bluuebunny/crossref_metadata_2025_split huggingface dataset:
Black‐backed woodpecker abundance in the Black Hills
Authors: Matseur Elizabeth A. , Thompson Frank R. , Dickerson Brian E. , Rumble Mark A. , Millspaugh Joshua J. 
Published: March 2018

ABSTRACTThe Black Hills population of black‐backed woodpeckers (Picoides arcticus) was petitioned, but deemed not warranted, to be listed as a threatened or endangered species under the Endangered Species Act and more information on their population size in the region is needed. Our objective was to map abundance and provide a population estimate of black‐backed woodpeckers in the Black Hills and Bear Lodge Mountains of South Dakota and Wyoming, USA. We conducted 3,666 and 3,384 5‐minute point count surveys from late‐March to late‐June in 2015 and 2016, respectively. We characterized vegetation around each point using geographic information system‐derived landscape variables and fit 3‐level hierarchical time‐removal models in R package unmarked using gmultmix. The global abundance model received the most support and included year, latitude, and percent area of green trees, beetle‐killed trees, dead trees, 1‐ to 2‐year‐old wildfire, 3‐year‐old wildfire, and 4‐ to 5‐year‐old wildfire. Points with high percent cover of beetle‐killed trees had the greatest density of black‐backed woodpeckers, followed by 1‐ to 2‐year‐old wildfires. After 4 years, areas burned by wildfire supported lower densities of black‐backed woodpeckers than undisturbed forests. Mean density was 0.528 birds/km2in 2015 and 0.626 birds/km2in 2016. There were an estimated 2,920 and 3,439 black‐backed woodpeckers in the Black Hills and Bear Lodge Mountains in 2015 and 2016, respectively. We suggest areas with high percent cover of beetle‐killed trees may support high densities of black‐backed woodpeckers and are important to sustaining populations when the availability of recent (<4 years old) wildfire is declining or scarce. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
Molecular population structure for feral swine in the United States
Authors: McCann Blake E. , Smyser Timothy J. , Schmit Brandon S. , Newman Robert A. , Piaggio Antoinette J. , Malek Mathew J. , Swafford Seth R. , Sweitzer Richard A. , Simmons Rebecca B. 
Published: March 2018

ABSTRACTFeral swine (Sus scrofa) have invaded most of the United States and continue to expand throughout North America. Given the ecological and economic threats posed by increasing feral swine abundance, it is imperative to develop an understanding of their patterns of natural range expansion and human‐mediated introductions. Towards this goal, we used molecular markers to elucidate the genetic structure of feral swine populations throughout the United States and evaluated the association between historical introductions and contemporary patterns of genetic organization. We used STRUCTURE and discriminant analysis of principal components (DAPC) to delineate genetic clusters for 959 individuals genotyped at 88 single nucleotide polymorphism loci. We identified 10 and 12 genetic clusters for the 2 clustering approaches, respectively. We observed strong agreement in clusters across approaches, with both describing clusters having strong geographic association at regional levels reflecting past introduction and range expansion patterns. In addition, we evaluated patterns of isolation by distance to test for and estimate spatial scaling of population structure within western, central, and eastern regions of North America. We found contrasting spatial patterns of genetic relatedness among regions, suggesting differences in the invasion process, likely as a result of regional variation in landscape heterogeneity and the influence of human‐mediated introductions. Our results indicate that molecular analyses of population genetic structure can provide reliable insights into the invasion processes of feral swine, thus providing a useful basis for management focused on minimizing continued range expansion by this problematic species. © 2018 The Wildlife Society.
A new method for selecting auricle positions in skull base reconstruction for temporal bone cancer
Authors: Tanaka Kentaro , Yano Tomoyuki , Homma Tsutomu , Tsunoda Atsunobu , Aoyagi Masaru , Kishimoto Seiji , Okazaki Mutsumi 
Published: March 2018

