bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating an Open Access Publishing Fund at a Comprehensive University
Authors: Beaubien Sarah , Garrison Julie , Way Doug
Published: February 2016

INTRODUCTION As the open access movement has fostered a shift from subscriber-funded journals to author-pays models, scholars seek funding for the dissemination of their research. In response to this need, some libraries have established open access funds at their institutions. This paper presents an evaluation of an open access fund at a comprehensive university. DESCRIPTION OF PROGRAM/SERVICE Wanting to learn how faculty have benefitted from an open access publishing fund, Grand Valley State University Libraries surveyed recipients of the fund. The survey asked authors why they chose an open access publishing option and whether the fund influenced this decision. Authors were also asked whether they perceived that selecting an open access option broadened exposure to their work and about their likelihood of choosing open access in the future. NEXT STEPS This article shares the results of this small survey and explores next steps in promoting and evaluating the fund and opportunities for focusing educational efforts across campus.
Four-dimensional noise reduction using the time series of medical computed tomography datasets with short interval times: a static-phantom study
Authors: Nishii Tatsuya , Kono Atsushi K. , Tani Wakiko , Suehiro Erina , Negi Noriyuki , Takahashi Satoru , Sugimura Kazuro
Published: February 2016

Backgrounds.This study examines the hypothesis that four-dimensional noise reduction (4DNR) with short interval times reduces noise in cardiac computed tomography (CCT) using “padding” phases. Furthermore, the capability of reducing the reduction dose in CCT using this post-processing technique was assessed.

Methods.Using base and quarter radiation doses for CCT (456 and 114 mAs/rot with 120 kVp), a static phantom was scanned ten times with retrospective electrocardiogram gating, and 4DNR with short interval times (50 ms) was performed using a post-processing technique. Differences in the computed tomography (CT) attenuation, contrast-to-noise ratio (CNR) and spatial resolution with modulation transfer function in each dose image obtained with and without 4DNR were assessed by conducting a Tukey–Kramer’s test and non-inferiority test.

Results.For the base dose, by using 4DNR, the CNR was improved from 1.18 ± 0.15 to 2.08 ± 0.20 (P= 0.001), while the CT attenuation and spatial resolution of the image of 4DNR did not were significantly inferior to those of reference image (P< 0.001). CNRs of the quarter-dose image in 4DNR also improved to 1.28 ± 0.11, and were not inferior to those of the non-4DNR images of the base dose (P< 0.001).

Conclusions.4DNR with short interval times significantly reduced noise. Furthermore, applying this method to CCT would have the potential of reducing the radiation dose by 75%, while maintaining a similar image noise level.
Eficiência do cloransulam-metílico no controle em pós-emergência de Conyza bonariensis na cultura da soja RR®
Authors: Blainski Éder , Maciel Cleber Daniel de Goes , Zobiole Luiz Henrique Saes , Rubin Rogério Da Silva , Silva André Augusto Pazinato , Karpinski Ricardo André Kloster , Helvig Enelise Osco
Published: February 2016

Com a introdução da soja transgênica resistente ao glyphosate, a qual foi amplamente difundida na região sul do Brasil, intensificou-se o número de aplicações e a seleção de biótipos de buva (Conyza bonarienses) resistente ao herbicida. Desta maneira, são fundamentais novas alternativas químicas para o controle eficiente de buva. Diante disso,  o objetivo deste trabalho foi avaliar a eficácia do cloransulam-metílico (Pacto®), aplicado em pós-emergência, no controle de C. bonariensis e produtividade da soja SYN 1059 RR Vtop®. O experimento foi conduzido no município de Assis Chateaubriand-PR, em delineamento experimental de blocos ao acaso, com quatro repetições. Os tratamentos constituíram das doses de cloransulam-metílico (25, 30, 35 e 40 g i.a. ha-1), clorimuron-etílico (20 g i.a. ha-1) e testemunhas capinada e sem capina. As plantas de buva encontravam-se entre 5 a 10 cm de altura e densidade média de 35 plantas por m2. Cloransulam-metílico, nas doses de 25 e 30 g ha-1, não controlou de forma eficiente a buva (<80%) a partir dos 28 DAA (dias após aplicação), sendo inferior ao clorimuron-etílico. Entretanto, cloransulam-metílico a 35 e 40 g ha-1 apresentou controle de buva (87,0% e 90,7%) não diferindo significativamente do clorimuron-etílico aos 42 DAA (85,7%), assim como não ocasionando sintomas de injúrias e redução de produtividade à cultura da soja. Cloransulam-metílico apesar de não ter sido eficiente no controle de C. bonariensis a 30 g ha-1, apresentou produtividade da soja semelhante à testemunha capinada, e superior ao clorimuron-etílico. A matointerferência ocasionada pela infestação de buva reduziu a produtividade da soja em 47,5%.
Época seca e textura do solo afetam o controle químico de Senna obtusifolia em cana-de-açúcar
Authors: Takano Hudson Kagueyama , Constantin Jamil , Braz Guilherme Braga Pereira , Lima Mariucélio Santos , Padovese Filho João Carlos , Gonçalves Vinícius Diniz Barizon , Colevate André Fillipe Klym
Published: February 2016

