bluuebunny/crossref_metadata_2025_split huggingface dataset:
Power integrated circuit implementation of optimal adaptive voltage positioning scheme using progressive waveform shaping algorithm
Authors: Liu Chih‐Wei , Chang‐Chien Le‐Ren 
Published: June 2016

Adaptive voltage positioning (AVP) scheme is widely adopted in the high‐load voltage regulation modules (VRMs) because it helps VRMs reducing almost half the number of output capacitors for the same design without using AVP. The AVP scheme is claimed to be optimal if its voltage transient behaviour is linear by tuning the current sensing parameter (Ri) to match the value of the output capacitor equivalent series resistor (ESR). In this study, a progressive waveform‐shaping method is proposed to automatically achieve optimal AVP for the VRMs without manually setting the optimal Ri. Hence, as long as a proper ESR of the output capacitor is determined, VRM designers can use the least output capacitor numbers to obtain the optimal AVP waveform. The proposed method is especially appealing for the power integrated circuit application. The overall controller design was implemented by the Taiwan semiconductor manufacturing company (TSMC) 0.18 μm manufacturing process. In the real implementation, an AVP‐based buck converter was devised to perform 5 μs linear transient in response to the 10 A/5 μs load current step at 1.2 V output voltage. Test of the circuit shows that the AVP performance is comparable to those state of the art.
Pädophile Neigungen offenbaren: Stigma-Management bei Patienten aus dem Berliner Präventionsprojekt Dunkelfeld
Authors: Wagner Tilmann , Jahnke Sara , Beier Klaus M. , Hoyer Jürgen , Scherner Gerold 
Published: June 2016

ÜbersichtVor dem Hintergrund der enormen Stigmatisierung von Menschen mit pädophilen Neigungen ist davon auszugehen, dass sich Betroffene häufig entscheiden müssen, diese preiszugeben oder geheim zu halten – mit zum Teil dramatischen Konsequenzen für ihr soziales Leben und ihr Selbstbild. Obwohl Formen des Stigma-Managements für andere stigmatisierte Gruppen bereits intensiv erforscht wurden, liegen bisher keine Daten zu den Erfahrungen pädophiler Personen vor. Zur Identifikation typischer Strategien und deren Konsequenzen wurden in der vorliegenden Studie Erstgespräche von 186 Patienten des Präventionsprojekts Dunkelfeld (PPD) qualitativ ausgewertet. 48 % der Patienten hatten sich einer anderen Person anvertraut (direkte Offenlegung), bei 37 % wurden pädophile Neigungen durch andere Personen aufgedeckt, ohne dass die Betroffenen es selbst entschieden hatten (indirekte Offenlegung) und 15 % der Patienten hatten zuvor noch nie über ihre sexuellen Neigungen gesprochen
(Geheimhaltung). Unsere Analysen der berichteten Konsequenzen legen nahe, dass bei einer direkten Offenlegung das Verhältnis von Vor- und Nachteilen am günstigsten ausfällt. Die Ergebnisse werden hinsichtlich des Risikos für sexuellen Kindesmissbrauch und ihrer Implikationen für präventive therapeutische Strategien diskutiert.
Investigating grammatical processing in bilinguals
Authors: Clahsen Harald , Veríssimo João 
Published: June 2016

Abstract
In this article we discuss methods for investigating grammatical processing in bilinguals. We will present a methodological approach that relies on: (i) linguistic theory (in our case, morphology) for the construction of experimental materials; (ii) a design that allows for direct (within-experiment, within-participant, and within-item) comparisons of the critical conditions; and (iii) data analysis techniques that make both linear and non-linear gradient effects visible. We review recent studies of masked morphological priming in bilinguals in which the application of these methodological principles revealed highly selective interactions of age of acquisition (and the native/non-native contrast) with the linguistic distinction between inflection and derivation. We believe that such considerations are not only relevant for grammatical processing experiments, but also for studying bilingualism, and its potential cognitive advantages, more generally.
Cooking pasta in La Paz
Authors: Bak Thomas H. 
Published: June 2016

