: O’Connor Erin E. , Langer David A.
Published: October 2018

Objective

This study investigates where parents learn about, and what parents know about child mental health services. Parents who are better informed about mental health services may be more likely to utilize services for their children.

Methods

In a national online survey, 196 parents of children between the ages of 4 and 17 years reported on their information‐seeking behaviors and their familiarity and experience with psychosocial approaches.

Results

Parents reported utilizing multiple information sources with mental health providers, pediatricians, and social networks being the most prominent. Parents’ trust in different sources varied, with parents generally trusting healthcare professionals the most. Parents exposed to mental health services were more aware of specific therapeutic approaches.

Conclusions

Data on how parents receive and understand mental health‐related information contributes to ongoing dissemination and implementation efforts.
To manualize, or not to manualize: Is that still the question? A systematic review of empirical evidence for manual superiority in psychological treatment
Authors: Truijens Femke , Zühlke‐van Hulzen Levin , Vanheule Stijn
Published: October 2018

Objective

Institutional promotion of psychotherapy manuals as a requirement for evidence‐based treatments (EBTs) yields the assumption that manualized treatment is more effective than nonmanualized treatment. This systematic review examines empirical evidence for this claim.

Methods

An electronic database search identified studies that directly or indirectly compared manual‐based and non‐manual‐based treatment.

Results

Six studies directly compared manualized and nonmanualized treatment (Hypothesis 1). None support manual superiority. Eight meta‐analyses indirectly assessed effect sizes of manual‐based treatment and control groups (Hypothesis 2). Three support manual superiority, five do not. One meta‐analysis and 15 further studies addressed manual adherence as an indirect indicator of manual efficacy (Hypothesis 3). The meta‐analysis concluded that manual adherence does not affect outcome, additional studies provided inconclusive results.

Conclusions

Manualized treatment is not empirically supported as more effective than nonmanualized treatment. While manual‐based treatment may be attractive as a research tool, it should not be promoted as being superior to nonmanualized psychotherapy for clinical practice.
Attachment assessment in clinical practice: Factor structure of the attachment questionnaire
Authors: Laverdière Olivier , Descôteaux Jean , Beaulieu‐Tremblay Thalie , Simard Valérie
Published: October 2018

Objective

Attachment theory is of great relevance to psychotherapy process and outcome. The labor‐intensive and time‐consuming nature of attachment codification impedes its widespread use in clinical practice. The Attachment Questionnaire (AQ), a clinician‐rated instrument, was developed to address these limitations. However, the status of validation of the AQ remains preliminary. The objective of this study is to further validate the AQ by evaluating its factor structure and convergent validity.

Methods

To this end, 389 psychotherapists completed the AQ and assessed patients’ personality disorders and level of functioning.

Results

Factor analyses revealed that a five‐factor solution provided a better fit than the original four‐factor solution. The additional factor, inhibited exploration, captured difficulties in open, nondefensive, exploration of memories and their effects. Correlations between AQ factors and criterion variables support the convergent validity of the AQ.

Conclusions

These results are discussed in light of patients’ characteristics and recent advances in attachment research.
The vacuolated morphology of chordoma cells is dependent on cytokeratin intermediate filaments
Authors: Resutek Lauren , Hsieh Adam H.
Published: October 2018

Notochordal cells (NCs), characterized by their vacuolated morphology and coexpression of cytokeratin and vimentin intermediate filaments (IFs), form the immature nucleus pulposus (NP) of the intervertebral disc. As humans age, NCs give way to mature NP cells, which do not possess a vacuolated morphology and typically only express vimentin IFs. In light of their concomitant loss, we investigated the relationship between cytosolic vacuoles and cytokeratin IFs, specifically those containing cytokeratin‐8 proteins, using a human chordoma cell line as a model for NCs. We demonstrate that the chemical disruption of IFs with acrylamide, F‐actin with cytochalasin‐D, and microtubules with nocodazole all result in a significant (p < 0.001) decrease in vacuolation. However, vacuole loss was the greatest in acrylamide‐treated cells. Examination of the individual roles of vimentin and cytokeratin‐8 IFs in the existence of vacuoles was accomplished using small interfering RNA–mediated RNA interference to knock down either vimentin or cytokeratin‐8 expression. Reduction of cytokeratin‐8 expression was associated with a less‐vacuolated cell morphology. These data demonstrate that cytokeratin‐8 IFs are involved in stabilizing vacuoles and that their diminished expression could play a role in the loss of vacuolation in NCs during aging. A better understanding of the NCs may assist in preservation of this cell type for NP maintenance and regeneration.
Matrix stiffness modulates the differentiation of neural crest stem cells in vivo
Authors: Zhu Yiqian , Li Xian , Janairo Randall Raphael R. , Kwong George , Tsou Anchi D. , Chu Julia S. , Wang Aijun , Yu Jian , Wang Dong , Li Song
Published: October 2018