ObjectiveIn advanced temporal bone carcinoma cases, we attempted to preserve as much of the auricle as possible from a cosmetic and functional perspective. Difficulties are associated with selecting an adequate position for reconstructed auricles intraoperatively. We improved the surgical procedure to achieve a good postoperative auricle position.MethodsNine patients were included in this study. All patients underwent subtotal removal of the temporal bone and resection of the external auditory canal while preserving most of the external ear, and lateral skull base reconstruction was performed with anterolateral thigh flaps. We invented a new device, the auricle localizer, to select the correct position for the replaced external ear. The head skin incision line and two points of three‐point pin fixation were used as criteria, and a Kirschner wire was shaped as a basic line to match these criteria. Another Kirschner wire was shaped by wrapping it around the inferior edge of the external ear as the positioning line, and these two lines were then combined. To evaluate the postoperative auricle position, the auricle inclination angle was measured using head frontal cephalogram imaging.ResultsThe external ear on the affected side clearly drooped postoperatively in nonlocalizer cases, whereas this was not obvious in localizer cases. Auricle inclination angles 1 year after surgery significantly differed between these two cases (P = 0.018).ConclusionThe surgical device, the auricle localizer, is useful for selecting intraoperative accurate auricle positions. The assessment index, the auricle inclination angle, is useful for quantitatively evaluating postoperative results.Level of Evidence4 Laryngoscope, 2605–2610, 2018
Stakeholders' perception of the relevance of water and sediment connectivity in water and land management
Authors: Smetanová Anna , Paton Eva Nora , Maynard Carly , Tindale Sophie , Fernández‐Getino Ana Patricia , Marqéus Pérez María José , Bracken Louise , Le Bissonnais Yves , Keesstra Saskia D. 
Published: March 2018

AbstractUsing concepts of connectivity in challenges regarding land and water management (flooding, erosion, nutrient leaching, landslides) can only be fully harnessed if knowledge is communicated well between scientists and stakeholders. Proper communication requires prior understanding of end‐users' perception of connectivity as a useful framework. Therefore, we analysed (a) perceptions of ‘connectivity’ for stakeholders involved in water and land management across Europe, (b) potential for stakeholders to apply connectivity‐related measures in their management decisions, (c) stakeholders' biggest challenges in water and land management, and (d) stakeholders' expectations for future connectivity research agendas. We studied 85 questionnaires from 19 countries using a grounded theory approach. One third of stakeholders understood connectivity in its scientific context, whereas 39% perceived connectivity indirectly through their personal experiences (e.g., water and sediment fluxes and erosion). Half of stakeholders' perceived links and challenges were related to availability of data and methods, communication, and institutions or policy, whereas others believed they were related to water quality and quantity, soil erosion and quality, and climate change. Half of the stakeholders considered connectivity management important, and one third showed high interest in managing connectivity. Adopting connectivity into management is hindered by institutional‐ and policy‐based management limitations, insufficient data and methods, and ineffective knowledge transfer. Explicitly considering heterogeneity of stakeholder perceptions is required for projects regarding management of connectivity at European, national, and local scales.
Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum
Authors: Guzman‐Chavez Fernando , Salo Oleksandr , Samol Marta , Ries Marco , Kuipers Jeroen , Bovenberg Roel A. L. , Vreeken Rob J. , Driessen Arnold J. M. 
Published: March 2018

AbstractThe Pc21 g14570 gene of Penicillium chrysogenum encodes an ortholog of a class 2 histone deacetylase termed HdaA which may play a role in epigenetic regulation of secondary metabolism. Deletion of the hdaA gene induces a significant pleiotropic effect on the expression of a set of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS)‐encoding genes. The deletion mutant exhibits a decreased conidial pigmentation that is related to a reduced expression of the PKS gene Pc21 g16000 (pks17) responsible for the production of the pigment precursor naphtha‐γ‐pyrone. Moreover, the hdaA deletion caused decreased levels of the yellow pigment chrysogine that is associated with the downregulation of the NRPS‐encoding gene Pc21 g12630 and associated biosynthetic gene cluster. In contrast, transcriptional activation of the sorbicillinoids biosynthetic gene cluster occurred concomitantly with the overproduction of associated compounds . A new compound was detected in the deletion strain that was observed only under conditions of sorbicillinoids production, suggesting crosstalk between biosynthetic gene clusters. Our present results show that an epigenomic approach can be successfully applied for the activation of secondary metabolism in industrial strains of P. chrysogenum.
A Proposed Circuit Computation in Basal Ganglia: History‐Dependent Gain
Authors: Yttri Eric Allen , Dudman Joshua Tate 
Published: March 2018