Devido às suas características intrínsecas, o fedegoso (Senna obtusifolia) tem ganhado importância em canaviais, principalmente onde há predomínio de palhada após a colheita mecânica. O objetivo deste trabalho foi avaliar a eficácia de herbicidas pré-emergentes utilizados na cultura da cana-de-açúcar no controle de fedegoso em solos de diferentes texturas e épocas de aplicação. Foram realizados dois experimentos para cada época de aplicação (seca e úmida), sendo um para cada classe textural de solo (muito-argiloso e franco-argilo-arenoso), totalizando quatro experimentos. Os tratamentos foram constituídos por 17 herbicidas na época úmida e 11 herbicidas na época seca (todos os herbicidas foram aplicados em 50 e 100% da dose recomendada), além da testemunha sem aplicação para cada época e solo, sendo o delineamento inteiramente ao acaso. O tipo de solo e a época de aplicação alteraram a eficiência dos herbicidas. Para a época úmida, inicialmente, todos os herbicidas, exceto trifluralin e s-metolachlor, resultaram em controle satisfatório de fedegoso. Tebuthiuron foi o herbicida que proporcionou maior período residual de controle. Para a época seca, amicarbazone, flumioxazin, hexazinone, imazapic, [diuron + hexazinone] F1 e isoxaflutole foram eficazes em ambos os solos, mas somente em avaliações iniciais; [diuron + hexazinone] F1 e amicarbazone foram os herbicidas que proporcionaram maior período residual de controle.
Seletividade dos herbicidas fomesafen e clomazone associados com outros herbicidas aplicados em pré-emergência do algodoeiro
Authors: Oliveira Neto Antonio Mendes de , Constantin Jamil , Oliveira Jr Rubem Silvério de , Barroso Alberto Leão de Lemos , Menezes Carlos César Evangelista de , Guerra Naiara , Takano Hudson Kagueyama
Published: February 2016

Um experimento de campo foi realizado em Santa Helena de Goiás para avaliar a seletividade dos herbicidas fomesafen e clomazone e outras associações ao algodoeiro, quando aplicados em pré-emergência. O experimento foi conduzido em delineamento de blocos casualizados em esquema de parcelas subdivididas, com quatro repetições. Os tratamentos herbicidas avaliados foram: clomazone, clomazone + fomesafen (0,45 kg ha-1 de i.a.), clomazone + fomesafen (0,625 kg ha-1 de i.a.), clomazone + fomesafen + diuron, clomazone + fomesafen + prometryn, clomazone + fomesafen + trifluralin e clomazone + fomesafen + s-metolachlor. Os sintomas visuais de fitointoxicação foram visualizados até a avaliação de 19 dias após a emergência, e de modo geral, as injúrias foram maiores onde foi associado três herbicidas na aplicação. Os tratamentos com clomazone isolado e as associações clomazone + fomesafen (1,0 + 0,45 kg ha-1 de i.a.), clomazone + fomesafen + diuron, clomazone + fomesafen + prometryn, clomazone + fomesafen + trifluralin e clomazone + fomesafen + s-metolachlor foram seletivas ao algodoeiro. A maior dose de fomesafen (0,625 kg ha-1 de i.a.) em associações com clomazone (1,0 kg ha-1 de i.a.) não foi seletiva ao algodoeiro (cultivar DP 555 BG RR e em solo de textura argilosa, com 3,1% de MO e pH de 6,0).
Eficiência e seletividade do flumioxazin e do S-metolachlor na aplicação em pré emergência da mandioca ‘Baianinha’
Authors: Costa Neumárcio Vilanova , Pompermaier Ramella João Ricardo , Sontag Daniel Adriano , Pavan Guilherme Cardoso , Dourado Rodrigo Fernando
Published: February 2016

Objetivou-se avaliar a seletividade e a eficiência no controle de plantas daninhas do flumioxazin e do S-metolachlor na cultura da mandioca ‘Baianinha’. O delineamento experimental utilizado foi de blocos casualizados com quatro repetições. Os tratamentos consistiram nas seguintes doses do flumioxazin 50, 75, 100 e 125 gha-1 i.a. e as doses do S-metolachlor foram 960, 1920, 2880 e 3840 g ha-1 i.a., além de uma testemunha sem capina e outra capinada. A aplicação dos tratamentos foi realizada em 11/10/2013, 13 dias após o plantio (DAP) e a maniva apresentava brotos subterrâneos com 3,0 a 4,5 cm.  O flumioxazin na maior dose proporcionou 61,5% de redução da biomassa das plantas daninhas, enquanto que o S-metolachlor na maior dose reduziu 63,7% na biomassa de plantas daninhas. Ambos os herbicidas não promoveram fitointoxicação e não alteraram a produtividade de raízes e teor de amido das plantas de mandioca. Concluiu-se que, os herbicidas foram seletivos para a mandioca ‘Baianinha’ e eficientes no controle das plantas daninhas. Entretanto, o nível de controle aumentou de acordo com incrementos das doses avaliadas.
Controle alternativo de biótipos de azevém resistentes ao clethodim
Authors: Schneider Theodoro , Vargas Leandro , Agostinetto Dirceu
Published: February 2016