Stem cells are often transplanted with scaffolds for tissue regeneration; however, how the mechanical property of a scaffold modulates stem cell fate in vivo is not well understood. Here we investigated how matrix stiffness modulates stem cell differentiation in a model of vascular graft transplantation. Multipotent neural crest stem cells (NCSCs) were differentiated from induced pluripotent stem cells, embedded in the hydrogel on the outer surface of nanofibrous polymer grafts, and implanted into rat carotid arteries by anastomosis. After 3 months, NCSCs differentiated into smooth muscle cells (SMCs) near the outer surface of the polymer grafts; in contrast, NCSCs differentiated into glial cells in the most part of the hydrogel. Atomic force microscopy demonstrated a stiffer matrix near the polymer surface but much lower stiffness away from the polymer graft. Consistently, in vitro studies confirmed that stiff surface induced SMC genes whereas soft surface induced glial genes. These results suggest that the scaffold’s mechanical properties play an important role in directing stem cell differentiation in vivo, which has important implications in biomaterials design for stem cell delivery and tissue engineering.
MicroRNA‐140‐5p targeting tumor necrosis factor‐α prevents pulmonary arterial hypertension
Authors: Zhu Tian‐Tian , Zhang Wei‐Fang , Yin Ya‐Ling , Liu Yu‐Hao , Song Ping , Xu Jian , Zhang Ming‐Xiang , Li Peng
Published: October 2018

Background

Pulmonary arterial hypertension (PAH) is characterized by the apoptosis resistance and hyperproliferation of pulmonary artery smooth muscle cells (PASMCs). Its pathogenesis has not been revealed. Here, we carried out experiments to investigate the functions of miR‐140‐5p and tumor necrosis factor‐α (TNF‐α).

Methods

We selected GSE703 from Gene Expression Omnibus (GEO) Database to conduct microarray analysis using R software and Gene Set Enrichment Analysis (GSEA). Combing bioinformatics results, the upregulation of miR‐140‐5p inhibited PAH progression through targeting TNF‐α. RNA expression was measured by quantitative real‐time polymerase chain reaction (RT‐qPCR) and protein level was measured by western blot analysis and enzyme‐linked immunosorbent assays (ELISA). We conducted monocrotaline (MCT) injection to rats to form PAH animal models. The lung tissues were observed by hematoxylin–eosin (HE) staining and Sirius red‐picric acid staining. Right ventricular systolic pressure (RVSP) and the ratio of right ventricle (RV)‐to‐left ventricle (LV) plus septum (S) weight (RV/[LV + S]) were measured in MCT‐induced animal models. Overexpression of miR‐140‐5p and TNF‐α were utilized to research the proliferation, migration, and phenotypic variation of hypoxia‐mediated PASMCs. The binding between miR‐140‐5p and TNF‐α 3′‐untranslated region (3′‐UTR) was confirmed via luciferase reporter assay.

Results

Downregulation of miR‐140‐5p and upregulation of TNF‐α were observed in PAH rat model and hypoxia‐mediated PASMCs. And we proved that overexpression of miR‐140‐5p could suppress the proliferation, migration, and phenotypic variation of PASMCs, therefore inhibiting PAH pathogenesis. Luciferase assay verified that miR‐140‐5p targeted TNF‐α directly. A converse correlation was also shown between miR‐140‐5p and TNF‐α in PASMCs.