AbstractIn this Scientific Perspectives we first review the recent advances in our understanding of the functional architecture of basal ganglia circuits. Then we argue that these data can best be explained by a model in which basal ganglia act to control the gain of movement kinematics to shape performance based on prior experience, which we refer to as a history‐dependent gain computation. Finally, we discuss how insights from the history‐dependent gain model might translate from the bench to the bedside, primarily the implications for the design of adaptive deep brain stimulation. Thus, we explicate the key empirical and conceptual support for a normative, computational model with substantial explanatory power for the broad role of basal ganglia circuits in health and disease. © 2018 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Strengths and challenges in conducting clinical trials in Parkinson's disease mild cognitive impairment
Authors: Litvan Irene , Kieburtz Karl , Tröster Alexander I. , Aarsland Dag 
Published: March 2018

ABSTRACTTreatments to slow the progression of cognitive dysfunction to dementia and improve the quality of life of persons with Parkinson's disease (PD) are desperately needed. Because PD mild cognitive impairment is considered a transitional stage before dementia, it opens a window to timely intervention. This article critically reviews the strengths and challenges of pharmacologic and nonpharmacologic clinical therapeutic trials in PD mild cognitive impairment conducted during the past 5 years, including ongoing trials. Relatively few high‐quality trials have been conducted, and some important factors in designing future clinical trials are discussed. © 2018 International Parkinson and Movement Disorder Society
Simultaneous measurement of glutamate, glutamine, GABA, and glutathione by spectral editing without subtraction
Authors: An Li , Araneta Maria Ferraris , Johnson Christopher , Shen Jun 
Published: March 2018

PurposeTo simultaneously measure glutamate, glutamine, γ‐aminobutyric acid (GABA), and glutathione using spectral editing without subtraction at 7T.MethodsA novel spectral editing approach was proposed to simultaneously measure glutamate, glutamine, GABA, and glutathione using a TE of 56 ms at 7T. By numerical optimization of sequence timing in the presence of an editing pulse, the 4 metabolites all form relatively intense pseudo singlets with maximized peak amplitudes and minimized peak linewidths in 1 of the 3 interleaved spectra. For measuring glutamate, glutamine, and glutathione, the editing pulse targets the H3 protons of these metabolites near 2.12 parts per million. Both GABA H2 and H4 resonances are fully utilized in spectral fitting.ResultsConcentration levels (/[total creatine]) of glutamate, glutamine, GABA, and glutathione from an 8 mL voxel in the pregenual anterior cingulate cortex of 5 healthy volunteers were found to be 1.26 ± 0.13, 0.33 ± 0.06, 0.13 ± 0.03, and 0.27 ± 0.03, respectively, with within‐subject coefficient of variation at 3.2%, 8.2%, 7.1%, and 10.2%, respectively. The total scan time was less than 4.5 min.ConclusionsThe proposed new technique does not require data subtraction. The 3 major metabolites of the glutamatergic and GABAergic systems and the oxidative stress marker glutathione were all measured in 1 short scan with high precision.
Food Restriction is Required to Preserve the Antisteatotic Effects of Central Leptin in the Liver of Middle‐Aged Rats
Authors: López Virginia , Bonzón‐Kulichenko Elena , Moltó Eduardo , Fernández‐Agulló Teresa , Arribas Carmen , Andrés Antonio , Gallardo Nilda 
Published: March 2018