O azevém é uma planta daninha de ciclo anual, presente em lavouras de inverno, em pomares e vinhedos da região Sul do Brasil. A espécie é normalmente controlada pelo herbicida clethodim, no entanto, o uso continuado desse produto selecionou biótipos resistentes. Diante disso, o objetivo desta pesquisa foi avaliar a resposta de populações de azevém resistentes ao clethodim a aplicação de herbicidas de diferentes mecanismos de ação, e propor alternativas de controle químico. Um experimento foi realizado em Coqueiros do Sul, no delineamento de blocos ao acaso com três repetições. Os tratamentos avaliados foram: nicosulfuron (60 e 120 gi.a.ha-1), iodosulfuron-metílico (6 e 12 g i.a.ha-1), paraquat (400 e 800 g i.a. ha-1), amônio-glufosinato (600 e 1200 g i.a. ha-1), clomazone (750 e 1500 g i.a. ha-1), tembotrione (100 e 200 g i.a. ha-1), clethodim (144 e 288 g i.a. ha-1), haloxifop-methyl (60 e 120 g i.a. ha-1) e uma testemunha sem aplicação de herbicida. Os herbicidas tembotrione, nicosulfuron, iodosulfuron-metílico, clomazone, clethodim e haloxifop-methyl não foram eficientes no controle de azevém. Todavia, somente os herbicidas paraquat e amônio-glufosinato causaram o controle da planta daninha e podem ser utilizados no controle de populações de azevém resistentes ao herbicida clethodim.
What drives interannual variability of hypoxia in Chesapeake Bay: Climate forcing versus nutrient loading?
Authors: Li Ming , Lee Younjoo J. , Testa Jeremy M. , Li Yun , Ni Wenfei , Kemp W. Michael , Di Toro Dominic M.
Published: February 2016

Oxygen depletion in estuaries is a worldwide problem with detrimental effects on many organisms. Although nutrient loading has been stabilized for a number of these systems, seasonal hypoxia persists and displays large year‐to‐year variations, with larger hypoxic volumes in wetter years and smaller hypoxic volumes in drier years. Data analysis points to climate as a driver of interannual hypoxia variability, but nutrient inputs covary with freshwater flow. Here we report an oxygen budget analysis of Chesapeake Bay to quantify relative contributions of physical and biogeochemical processes. Vertical diffusive flux declines with river discharge, whereas longitudinal advective flux increases with river discharge, such that their total supply of oxygen to bottom water is relatively unchanged. However, water column respiration exhibits large interannual fluctuations and is correlated with primary production and hypoxic volume. Hence, the model results suggest that nutrient loading is the main mechanism driving interannual hypoxia variability in Chesapeake Bay.
Is the Brewer‐Dobson circulation increasing or moving upward?
Authors: Oberländer‐Hayn Sophie , Gerber Edwin P. , Abalichin Janna , Akiyoshi Hideharu , Kerschbaumer Andreas , Kubin Anne , Kunze Markus , Langematz Ulrike , Meul Stefanie , Michou Martine , Morgenstern Olaf , Oman Luke D.
Published: February 2016

The meridional circulation of the stratosphere, or Brewer‐Dobson circulation (BDC), is projected to accelerate with increasing greenhouse gas (GHG) concentrations. The acceleration is typically quantified by changes in the tropical upward mass flux (Ftrop) across a given pressure surface. Simultaneously, models project a lifting of the entire atmospheric circulation in response to GHGs; notably, the tropopause rises about a kilometer over this century. In this study, it is shown that most of the BDC trend is associated with the rise in the circulation. Using a chemistry‐climate model (CCM), Ftrop trends across 100 hPa are contrasted with those across the tropopause: while Ftrop at 100 hPa increases 1–2 %/decade, the mass flux entering the atmosphere above the tropopause actually decreases. Similar results are found for other CCMs, suggesting that changes in the BDC may better be described as an upward shift of the circulation, as opposed to an increase, with implications for the mechanism and stratosphere‐troposphere exchange.
Whistler emission in the separatrix regions of asymmetric magnetic reconnection
Authors: Graham D. B. , Vaivads A. , Khotyaintsev Yu. V. , André M.
Published: February 2016

At Earth's dayside magnetopause asymmetric magnetic reconnection occurs between the cold dense magnetosheath plasma and the hot tenuous magnetospheric plasma, which differs significantly from symmetric reconnection. During magnetic reconnection the separatrix regions are potentially unstable to a variety of instabilities. In this paper observations of the separatrix regions of asymmetric reconnection are reported as Cluster crossed the magnetopause near the subsolar point. The small relative motion between the spacecraft and plasma allows spatial changes of electron distributions within the separatrix regions to be resolved over multiple spacecraft spins. The electron distributions are shown to be unstable to the electromagnetic whistler mode and the electrostatic beam mode. Large‐amplitude whistler waves are observed in the magnetospheric and magnetosheath separatrix regions, and outflow region. In the magnetospheric separatrix regions the observed whistler waves propagate toward the X line, which are shown to be driven by the loss in magnetospheric electrons propagating away from the X line and are enhanced by the presence of magnetosheath electrons. The beam mode waves are predicted to be produced by beams of magnetosheath electrons propagating away from the X line and potentially account for some of the electrostatic fluctuations observed in the magnetospheric separatrix regions.
Statistical correlation of low‐altitude ENA emissions with geomagnetic activity from IMAGE/MENA observations
Authors: Mackler D. A. , Jahn J.‐M. , Perez J. D. , Pollock C. J. , Valek P. W.
Published: February 2016