Conclusions

miR‐140‐5p and TNF‐α are important regulators in PAH pathology and may serve as a therapeutic target for PAH.
An optimized sample preparation approach for atomic resolution in situ studies of thin films
Authors: Moatti Adele , Sachan Ritesh , Prater John , Narayan Jagdish
Published: October 2018

This work provides the details of a simple and reliable method with less damage to prepare electron transparent samples for in situ studies in scanning/transmission electron microscopy. In this study, we use epitaxial VO2 thin films grown on c‐Al2O3 by pulsed laser deposition, which have a monoclinic–rutile transition at ~68°C. We employ an approach combining conventional mechanical wedge‐polishing and Focused Ion beam to prepare the electron transparent samples of epitaxial VO2 thin films. The samples are first mechanically wedge‐polished and ion‐milled to be electron transparent. Subsequently, the thin region of VO2 films are separated from the rest of the polished sample using a focused ion beam and transferred to the in situ electron microscopy test stage. As a critical step, carbon nanotubes are used as connectors to the manipulator needle for a soft transfer process. This is done to avoid shattering of the brittle substrate film on the in situ sample support stage during the transfer process. We finally present the atomically resolved structural transition in VO2 films using this technique. This approach significantly increases the success rate of high‐quality sample preparation with less damage for in situ studies of thin films and reduces the cost and instrumental/user errors associated with other techniques.

The present work highlights a novel, simple, reliable approach with reduced damage to make electron transparent samples for atomic‐scale insights of temperature‐dependent transitions in epitaxial thin film heterostructures using in situ TEM studies.
Locomotor kinematics of tree squirrels (Sciurus carolinensis) in free‐ranging and laboratory environments: Implications for primate locomotion and evolution
Authors: Dunham Noah T. , McNamara Allison , Shapiro Liza , Phelps Taylor , Wolfe Adrienne N. , Young Jesse W.
Published: October 2018

The grasping capabilities and gait kinematics characteristic of primates are often argued to be adaptations for safely moving on small terminal branches. The goal of this study was to identify whether Eastern gray squirrels (Sciurus carolinensis)—arboreal rodents that frequently move and forage on small branches, lack primate‐like grasping and gait patterns, and arguably represent extant analogs of a stem primate ancestor—adjust gait kinematics to narrow and nonhorizontal branches. We studied locomotor kinematics of free‐ranging and laboratory‐housed squirrels moving over various substrates. We used high‐speed video to film (a) a population of free‐ranging squirrels moving on natural substrates and (b) laboratory‐housed squirrels moving on horizontal poles. Substrates were coded as small, medium, or large relative to squirrel trunk diameter, and as inclined, declined, or horizontal. Free‐ranging squirrels used more gallops and half‐bounds on small‐ and medium‐sized substrates, and more high‐impact bounds, with reduced limb‐lead durations, on declined substrates. Laboratory squirrels moved at higher speeds than free‐ranging squirrels and responded to decreasing diameter by using more gallops and half‐bounds, lowering speed, and—controlling for speed—increasing mean duty factor, mean number of supporting limbs, and relative forelimb lead duration. Our inability to detect substantial diameter or orientation‐related gait adjustments in the wild may be due to a limited accounting of confounding influences (e.g., substrate compliance). Ultimately, studies assessing stability measures (e.g., center of mass fluctuations and peak vertical force) are required to assess whether primates' enhanced grasping and gait patterns engender performance advantages on narrow or oblique substrates.
The Salmonella pathogenicity island-2 subverts human NLRP3 and NLRC4 inflammasome responses
Authors: Bierschenk Damien , Monteleone Mercedes , Moghaddas Fiona , Baker Paul J , Masters Seth L , Boucher Dave , Schroder Kate
Published: October 2018

Inflammasomes are signaling hubs that activate inflammatory caspases to drive cytokine maturation and cell lysis. Inflammasome activation by Salmonella Typhimurium infection or Salmonella-derived molecules is extensively studied in murine myeloid cells. Salmonella-induced inflammasome signaling in human innate immune cells, is however, poorly characterized. Here, we show that Salmonella mutation to inactivate the Salmonella pathogenicity island-2 type III secretion system (SPI2 T3SS) potentiates S. Typhimurium-induced inflammasome responses from primary human macrophages, resulting in strong IL-1β production and macrophage death. Inactivation of the SPI1 T3SS diminished human macrophage responses to WT and ΔSPI2 Salmonella. Salmonella ΔSPI2 elicited a mixed inflammasome response from human myeloid cells, in which NLR family CARD-domain containing protein 4 (NLRC4) and NLR family PYRIN-domain containing protein 3 (NLRP3) perform somewhat redundant functions in generating IL-1β and inducing pyroptosis. Our data suggest that Salmonella employs the SPI2 T3SS to subvert SPI1-induced NLRP3 and NLRC4 inflammasome responses in human primary macrophages, in a species-specific immune evasion mechanism.