ObjectiveAging is a significant risk factor for the development of obesity and hepatic steatosis associated with insulin and leptin resistance. Food restriction (FR) is commonly used for reducing body weight (BW), adiposity, and liver steatosis. Thus, this study aimed to determine whether FR in middle‐aged rats can recover the central leptin antisteatotic effects observed in the liver in young animals.MethodsTwo groups of 4‐month‐old Wistar rats were fed ad libitum (AL) or were on FR for 3 months. At 7 months of age, both groups were centrally treated with rat leptin (0.2 μg/d, 7 days) or saline.ResultsCentral leptin reduced food intake and BW, but not the hepatic triglyceride content, in 7‐month‐old rats fed AL. However, in 7‐month‐old FR rats, leptin did not affect BW but markedly reduced serum leptin, serum and hepatic triglyceride levels, and the expression of hepatic lipogenic genes. In addition, central leptin decreased serum and hepatic endogenous norepinephrine levels of FR rats, exerting a homeostatic effect beyond its antisteatotic actions.ConclusionsThese findings suggest that in middle‐aged rats, moderate FR is required for both preserving the antisteatotic actions of central leptin and avoiding excessive weight loss.
Deep surface Cu depletion induced by K in high‐efficiency Cu(In,Ga)Se2 solar cell absorbers
Authors: Donzel‐Gargand Olivier , Thersleff Thomas , Keller Jan , Törndahl Tobias , Larsson Fredrik , Wallin Erik , Stolt Lars , Edoff Marika 
Published: March 2018

AbstractIn this work, we used K‐rich glass substrates to provide potassium during the coevaporation of Cu(In,Ga)Se2 (CIGS) absorber layers. Subsequently, we applied a postdeposition treatment (PDT) using KF or RbF to some of the grown absorbers. It was found that the presence of K during the growth of the CIGS layer led to cell efficiencies beyond 17%, and the addition of a PDT pushed it beyond 18%. The major finding of this work is the observation of discontinuous 100‐ to 200‐nm‐deep Cu‐depleted patches in the vicinity of the CdS buffer layer, correlated with the presence of K during the growth of the absorber layer. The PDT had no influence on the formation of these patches. A second finding concerns the composition of the Cu‐depleted areas, where an anticorrelation between Cu and both In and K was measured using scanning transmission electron microscopy. Furthermore, a steeper Ga/(In+Ga) ratio gradient was measured for the absorbers grown with the presence of K, suggesting that K hinders the group III element interdiffusion. Finally, no Cd in‐diffusion to the CIGS layer could be detected. This indicates that if CdCu substitution occurs, either their concentration is below our instrumental detection limit or its presence is contained within the first 6 nm from the CdS/CIGS interface.
Membrane‐Based SDS Depletion Ahead of Peptide and Protein Analysis by Mass Spectrometry
Authors: Unterlander Nicole , Doucette Alan A. 
Published: March 2018

AbstractSDS interferes with both bottom‐up and top‐down MS analysis, requiring removal prior to detection. Filter‐aided sample preparation (FASP) is favored for bottom‐up proteomics (BUP) while acetone precipitation is popular for top‐down proteomics (TDP). We recently demonstrated acetone precipitation in a membrane filter cartridge. Alternatively, our automated electrophoretic device, termed transmembrane electrophoresis (TME), depletes SDS for both TDP and BUP studies. Here TME is compared to these two alternative methods of SDS depletion in both BUP and TDP workflows. To do so, a modified FASP method is described applicable to the SDS purification and recovery of intact proteins, suitable for LC/MS. All three methods reliably deplete >99.8% SDS. TME provide higher sample yields (average 90%) than FASP (55%) or acetone precipitation (57%), translating into higher total protein identifications (973 vs 877 FASP or 890 acetone) and higher spectral matches (2.5 times) per protein. In a top down workflow, each SDS‐depletion method yields high‐quality MS spectra for intact proteins. These results show each of these membrane‐based strategies is capable of depleting SDS with high sample recovery and high spectra quality for both BUP and TDP studies.
Modifications generated by fast photochemical oxidation of proteins reflect the native conformations of proteins
Authors: Chea Emily E. , Jones Lisa M. 
Published: March 2018