Plasma sheet particles transported Earthward during times of active magnetospheric convection can interact with exospheric/thermospheric neutrals through charge exchange. The resulting Energetic Neutral Atoms (ENAs) are free to leave the influence of the magnetosphere and can be remotely detected. ENAs associated with low‐altitude (300–800 km) ion precipitation in the high‐latitude atmosphere/ionosphere are termed low‐altitude emissions (LAEs). Remotely observed LAEs are highly nonisotropic in velocity space such that the pitch angle distribution at the time of charge exchange is near 90°. The Geomagnetic Emission Cone of LAEs can be mapped spatially, showing where proton energy is deposited during times of varying geomagnetic activity. In this study we present a statistical look at the correlation between LAE flux (intensity and location) and geomagnetic activity. The LAE data are from the MENA imager on the IMAGE satellite over the declining phase of solar cycle 23 (2000–2005). The SYM‐H, AE, and Kp indices are used to describe geomagnetic activity. The goal of the study is to evaluate properties of LAEs in ENA images and determine if those images can be used to infer properties of ion precipitation. Results indicate a general positive correlation to LAE flux for all three indices, with the SYM‐H showing the greatest sensitivity. The magnetic local time distribution of LAEs is centered about midnight and spreads with increasing activity. The invariant latitude for all indices has a slightly negative correlation. The combined results indicate LAE behavior similar to that of ion precipitation.
The influence of external forcing on subdecadal variability of regional surface temperature in CMIP5 simulations of the last millennium
Authors: Le Thanh , Sjolte Jesper , Muscheler Raimund
Published: February 2016

We use Granger causality to investigate the influences of external forcings on subdecadal variability of regional near‐surface air temperature (SAT) in past millennium simulations (period 850–1850 A.D.) of the Coupled Model Intercomparison Project Phase 5 (CMIP5) models. Our results strengthen the conclusion for robust influence of volcanic forcing on SAT during preindustrial times of the last millennium. The SAT response to solar variations is detected in tropical and subtropical regions. In other regions, this response is weak. The impact of greenhouse gases (GHGs) radiative forcing to regional SAT is weak and uncertain. This is most probably due to the low amplitude of the variations in GHGs and hence weak GHGs forcing during the preindustrial millennium. The low agreement between models in simulating the impacts of solar variations on SAT in several regions suggests the different dynamical responses in these models, possibly associated with inaccurate parameterization of the processes related to solar forcing. Our analysis suggests that internal climate variability played a more significant role than external forcings in short‐term SAT variability in the regions of the North Atlantic, the North Pacific, the Arctic, the Antarctic Peninsula, and its surrounding oceans. The possibility of long‐term impacts of external forcings on SAT and the uncertainties that might be contained due to effects of internal climate modes other than El Niño–Southern Oscillation underscore the necessity for a more detailed understanding of the dynamical response of SAT to external forcings.
Benchmarking historical CMIP5 plant functional types across the Upper Midwest and Northeastern United States
Authors: Matthes Jaclyn Hatala , Goring Simon , Williams John W. , Dietze Michael C.
Published: February 2016

Centennial‐scale climate‐ecosystem feedbacks are a major source of predictive uncertainty for land‐atmosphere fluxes of energy, carbon, and water. Accurate representations of plant functional type (PFT) distributions through time and space are required for modeling centennial‐scale feedbacks within Earth system models (ESMs). We tested the ability of ESMs from the Coupled Model Intercomparison Project Phase 5 (CMIP5) to capture historical PFT distributions at the time of Euro‐American settlement in the Northeastern United States against a new subcontinental‐scale data set of historical tree abundances derived from forest composition surveys. To identify and diagnose errors in ESM‐simulated PFT distributions and quantify impacts on modeled albedo, net primary productivity, and transpiration, we analyzed actual and modeled PFT distributions with respect to historical mean annual climate and modeled elasticity among PFTs, climate, and vegetation‐atmosphere fluxes. Historical PFT distributions were poorly matched between ESMs and the settlement‐era data, often due to inaccurate PFT‐climate relationships within ESMs, particularly for evergreen trees. Some models exhibited large local, but regionally compensating, errors in simulated albedo, net primary productivity, and transpiration due to inaccurate PFT distributions, while others had systematic regional biases in vegetation‐atmosphere fluxes. Internal variable elasticity varied among ESMs, and these differences closely corresponded to model skill in predicting PFT distributions. New historical benchmarks like the settlement‐era vegetation data provide opportunities to confront ESMs, parse sources of error, and improve simulations of historical and future vegetation‐atmosphere feedbacks.
From channelization to restoration: Sociohydrologic modeling with changing community preferences in the Kissimmee River Basin, Florida
Authors: Chen Xi , Wang Dingbao , Tian Fuqiang , Sivapalan Murugesu
Published: February 2016