The Gram-negative bacterium Salmonella Typhimurium suppresses human macrophage inflammasome responses via the Salmonella Pathogenicity Island 2.
An embryonic staging series up to hatching for Cyprinodon variegatus: An emerging fish model for developmental, evolutionary, and ecological research
Authors: Lencer Ezra S. , McCune Amy R.
Published: October 2018

Using multiple taxa to research development is necessary for making general conclusions about developmental patterns and mechanisms. We present a staging series for Cyprinodon variegatus as a basis for further study of the developmental biology of fishes in the genus Cyprinodon and for comparative work on teleost fishes beyond the standard models. Cyprinodon are small, euryhaline fishes, widely distributed in fresh, brackish, and hypersaline waters of southern and eastern North America. Cyprinodontids are closely related to fundulids, providing a comparative reference point to the embryological model, Fundulus heteroclitus. Ecologists and evolutionary biologists commonly study Cyprinodon, and we have been using Cyprinodon to study skull variation and its genetic basis among closely related species. We divided embryonic development of C. variegatus into 34 morphologically identifiable stages. We reference our staging series to that already defined for a related model species, Oryzias latipes (medaka) that is studied by a large community of researchers. We provide a description of the early chondrogenesis and ossification of skull and caudal fin bones during the latter stages of embryonic development. We show that Cyprinodon are tractable for studying development. Eggs can be obtained easily from breeding pairs and our study provides a staging system to facilitate future developmental studies.
Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes
Authors: Ghedotti Michael J. , Gruber Josephine N. , Barton Ryan W. , Davis Matthew P. , Smith W. Leo
Published: October 2018

Bioluminescent organs have evolved many times within teleost fishes and exhibit a wide range of complexity and anatomical derivation. Although some bioluminescent organs have been studied in detail, the morphology of the bacterial light organs in glowbellies (Acropoma) is largely unknown. This study describes the anatomy of the bioluminescent organs in Haneda's Glowbelly (Acropoma hanedai) and the Glowbelly (Acropoma japonicum) and places the evolution of this light‐producing system in the context of a new phylogeny of glowbellies and their relatives. Gross and histological examination of the bioluminescent organs indicate that they are derived from perianal ectodermal tissue, likely originating from the developmental proctodeum, contrary to at least one prior suggestion that the bioluminescent organ in Acropoma is of endodermal intestinal derivation. Additionally, anterior bioluminescent organ development in both species is associated with lateral spreading of the bacteria‐containing arms of the bioluminescent organ from an initial median structure. In the context of a 16‐gene molecular phylogeny, the bioluminescent organ in Acropoma is shown to have evolved within the Acropomatidae in the ancestor of Acropoma. Further, ancestral‐states reconstruction demonstrates that the bioluminescent organs in Acropoma evolved independently from the light organs in related howellid and epigonid taxa which have esophageal or intestinally derived bioluminescent organs. Across the acropomatiforms, our reconstructions indicate that bioluminescent organs evolved independently four or five times. Based on the inferred phylogeny of the order where Acropoma and Doederleinia were separated from other traditional acropomatids, the familial taxonomy of the Acropomatidae was modified such that the previously described Malakichthyidae and Synagropidae were recognized. We also morphologically diagnose and describe the family Lateolabracidae.
Stable 3D FDTD method for arbitrary fully electric and magnetic anisotropic Maxwell's equations
Authors: Nehls John , Dineen Colm , Liu Jinjie , Poole Cody , Brio Moysey , Moloney Jerome V.
Published: October 2018

We have developed a new fully anisotropic 3D FDTD Maxwell solver for arbitrary electrically and magnetically anisotropic media for piecewise constant electric and magnetic materials that are co‐located over the primary computational cells. Two numerical methods were developed that are called nonaveraged and averaged methods, respectively. The nonaveraged method is first‐order accurate, while the averaged method is second‐order accurate for smoothly‐varying materials and reduces to first order for discontinuous material distributions. For the standard FDTD field locations with the co‐location of the electric and magnetic materials at the primary computational cells, the averaged method required development of the different inversion algorithms of the constitutive relations for the electric and magnetic fields. We provide a mathematically rigorous stability proof followed by extensive numerical testing that includes long‐time integration, eigenvalue analysis, tests with extreme, randomly placed material parameters, and various boundary conditions. For accuracy evaluation, we have constructed a test case with an explicit analytic solution. Using transformation optics, we have constructed complex, spatially inhomogeneous geometrical object with fully‐anisotropic materials and a large dynamic range of
and
, such that a plane wave incident on the object is perfectly reconstructed downstream.
Poly glycidyl methacrylate‐co‐ethylene dimethacrylate porous monolith as a versatile platform for the development of separations and solid‐phase extractions in sequential injection analyzers
Authors: Ribeiro Luiz F. , Lopes Martins Renan , de Souza Costa Diego M. , Masini Jorge C.
Published: October 2018