Abstract
Literature on bilingualism and cognition is characterised by a large amount of conflicting evidence. In some studies, bilinguals perform better then monolinguals on executive tasks involving inhibition, monitoring and switching but are slower on tasks of lexical processing. Other studies don’t find any significant effects and challenge the very existence of cognitive differences between monolinguals and bilinguals. In this paper I question the assumption that different studies performed in different parts of the world should yield the same results. I argue that the environment (in the widest sense of the word) in which an experiment is conducted can exert profound influence on its outcome. Against the background of the current debate about the replication crisis in science, I propose that conflicting evidence is not a threat to the trustworthiness of scientific research but a sign of the health of a discipline and a welcome opportunity to identify new relevant variables.
Feeding Ecology of Dolphinfish in the Western Gulf of Mexico
Authors: Brewton Rachel A. , Ajemian Matthew J. , Young Peter C. , Stunz Gregory W. 
Published: June 2016

AbstractDolphinfish Coryphaena hippurus support important commercial and recreational fisheries in the Gulf of Mexico. Understanding the feeding ecology of this economically important pelagic fish is key to its sustainable management; however, dietary data from this region are sparse. We conducted a comprehensive diet study to develop new trophic baselines and investigate potential ontogenetic and sex‐related shifts in Dolphinfish feeding ecology. The stomach contents of 357 Dolphinfish (27.6–148.5 cm TL) were visually examined from fishery‐dependent sources off Port Aransas, Texas. Our analyses revealed a highly piscivorous diet with Actinopterygii comprising 70.44% of the stomach contents by number. The most commonly observed taxa were carangid (12.45%N) and tetraodontiform (12.08%N; families Balistidae, Monacanthidae, and Tetraodontidae) fishes. Malacostracans were also common (24.83%N), mostly in the form of pelagic megalopae. Other prey categories included squid and the critically endangered Kemp's Ridley sea turtles Lepidochelys kempii. Although increasingly commom in larger fish, Sargassum spp. was found across a range of sizes in Dolphinfish, indicating that these fish feed from this drifting macroalgae throughout ontogeny. An ontogenetic shift from primary consumption of carangids and brachyurans in smaller size‐classes to tetraodontids, monocanthids, and squid in larger size‐classes was also observed. No sex‐related difference in diet was observed. The overall infection rate for gastric parasites was 54%, an order of magnitude increase from that previously reported in the region, but consistent with recent studies from other areas. Trematode parasites in the genus Dinurus were found in 55% of stomachs and nematode parasites of the family Raphidascarididae in 16% of stomachs. Overall, Dolphinfish in the western Gulf of Mexico are highly opportunistic carnivores with a gastrointestinal parasite burden consistent with that reported in other ocean basins. These data will be important for sustainable management of this economically important species.Received November 20, 2015; accepted February 17, 2016 Published online June 24, 2016
Comparison of Pulsed Gastric Lavage and Acrylic Stomach Tubes for Sampling the Diet of Butterfly Peacock Bass
Authors: Bies Jason M. , Neal J. Wesley 
Published: June 2016

AbstractNonlethal techniques for sampling the stomach contents of fishes have been developed for a variety of fish species. The goal of this study was to determine whether pulsed gastric lavage or acrylic stomach tubes were more effective for extracting stomach contents from Butterfly Peacock Bass Cichla ocellaris, specifically which was least injurious, retrieved the greatest percentage of stomach contents, and was least biased. Pulsed gastric lavage was less injurious than stomach tubes, with bruising of the stomach wall the most common injury being observed. The mean percent of stomach contents removed by pulsed gastric lavage (70.0%) was greater than the percent removed by stomach tubes (57.2%). Both gears were less successful at removing contents from larger fish and had difficulties retrieving contents from fuller stomachs. Pulsed gastric lavage is the recommended method for sampling stomach contents from Butterfly Peacock Bass, as it is both less injurious and more effective than stomach tubes. However, given the low average percent of diet recovered, pulsed gastric lavage may be more appropriate for studies that require only the presence or absence of a species in Butterfly Peacock Bass diets rather than for studies that require quantitative depictions of diet composition.Received December 19, 2015; accepted March 10, 2016 Published online June 24, 2016
Moral uncertainty and permissibility: Evaluating Option Sets
Authors: Barry Christian , Tomlin Patrick 
Published: June 2016