The Kissimmee River Basin (Florida, USA) underwent river channelization in the 1960s and subsequent restoration in the 1990s, revealing a shift in management emphasis from flood protection to wetland health. In this paper, this shift is hypothesized to result from changing human values and preferences, and a power differential between the more numerous and affluent upstream urban residents (who prioritize wetland restoration) and downstream rural residents (who prioritize flood protection). We develop a conceptual sociohydrologic model to simulate the interactions between community interests and hydrology. The modeling results show that flood intensity decreased after channelization, which reduced concern about flooding. However, channelization also led to a decrease in wetland storage, which caused an increase of wetland concern, especially among the urban residents. Eventually, the community sensitivity switched from favoring flood protection to favoring wetlands, and subsequent management strategies switched from channelization to restoration. Using the model, we project that the wetlands will be recovering for the next 20 years and community sensitivity will slowly go back to a neutral state. However, possible rainfall intensification in the future could return the community sensitivity to favoring flood protection again. The preferential increase of upstream population growth will raise the community's concern about wetlands and the preferential increase of downstream population growth will magnify concern about flooding. This study provides insight into the driving forces behind human‐water interactions in the Kissimmee River Basin while simultaneously demonstrating the potential of sociohydrologic modeling to describe complex human‐water coupled systems with simple concepts and equations.
Impact of rising greenhouse gas concentrations on future tropical ozone and UV exposure
Authors: Meul Stefanie , Dameris Martin , Langematz Ulrike , Abalichin Janna , Kerschbaumer Andreas , Kubin Anne , Oberländer‐Hayn Sophie
Published: February 2016

Future projections of tropical total column ozone (TCO) are challenging, as its evolution is affected not only by the expected decline of ozone depleting substances but also by the uncertain increase of greenhouse gas (GHG) emissions. To assess the range of tropical TCO projections, we analyze simulations with a chemistry‐climate model forced by three different GHG scenarios (Representative Concentration Pathway (RCP) 4.5, RCP6.0, and RCP8.5). We find that tropical TCO will be lower by the end of the 21st century compared to the 1960s in all scenarios with the largest decrease in the medium RCP6.0 scenario. Uncertainties of the projected TCO changes arise from the magnitude of stratospheric column decrease and tropospheric ozone increase which both strongly vary between the scenarios. In the three scenario simulations the stratospheric column decrease is not compensated by the increase in tropospheric ozone. The concomitant increase in harmful ultraviolet irradiance reaches up to 15% in specific regions in the RCP6.0 scenario.
On the relationship between extratropical cyclone precipitation and intensity
Authors: Pfahl S. , Sprenger M.
Published: February 2016

Extratropical precipitation is largely associated with the passage of cyclones. Here the relative importance of cyclone intensity and moisture availability for cyclone precipitation is investigated using reanalysis data. It is shown that 69% of the event‐to‐event variability of precipitation in the cyclones' intensification phase is explained by a simple scaling relationship using as predictor the product of cyclone intensity (measured in terms of near‐surface wind speed) and total column water vapor (TCWV) in the cyclone region. Differences in the correlation of cyclone intensity with precipitation before and after the time of maximum intensity are potentially related to effects of latent heating on cyclone intensification. For subtropical cyclones, intensity alone is a good predictor of the associated precipitation, whereas at higher latitudes, where moisture availability is more limited, TCWV is an important independent factor. The results from this study may be used to better understand and constrain future regional‐scale precipitation changes.
A Radical Pathway for Direct Substitution of Benzyl Alcohols with Water‐Soluble Copper Catalyst in Water
Authors: Hikawa Hidemasa , Mori Yuki , Kikkawa Shoko , Azumaya Isao
Published: February 2016

We have developed a novel strategy for the direct substitution of benzyl alcohols with anthranilic acids using water‐soluble copper catalysts through a radical pathway in water, which offers efficient and environmentally friendly N‐, S‐, and C‐benzylations under neutral conditions. Radical scavengers strongly inhibited the benzylation. Radical clock experiments using α‐cyclopropylbenzyl alcohol were conducted to observe the rapid isomerization of the cyclopropylmethyl radical to the allylmethyl radical. Hammett plots could be fitted to a two‐parameter Hammett relationship containing both radical and polar contributions [log (kX/kH)=−1.24 σ.–0.38 σ, R2=0.99]. The relative parameter ρ./ρ of 3.3 suggested that these reactions involved a strong radical character with minor polar influence at the transition state.

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Ohmic Contacts to 2D Semiconductors through van der Waals Bonding
Authors: Farmanbar Mojtaba , Brocks Geert
Published: February 2016

High contact resistances have blocked the progress of devices based on MX2 (M = Mo, W; X = S, Se, Te) 2D semiconductors. Interface states formed at MX2/metal contacts pin the Fermi level, leading to sizable Schottky barriers for p‐type contacts in particular. It is shown that i) one can remove the interface states by covering the metal by a 2D layer, which is van der Waals‐bonded to the MX2 layer, and ii) one can choose the buffer layer such that it yields a p‐type contact with a zero Schottky barrier height. Possible buffer layers are graphene, a monolayer of h‐BN, or an oxide layer with a high electron affinity, such as MoO3. The most elegant solution is a metallic M′ X′2 layer with a high work function. A NbS2 monolayer adsorbed on a metal yields a high work function contact, irrespective of the metal, which gives a barrierless contact to all MX2 layers.
Duplication 2p25 in a child with clinical features of CHARGE syndrome
Authors: Sperry Ethan D. , Schuette Jane L. , van Ravenswaaij‐Arts Conny M. A. , Green Glenn E. , Martin Donna M.
Published: February 2016