We demonstrated that the porous structure and the reactivity of the epoxy group in the poly glycidyl methacrylate‐co‐ethylene dimethacrylate monolith can be a platform for the development of separation and extraction methods based on sequential injection analysis. The epoxy group was functionalized to produce monoliths affording complexing and ion exchange properties. Derivatization with iminodiacetate and sodium sulfite produced weak and strong cation exchangers, respectively. Derivatization with ethylenediamine produced a weak anion exchanger, and the treatment of the ethylenediamine‐modified monolith with chloroacetate produced another weak cation exchanger. All the monoliths also worked as chelating sorbents. The columns were prepared inside 50 × 2.01 mm id fused‐silica lined stainless steel tubing and exhibited permeabilities between 0.76 and 4.92 × 10−13 m2, which enabled the application of flow rates between 5 and 15 μL/s by the syringe pumps used in sequential injection analyzers. These columns separated proteins by cation or anion exchange in a sequential injection chromatograph in both synthetic mixtures and in egg white. Additionally, the online solid‐phase extraction of copper ions was demonstrated in a sequential injection analyzer with the same columns. Postcolumn derivatization with ethylenediamine and spectrophotometric detection was used for the copper detection.
Effects of prescribed fire on San Francisco gartersnake survival and movement
Authors: Halstead Brian J. , Thompson Michelle E. , Amarello Melissa , Smith Jeffrey J. , Wylie Glenn D. , Routman Eric J. , Casazza Michael L.
Published: October 2018

The application of fire is prescribed for management of habitats for many plant and animal communities, but its effects on herpetofauna are diverse and remain poorly understood. To date no studies have examined the effects of prescribed fire on endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) populations, despite a call for prescribed fire in the recovery plan for the species. We used multi‐state capture‐mark‐recapture models to assess whether effects of prescribed fire were ephemeral, occurring only during the year of the fire, or persisted for 3 years following the fire, and to estimate the effects of prescribed fire on demographic parameters of San Francisco gartersnakes inhabiting California coastal prairie. Ephemeral fire effects were better supported for transitions (movement) between burned and unburned areas, but persistent fire effects were better supported for apparent survival and recapture probabilities. Movement between burned and unburned areas decreased during the year of the fire, but transition rates from burned to unburned areas decreased less than transition rates from unburned to burned areas in the year of the fire. Apparent survival probabilities increased in the unburned areas following the fire but were largely unchanged, though more uncertain, in burned areas following the fire. Recapture probabilities decreased site‐wide following the fire, though the decrease was greater in burned areas than in unburned areas. Although imprecise, our estimates of the effects of prescribed fire suggest that under the conditions of this fire (low‐intensity fall burn applied to a small area within a robust population and followed by wet weather), prescribed fire is a viable management tool for maintaining open habitats where San Francisco gartersnakes occur. © 2018 The Wildlife Society.
Seasonal metabolism and carbon export potential of a key coastal habitat: The perennial canopy‐forming macroalga Fucus vesiculosus
Authors: Attard K. M. , Rodil I. F. , Berg P. , Norkko J. , Norkko A. , Glud R. N.
Published: October 2018

The important role of macroalgal canopies in the oceanic carbon (C) cycle is increasingly being recognized, but direct assessments of community productivity remain scarce. We conducted a seasonal study on a sublittoral Baltic Sea canopy of the brown alga Fucus vesiculosus, a prominent species in temperate and Arctic waters. We investigated community production on hourly, daily, and seasonal timescales. Aquatic eddy covariance (AEC) oxygen flux measurements integrated ~ 40 m2 of the seabed surface area and documented considerable oxygen production by the canopy year‐round. High net oxygen production rates of up to 35 ± 9 mmol m−2 h−1 were measured under peak irradiance of ~ 1200 μmol photosynthetically active radiation (PAR) m−2 s−1 in summer. However, high rates > 15 mmol m−2 h−1 were also measured in late winter (March) under low light intensities < 250 μmol PAR m−2 s−1 and water temperatures of ~ 1°C. In some cases, hourly AEC fluxes documented an apparent release of oxygen by the canopy under dark conditions, which may be due to gas storage dynamics within internal air spaces of F. vesiculosus. Daily net ecosystem metabolism (NEM) was positive (net autotrophic) in all but one of the five measurement campaigns (December). A simple regression model predicted a net autotrophic canopy for two‐thirds of the year, and annual canopy NEM amounted to 25 mol O2 m−2 yr−1, approximately six‐fold higher than net phytoplankton production. Canopy C export was ~ 0.3 kg C m−2 yr−1, comparable to canopy standing biomass in summer. Macroalgal canopies thus represent regions of intensified C assimilation and export in coastal waters.
Environmental controls on pteropod biogeography along the Western Antarctic Peninsula
Authors: Thibodeau P. S. , Steinberg D. K. , Stammerjohn S. E. , Hauri C.
Published: October 2018