AbstractHydroxyl radical footprinting (HRF) is a nonspecific protein footprinting method that has been increasingly used in recent years to analyze protein structure. The method oxidatively modifies solvent accessible sites in proteins, which changes upon alterations in the protein, such as ligand binding or a change in conformation. For HRF to provide accurate structural information, the method must probe the native structure of proteins. This requires careful experimental controls since an abundance of oxidative modifications can induce protein unfolding. Fast photochemical oxidation of proteins (FPOP) is a HRF method that generates hydroxyl radicals via photo‐dissociation of hydrogen peroxide using an excimer laser. The addition of a radical scavenger to the FPOP reaction reduces the lifetime of the radical, limiting the levels of protein oxidation. A direct assay is needed to ensure FPOP is probing the native conformation of the protein. Here, we report using enzymatic activity as a direct assay to validate that FPOP is probing the native structure of proteins. By measuring the catalytic activity of lysozyme and invertase after FPOP modification, we demonstrate that FPOP does not induce protein unfolding.
Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way
Authors: Wang Jia , Chen Jingfei , Li Jingwen , An Liaoyuan , Wang Yefei , Huang Qingshan , Yao Lishan 
Published: March 2018

AbstractA combined experimental and computational study is performed for arginine side chain stacking with the protein α‐helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R‐PP stacking has an energy of ∼0.2‐0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone‐backbone h‐bonds (i→i‐4 and i‐3→i‐7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the i→i‐4 and i‐3→i‐7 h‐bonds, respectively. This cooperativity is supported by a protein α‐helices h‐bond survey in the pdb databank where stacking shortens the corresponding h‐bond distances.
Hydrogen jet vapor cloud explosion: A model for predicting blast size and application to risk assessment
Authors: Jallais Simon , Vyazmina Elena , Miller Derek , Thomas J. Kelly 
Published: March 2018

Releases of hydrogen at elevated pressures form turbulent jets in unconfined & uncongested regions may trigger vapor cloud explosion (VCE) as well as jet fire hazards. In the case of a delayed ignition of an unconfined & uncongested jet the turbulence induced by the jet release can lead to flame speeds sufficient to produce damaging blast loads, even in the absence of confinement or congestion. The VCE hazard posed by such high‐pressure hydrogen releases is not well‐recognized.The authors have previously presented test data and computational fluid dynamic (CFD) modeling analyses which characterize high pressure hydrogen releases and the associated VCE hazard in unconfined & uncongested regions. The current paper provides an overview of this VCE hazard. It presents both CFD simulations and a new simplified method. The new method determines the blast strength based on a blast curve method (i.e., TNO multienergy or BST) with the strength index correlated to the mass flow rate of the accidental release. The paper discusses also the implications of such events for building siting analyses and risk assessments. © 2018 American Institute of Chemical Engineers Process Process Saf Prog 37:397–410, 2018
Phylogeography of Diaphorina citri (Hemiptera: Liviidae) and its primary endosymbiont, ‘Candidatus Carsonella ruddii’: an evolutionary approach to host–endosymbiont interaction
Authors: Wang Yanjing , Lu Jinming , Beattie George AC , Islam Mohammad R , Om Namgay , Dao Hang T , Van Nguyen Liem , Zaka Syed M , Guo Jun , Tian Mingyi , Deng Xiaoling , Tan Shunyun , Holford Paul , He Yurong , Cen Yijing 
Published: March 2018

AbstractBACKGROUNDIn insects, little is known about the co‐evolution between their primary endosymbionts and hosts at the intraspecific level. This study examined co‐diversification between the notorious agricultural pest Diaphorina citri and its primary endosymbionts (P‐endosymbiont), ‘Candidatus Carsonella ruddii’ at the population level.RESULTSMaximum likelihood, haplotype network, principal components and Bayesian clustering identified three lineages for D. citri and its P‐endosymbiont: a Western clade containing individuals from Pakistan, Bhutan (Phuentsholing), Vietnam (Son La), USA, Myanmar and China (Ruili, Yunnan); a Central clade, with accessions originating from Southwest China, Bhutan (Tsirang) and Bangladesh; and an Eastern clade containing individuals from Southeast Asia, and East and South China. A more diverse genetic structure was apparent in the host mitochondrial DNA than their P‐endosymbionts; however, the two sets of data were strongly congruent.CONCLUSIONThis study provides evidence for the co‐diversification of D. citri and its P‐endosymbiont during the migration from South Asia to East and Southeast Asia. We also suggest that the P‐endosymbiont may facilitate investigations into the genealogy and migration history of the host. The biogeography of D. citri and its P‐endosymbiont indicated that D. citri colonized and underwent a secondary dispersal from South Asia to East and Southeast Asia. © 2018 Society of Chemical Industry