CHARGE syndrome is a dominant disorder characterized by ocular colobomata, heart defects, choanal atresia, retardation of growth and development, genital hypoplasia, and ear abnormalities including deafness and vestibular disorders. The majority of individuals with CHARGE have pathogenic variants in the gene encoding CHD7, a chromatin remodeling protein. Here, we present a 15‐year‐old girl with clinical features of CHARGE syndrome and a de novo 6.5 Mb gain of genomic material at 2p25.3–p25.2. The duplicated region contained 24 genes, including the early and broadly expressed transcription factor gene SOX11. Analysis of 28 other patients with CHARGE showed no SOX11 copy number changes or pathogenic sequence variants. To our knowledge, this child's chromosomal abnormality is unique and represents the first co‐occurrence of duplication 2p25 and clinical features of CHARGE syndrome. We compare our patient's phenotype to ten previously published patients with isolated terminal duplication 2p, and elaborate on the clinical diagnosis of CHARGE in the context of atypical genetic findings. © 2016 Wiley Periodicals, Inc.
Variation in body mass and morphological characters in Macaca mulatta brevicaudus from Hainan, China
Authors: Zhang Peng , Lyu Mu‐Yang , Wu Cheng‐Feng , Chu Yuan‐Meng‐Ran , Han Ning , Yang Danhe , Hu Kaijin
Published: February 2016

The rhesus macaque (Macaca mulatta) is the most widely distributed nonhuman primate species in the world, with six subspecies distributed through China. From 2012 to 2014, we conducted studies on the body mass and morphological variation of the southernmost subspecies M. m. brevicaudus in Nanwan Nature Reserve for Rhesus Macaque, Hainan, China. We compared measurements with other populations of this species. We also investigated the inter‐group body mass variation from seven provisioned free‐ranging groups in our study site. Our results show that M. m. brevicaudus has the smallest body size, the smallest body mass, and the shortest tail among rhesus macaque subspecies. Its sexual dimorphism score is also among the lowest, which is similar to other southern distributed subspecies in China, but smaller than northern distributed subspecies. We found that the average body mass of female macaques is not correlated with their dominance ranks. There are significant differences in body mass among the seven adjacent study groups at the same site, suggesting the existence of inter‐group competition. Average body mass of a group is better described by a quadratic function of group size than a linear one as predicted by the socio‐ecological model. Am. J. Primatol. 78:679–698, 2016. © 2016 Wiley Periodicals, Inc.
Structure and Composition of the 200 K‐Superconducting Phase of H2S at Ultrahigh Pressure: The Perovskite (SH−)(H3S+)
Authors: Gordon Elijah E. , Xu Ke , Xiang Hongjun , Bussmann‐Holder Annette , Kremer Reinhard K. , Simon Arndt , Köhler Jürgen , Whangbo Myung‐Hwan
Published: February 2016

At ultrahigh pressure (>110 GPa), H2S is converted into a metallic phase that becomes superconducting with a record Tc of approximately 200 K. It has been proposed that the superconducting phase is body‐centered cubic H3S (Im
m, a=3.089 Å) resulting from the decomposition reaction 3 H2S→2 H3S+S. The analogy between H2S and H2O led us to a very different conclusion. The well‐known dissociation of water into H3O+ and OH− increases by orders of magnitude under pressure. H2S is anticipated to behave similarly under pressure, with the dissociation process 2 H2S→H3S++SH− leading to the perovskite structure (SH−)(H3S+). This phase consists of corner‐sharing SH6 octahedra with SH− ions at each A site (the centers of the S8 cubes). DFT calculations show that the perovskite (SH−)(H3S+) is thermodynamically more stable than the Im
m structure of H3S, and suggest that the A site hydrogen atoms are most likely fluxional even at Tc .
A Water‐Stable Cationic Metal–Organic Framework as a Dual Adsorbent of Oxoanion Pollutants
Authors: Desai Aamod V. , Manna Biplab , Karmakar Avishek , Sahu Amit , Ghosh Sujit K.
Published: February 2016

A three‐dimensional water‐stable cationic metal–organic framework (MOF) pillared by a neutral ligand and with NiII metal nodes has been synthesized employing a rational design approach. Owing to the ordered arrangement of the uncoordinated tetrahedral sulfate (SO42−) ions in the channels, the compound has been employed for aqueous‐phase ion‐exchange applications. The compound exhibits rapid and colorimetric aqueous‐phase capture of environmentally toxic oxoanions (with similar geometries) in a selective manner. This system is the first example of a MOF‐based system which absorbs both dichromate (Cr2O72−) and permanganate (MnO4−) ions, with the latter acting as a model for the radioactive contaminant pertechnetate (TcO4−).
Numeric Estimates of Teratogenic Severity from Embryo–Fetal Developmental Toxicity Studies
Authors: Wise L. David
Published: February 2016