Abstract

Pteropods are abundant zooplankton in the Western Antarctic Peninsula (WAP) and important grazers of phytoplankton and prey for higher trophic levels. We analyzed long‐term (1993–2017) trends in summer (January–February) abundance of WAP pteropods in relation to environmental controls (sea ice, sea surface temperature, climate indices, phytoplankton biomass and productivity, and carbonate chemistry) and interspecies dynamics using general linear models. There was no overall directional trend in abundance of thecosomes, Limacina helicina antarctica and Clio pyramidata, throughout the entire WAP, although L. antarctica abundance increased in the slope region and C. pyramidata abundance increased in the South. High L. antarctica abundance was strongly tied to a negative Multivariate El Niño Southern Oscillation Index the previous year. C. pyramidata abundance was best explained by early sea ice retreat 1‐yr prior. Abundance of the gymnosome species, Clione antarctica and Spongiobranchaea australis, increased over the time series, particularly in the slope region. Gymnosome abundance was positively influenced by abundance of their prey, L. antarctica, during the same season, and late sea ice advance 2‐yr prior. These trends indicate a shorter ice season promotes longer periods of open water in spring/summer favoring all pteropod species. Weak relationships were found between pteropod abundance and carbonate chemistry, and no long‐term trend in carbonate parameters was detected. These factors indicate ocean acidification is not presently influencing WAP pteropod abundance. Pteropods are responsive to the considerable environmental variability on both temporal and spatial scales—key for predicting future effects of climate change on regional carbon cycling and plankton trophic interactions.
The euphausiid prey field for blue whales around a steep bathymetric feature in the southern California current system
Authors: Nickels Catherine F. , Sala Linsey M. , Ohman Mark D.
Published: October 2018

Euphausiids are important prey for many marine organisms and often occur in patchy aggregations. Euphausiid predators, such as blue whales, may become concentrated in the vicinity of these aggregations. We investigated an area called Nine Mile Bank (NMB) near San Diego, California, defined by an area of steep bathymetry, to determine whether the frequent whale sightings in that locality can be explained by the distribution of euphausiids across the bank and by the vertical distribution of euphausiids in the water column. Thysanoessa spinifera, the strongly preferred blue whale prey euphausiid in this area, was consistently more abundant on the bank or inshore of it than offshore. In contrast, Euphausia pacifica, a minor blue whale prey item, was much more abundant and distributed across the study region. Adults of both species were concentrated in a stratum corresponding to the feeding depth of blue whales. Other euphausiids that form a negligible part of the blue whale diet also showed no association with NMB. Both blue whales and their primary prey species Thysanoessa spinifera were more abundant on or inshore of the bank than offshore, suggesting that the bank may serve as an offshore limit of high prey abundance that helps to concentrate blue whales.
Automated plankton image analysis using convolutional neural networks
Authors: Luo Jessica Y. , Irisson Jean‐Olivier , Graham Benjamin , Guigand Cedric , Sarafraz Amin , Mader Christopher , Cowen Robert K.
Published: October 2018

The rise of in situ plankton imaging systems, particularly high‐volume imagers such as the In Situ Ichthyoplankton Imaging System, has increased the need for fast processing and accurate classification tools that can identify a high diversity of organisms and nonliving particles of biological origin. Previous methods for automated classification have yielded moderate results that either can resolve few groups at high accuracy or many groups at relatively low accuracy. However, with the advent of new deep learning tools such as convolutional neural networks (CNNs), the automated identification of plankton images can be vastly improved. Here, we describe an image processing procedure that includes preprocessing, segmentation, classification, and postprocessing for the accurate identification of 108 classes of plankton using spatially sparse CNNs. Following a filtering process to remove images with low classification scores, a fully random evaluation of the classification showed that average precision was 84% and recall was 40% for all groups. Reliably classifying rare biological classes was difficult, so after excluding the 12 rarest taxa, classification accuracy for the remaining biological groups became > 90%. This method provides proof of concept for the effectiveness of an automated classification scheme using deep‐learning methods, which can be applied to a range of plankton or biological imaging systems, with the eventual application in a variety of ecological monitoring and fisheries management contexts.
Exploring Time‐Resolved Multiphysics of Active Plasmonic Systems with Experiment‐Based Gain Models
Authors: Azzam Shaimaa I. , Fang Jieran , Liu Jingjing , Wang Zhuoxian , Arnold Nikita , Klar Thomas A. , Prokopeva Ludmila J. , Meng Xiangeng , Shalaev Vladimir M. , Kildishev Alexander V.
Published: October 2018

A systematic approach to investigate lasing and net amplification in plasmonic structures with a finite‐difference time‐domain method coupled to the rate equations of four‐level and six‐level atomic systems is developed. The experiment‐fitted kinetic parameters are fed into the model to study the mechanism of the coupling of metamaterials and metasurfaces with the gain medium. With the help of such an accurate model, net amplification can be distinguished from time‐resolved lasing dynamics for the plasmonic systems coupled with gain.
Direction‐Controlled Bifunctional Metasurface Polarizers
Authors: Chen Yang , Gao Jie , Yang Xiaodong
Published: October 2018

Metasurfaces composed of in‐plane subwavelength nanostructures have unprecedented capability in manipulating the amplitude, phase, and polarization states of light. Here, a unique type of direction‐controlled bifunctional metasurface polarizer is proposed and experimentally demonstrated based on plasmonic stepped slit‐groove dimers. In the forward direction, a chiral linear polarizer is enabled which only allows the transmission of a certain incident handedness and converts it into the specified linear polarization. In the backward direction, the metasurface functions as an anisotropic circular polarizer to selectively convert a certain linear polarization component into the desired circularly polarized transmission. The observed direction‐controlled polarization selection and conversion are explained by the spin‐dependent mode coupling process inside the bilayer structure. Anisotropic chiral imaging based on the proposed metasurface polarizer is further demonstrated. The results provide new degrees of freedom to realize future multifunctional photonic integrated devices for structured light conversion, vector beam generation, optical imaging and sensing, and optical communication.
Association of Pretransplant Renal Function With Liver Graft and Patient Survival After Liver Transplantation in Patients With Nonalcoholic Steatohepatitis
Authors: Molnar Miklos Z. , Joglekar Kiran , Jiang Yu , Cholankeril George , Abdul Mubeen Khan Mohammed , Kedia Satish , Gonzalez Humberto C. , Ahmed Aijaz , Singal Ashwani , Bhamidimarri Kalyan Ram , Aithal Guruprasad Padur , Duseja Ajay , Wong Vincent Wai‐Sun , Gulnare Agayeva , Puri Puneet , Nair Satheesh , Eason James D. , Satapathy Sanjaya K. ,   for the Global NAFLD Consortium
Published: October 2018