A developing organism exposed to a toxicant will have a response that ranges from none to severe (i.e., death or malformation). The response at a given dosage may be termed teratogenic (or developmental toxic) severity and is dependent on exposure conditions. Prenatal/embryo–fetal developmental (EFD) toxicity studies in rodents and rabbits are the most consistent and definitive assessments of teratogenic severity, and teratogenesis screening assays are best validated against their results. A formula is presented that estimates teratogenic severity for each group, including control, within an EFD study. The developmental components include embryonic/fetal death, malformations, variations, and mean fetal weight. The contribution of maternal toxicity is included with multiplication factors to adjust for the extent of mortality, maternal body weight change, and other parameters deemed important. The derivation of the formula to calculate teratogenic severity is described. Various EFD data sets from the literature are presented to highlight considerations to the calculation of the various components of the formula. Each score is compared to the concurrent control group to obtain a relative teratogenic severity. The limited studies presented suggest relative scores of two‐ to <fivefold higher than control have detectable but a low level of teratogenic severity, and scores ≥fivefold higher than control have increasingly more severe teratogenicity. Such scores may help refine the concept of an exposure‐based validation list for use by proponents of screening assays (Daston et al., 2014) by estimating the severity of “positive” exposures, or in other situations by defining the severity of a LOAEL (lowest observed adverse effect level)
Position‐effect variegation revisited: HUSHing up heterochromatin in human cells
Authors: Timms Richard T. , Tchasovnikarova Iva A. , Lehner Paul J.
Published: February 2016

Much of what we understand about heterochromatin formation in mammals has been extrapolated from forward genetic screens for modifiers of position‐effect variegation (PEV) in the fruit fly Drosophila melanogaster. The recent identification of the HUSH (Human Silencing Hub) complex suggests that more recent evolutionary developments contribute to the mechanisms underlying PEV in human cells. Although HUSH‐mediated repression also involves heterochromatin spreading through the reading and writing of the repressive H3K9me3 histone modification, clear orthologues of HUSH subunits are not found in Drosophila but are conserved in vertebrates. Here we compare the insights into the mechanisms of PEV derived from genetic screens in the fly, the mouse and in human cells, review what is currently known about the HUSH complex and discuss the implications of HUSH‐mediated silencing for viral latency. Future studies will provide mechanistic insight into HUSH complex function and reveal the relationship between HUSH and other epigenetic silencing complexes.
Modeling bond correlations in denatured proteins and polypeptides
Authors: Betancourt Marcos R.
Published: February 2016

Bond‐orientational correlations for finite‐length homopolypeptides and a selected group of denatured proteins are obtained by numerical simulations using a polypeptide model with a potential of mean force. These correlations characterize the stiffness of the polypeptide backbone and are generally described by either an exponential or a power‐law decay in the asymptotic limit. However, for finite length polypeptides and unfolded proteins the correlations significantly deviate from either single exponential or power‐law behavior. A heuristic model is developed to analyze the correlations of homopolypeptides, which depends on the chain length and the side‐chain properties. The model contains power‐law and multi‐exponential terms, the latter which could be interpreted as local persistence lengths. In the asymptotic limit, the model reduces to the expected power‐law behavior. Simulations of denatured proteins show that the power‐law behavior of the correlations is significantly suppressed and only the multi‐exponential term is needed to model the correlations. In addition, average persistence lengths (ranging from 2.0 to 2.5 nm) are obtained from the correlations by fitting single exponentials and shown to be in general agreement with experiments, which also assume single exponential decay. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 312–323, 2016.
Virtual substitution scan via single‐step free energy perturbation
Authors: Chiang Ying‐Chih , Wang Yi
Published: February 2016

With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the “recycling” of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open‐source visualization and analysis software VMD. Based on the single‐step free energy perturbation (sFEP) method, VSS enables the user to post‐process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof‐of‐concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi‐step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 324–336, 2016.
CFD of mixing of multi‐phase flow in a bioreactor using population balance model
Authors: Sarkar Jayati , Shekhawat Lalita Kanwar , Loomba Varun , Rathore Anurag S.
Published: February 2016

Mixing in bioreactors is known to be crucial for achieving efficient mass and heat transfer, both of which thereby impact not only growth of cells but also product quality. In a typical bioreactor, the rate of transport of oxygen from air is the limiting factor. While higher impeller speeds can enhance mixing, they can also cause severe cell damage. Hence, it is crucial to understand the hydrodynamics in a bioreactor to achieve optimal performance. This article presents a novel approach involving use of computational fluid dynamics (CFD) to model the hydrodynamics of an aerated stirred bioreactor for production of a monoclonal antibody therapeutic via mammalian cell culture. This is achieved by estimating the volume averaged mass transfer coefficient (kLa) under varying conditions of the process parameters. The process parameters that have been examined include the impeller rotational speed and the flow rate of the incoming gas through the sparger inlet. To undermine the two‐phase flow and turbulence, an Eulerian‐Eulerian multiphase model and k‐ε turbulence model have been used, respectively. These have further been coupled with population balance model to incorporate the various interphase interactions that lead to coalescence and breakage of bubbles. We have successfully demonstrated the utility of CFD as a tool to predict size distribution of bubbles as a function of process parameters and an efficient approach for obtaining optimized mixing conditions in the reactor. The proposed approach is significantly time and resource efficient when compared to the hit and trial, all experimental approach that is presently used. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:613–628, 2016
Reimagining care for adolescent and young adult cancer programs: Moving with the times
Authors: Gupta Abha A. , Papadakos Janet K. , Jones Jennifer M. , Amin Leila , Chang Eugene K. , Korenblum Chana , Mina Daniel Santa , McCabe Lianne , Mitchell Laura , Giuliani Meredith E.
Published: February 2016