Nonalcoholic steatohepatitis (NASH) is one of the top 3 indications for liver transplantation (LT) in Western countries. It is unknown whether renal dysfunction at the time of LT has any effect on post‐LT outcomes in recipients with NASH. From the United Network for Organ Sharing–Standard Transplant Analysis and Research data set, we identified 4088 NASH recipients who received deceased donor LT. We divided our recipients a priori into 3 categories: group 1 with estimated glomerular filtration rate (eGFR) <30 mL/minute/1.73 m2 at the time of LT and/or received dialysis within 2 weeks preceding LT (n = 937); group 2 with recipients who had eGFR ≥30 mL/minute/1.73 m2 and who did not receive renal replacement therapy prior to LT (n = 2812); and group 3 with recipients who underwent simultaneous liver‐kidney transplantation (n = 339). We examined the association of pretransplant renal dysfunction with death with a functioning graft, all‐cause mortality, and graft loss using competing risk regression and Cox proportional hazards models. The mean ± standard deviation age of the cohort at baseline was 58 ± 8 years, 55% were male, 80% were Caucasian, and average exception Model for End‐Stage Liver Disease score was 24 ± 9. The median follow‐up period was 5 years (median, 1816 days; interquartile range, 1090‐2723 days). Compared with group 1 recipients, group 2 recipients had 19% reduced trend for risk for death with a functioning graft (subhazard ratio [SHR], 0.81; 95% confidence interval [CI], 0.64‐1.02) and similar risk for graft loss (SHR, 1.25; 95% CI, 0.59‐2.62), whereas group 3 recipients had similar risk for death with a functioning graft (SHR, 1.23; 95% CI, 0.96‐1.57) and graft loss (SHR, 0.18; 95% CI, 0.02‐1.37) using an adjusted competing risk regression model. In conclusion, recipients with preserved renal function before LT showed a trend toward lower risk of death with a functioning graft compared with SLKT recipients and those with pretransplant severe renal dysfunction in patients with NASH.
Impact of Prior Bariatric Surgery on Perioperative Liver Transplant Outcomes
Authors: Idriss Rajab , Hasse Jeanette , Wu Tiffany , Khan Fatima , Saracino Giovanna , McKenna Greg , Testa Giuliano , Trotter James , Klintmalm Goran , Asrani Sumeet K.
Published: October 2018

Bariatric surgery (BS) is effective in treating morbid obesity, but the impact of prior BS on candidacy for liver transplantation (LT) is unclear. We examined 78 patients with cirrhosis with prior BS compared with a concurrent cohort of 156 patients matched by age, Model for End‐Stage Liver Disease score, and underlying liver disease. We compared rates of transplant denial after evaluation, delisting on the waiting list, and survival after LT. The median time from BS to LT evaluation was 7 years. Roux‐en‐Y gastric bypass was the most common BS procedure performed (63% of cohort). Nonalcoholic fatty liver disease was the leading etiology for liver cirrhosis (47%). Delisting/death on the waiting list was higher among patients with BS (33.3% versus 10.1%; P = 0.002), and the transplantation rate was lower (48.9% versus 65.2%; P = 0.03). Intention‐to‐treat (ITT) survival from listing to 1 year after LT was lower in the BS cohort versus concurrent cohort (1‐year survival, 84% versus 90%; P = 0.05). On adjusted analysis, a history of BS was associated with an increased risk of death on the waiting list (hazard ratio [HR], 5.7; 95% confidence interval [CI], 2.2‐15.1), but this impact was attenuated (HR, 4.9; 95% CI, 1.8‐13.4) by the presence of malnutrition. When limited to matched controls by sex, mortality attributed to BS was no longer significant for females (P = 0.37) but was significant for males (P = 0.046). Sarcopenia, as captured by skeletal muscle index, was calculated in a subset of patients (n = 49). The total skeletal surface area was lower in the BS group (127 [105‐141] cm2 versus 153 [131‐191] cm2; P = 0.005). Rates of sarcopenia were higher among patients delisted after listing (71.4% versus 16.7%; P = 0.04). In conclusion, a history of BS was associated with higher rates of delisting on the waiting list as well as lower survival from the time of listing on ITT analysis. Presence of malnutrition and sarcopenia among patients with BS may contribute to worse outcomes.
Anion‐Mediated Effects on the Size and Mechanical Properties of Enzymatically Crosslinked Suckerin Hydrogels
Authors: Buck Chelsea C. , Dennis Patrick B. , Gupta Maneesh K. , Grant Marcus T. , Crosby Marquise G. , Slocik Joseph M. , Mirau Peter A. , Becknell Kellie A. , Comfort Kristen K. , Naik Rajesh R.
Published: October 2018

The suckerin family of proteins, identified from the squid sucker ring teeth assembly, offers unique mechanical properties and potential advantages over other natural biomaterials. In this study, a small suckerin isoform, suckerin‐12, is used to create enzymatically crosslinked, macro‐scale hydrogels. Upon exposure to specific salt conditions, suckerin‐12 hydrogels contracted into a condensed state where mechanical properties are found to be modulated by the salt anion present. The rate of contraction is found to correlate well with the kosmotropic arm of the Hofmeister anion series. However, the observed changes in hydrogel mechanical properties are better explained by the ability of the salt to neutralize charges in suckerin‐12 by deprotonization or charge screening. Thus, by altering the anions in the condensing salt solution, it is possible to tune the mechanical properties of suckerin‐12 hydrogels. The potential for suckerins to add new properties to materials based on naturally‐derived proteins is highlighted.