Literature regarding the development of adolescent and young adult (AYA) cancer programs has been dominantly informed by pediatric centers and practitioners. However, the majority of young adults are seen and treated at adult cancer centers, in which cancer volumes afford the development of innovative supportive care services. Although the supportive care services in adult cancer centers are helpful to AYAs, some of the most prominent and distinct issues faced by AYAs are not adequately addressed through these services alone. This article describes how the AYA Program at Princess Margaret Cancer Centre has collaborated with existing supportive care services in addition to supplying its own unique services to meet the comprehensive needs of AYAs in the domains of: symptom management (sexuality and fatigue), behavior modification (return to work and exercise), and health services (advanced cancer and survivorship). These collaborations are augmented by patient education interventions and timely referrals. The objective of this article was to assist other centers in expanding existing services to address the needs of AYA patients with cancer. Cancer 2016;122:1038–1046. © 2016 American Cancer Society
Biologic and clinical characteristics of adolescent and young adult cancers: Acute lymphoblastic leukemia, colorectal cancer, breast cancer, melanoma, and sarcoma
Authors: Tricoli James V. , Blair Donald G. , Anders Carey K. , Bleyer W. Archie , Boardman Lisa A. , Khan Javed , Kummar Shivaani , Hayes‐Lattin Brandon , Hunger Stephen P. , Merchant Melinda , Seibel Nita L. , Thurin Magdalena , Willman Cheryl L.
Published: February 2016

Adolescent and young adult (AYA) patients with cancer have not attained the same improvements in overall survival as either younger children or older adults. One possible reason for this disparity may be that the AYA cancers exhibit unique biologic characteristics, resulting in differences in clinical and treatment resistance behaviors. This report from the biologic component of the jointly sponsored National Cancer Institute and LiveStrong Foundation workshop entitled “Next Steps in Adolescent and Young Adult Oncology” summarizes the current status of biologic and translational research progress for 5 AYA cancers; colorectal cancer breast cancer, acute lymphoblastic leukemia, melanoma, and sarcoma. Conclusions from this meeting included the need for basic biologic, genomic, and model development for AYA cancers as well as translational research studies to elucidate any fundamental differences between pediatric, AYA, and adult cancers. The biologic questions for future research are whether there are mutational or signaling pathway differences (for example, between adult and AYA colorectal cancer) that can be clinically exploited to develop novel therapies for treating AYA cancers and to develop companion diagnostics. Cancer 2016;122:1017–1028. © 2016 American Cancer Society
Feedback from each retinal neuron population drives expression of subsequent fate determinant genes without influencing the cell cycle exit timing
Authors: Kei Jeremy Ng Chi , Dudczig Stefanie , Currie Peter D. , Jusuf Patricia R.
Published: February 2016

During neurogenesis, progenitors balance proliferation and cell cycle exit together with expression of fate determinant genes to ensure that the correct number of each of these neuron types is generated. Although intrinsic gene expression acting cell autonomously within each progenitor drives these processes, the final number of neurons generated is also influenced by extrinsic cues, representing a potential avenue to direct neurogenesis in developmental disorders or regenerative settings without the requirement to change intrinsic gene expression. Thus, it is important to understand which of these stages of neurogenesis are amenable to such extrinsic influences. Additionally, all types of neurons are specified in a highly conserved histogenic order, although its significance is unknown. This study makes use of conserved patterns of neurogenesis in the relatively simple yet highly organized zebrafish retina model, in which such histogenic birth order is well characterized. We directly visualize and quantify birth dates and cell fate determinant expression in WT vs. environments lacking different neuronal populations. This study shows that extrinsic feedback from developing retinal neurons is important for the temporal expression of intrinsic fate determinants but not for the timing of birth dates. We found no changes in cell cycle exit timing but did find a significant delay in the expression of genes driving the generation only of later‐ but not earlier‐born cells, suggesting that the robustness of this process depends on continuous feedback from earlier‐formed cell types. Thus, extrinsic cues selectively influence cell fate determinant progression, which may explain the function of the retinal histogenic order observed. J. Comp. Neurol. 524:2553–2566, 2016. © 2016 Wiley Periodicals, Inc.
Dendritic branching angles of pyramidal cells across layers of the juvenile rat somatosensory cortex
Authors: Leguey Ignacio , Bielza Concha , Larrañaga Pedro , Kastanauskaite Asta , Rojo Concepción , Benavides‐Piccione Ruth , DeFelipe Javier
Published: February 2016

The characterization of the structural design of cortical microcircuits is essential for understanding how they contribute to function in both health and disease. Since pyramidal neurons represent the most abundant neuronal type and their dendritic spines constitute the major postsynaptic elements of cortical excitatory synapses, our understanding of the synaptic organization of the neocortex largely depends on the available knowledge regarding the structure of pyramidal cells. Previous studies have identified several apparently common rules in dendritic geometry. We study the dendritic branching angles of pyramidal cells across layers to further shed light on the principles that determine the geometric shapes of these cells. We find that the dendritic branching angles of pyramidal cells from layers II–VI of the juvenile rat somatosensory cortex suggest common design principles, despite the particular morphological and functional features that are characteristic of pyramidal cells in each cortical layer. J. Comp. Neurol. 524:2567–2576, 2016. © 2016 Wiley Periodicals, Inc.