AbstractIn this essay, we explore an issue of moral uncertainty: what we are permitted to do when we are unsure about which moral principles are correct. We develop a novel approach to this issue that incorporates important insights from previous work on moral uncertainty, while avoiding some of the difficulties that beset existing alternative approaches. Our approach is based on evaluating and choosing between optionsetsrather than particular conductoptions.We show how our approach is particularly well-suited to address this issue of moral uncertainty with respect to agents that have credence in moral theories that are not fully consequentialist.
Experimental assessment of factors mediating the naturalization of a globally invasive tree on sandy coastal plains: a case study from Brazil
Authors: Zimmermann Thalita G. , Andrade Antonio C. S. , Richardson David M. 
Published: June 2016

Abstract
As all naturalized species are potential invaders, it is important to better understand the determinants of naturalization of alien plants. This study sought to identify traits that enable the alien tree Casuarina equisetifolia to overcome barriers to survival and reproductive and to become naturalized on sandy coastal plains. Restinga vegetation in Brazil was used as a model system to conceptualize and quantify key stressors (high temperature, solar radiation, drought and salinity) which can limit the initial establishment of the plants. Experiments were conducted to evaluate the effects of these environmental factors on seed persistence in the soil (field), germination (laboratory), survival, growth, phenotypic plasticity and phenotypic integration (greenhouse). Results show that the expected viability of the seeds in the soil was 50 months. Seeds germinated in a similar way in constant and alternating temperatures (20–40 °C), except at 40 °C. Low light, and water and salt stresses reduced germination, but seeds recovered germination when stress diminished. Young plants did not tolerate water stress (&lt;2 % of soil moisture) or deep shade. Growth was greater in sunny than in shady conditions. Although a low degree of phenotypic plasticity is important in habitats with multiple stress factors, this species exhibited high germination plasticity, although young plants showed low plasticity. The positive effect of phenotypic integration on plastic expression in the shade shows that in stressful environments traits that show greater phenotypic plasticity values may have significant phenotypic correlations with other characters, which is an important factor in the evolutionary ecology of this invasive species. Long-term seed persistence in the soil, broad germination requirements (temperature and light conditions) and the capacity to survive in a wide range of light intensity favours its naturalization. However, C. equisetifolia did not tolerate water stress and deep shade, which limit its potential to become naturalized on sandy coastal plain.
Effects of topoclimatic complexity on the composition of woody plant communities
Authors: Oldfather Meagan F. , Britton Matthew N. , Papper Prahlad D. , Koontz Michael J. , Halbur Michelle M. , Dodge Celeste , Flint Alan L. , Flint Lorriane E. , Ackerly David D. 
Published: June 2016

Abstract
Topography can create substantial environmental variation at fine spatial scales. Shaped by slope, aspect, hill-position and elevation, topoclimate heterogeneity may increase ecological diversity, and act as a spatial buffer for vegetation responding to climate change. Strong links have been observed between climate heterogeneity and species diversity at broader scales, but the importance of topoclimate for woody vegetation across small spatial extents merits closer examination. We established woody vegetation monitoring plots in mixed evergreen-deciduous woodlands that spanned topoclimate gradients of a topographically heterogeneous landscape in northern California. We investigated the association between the structure of adult and regenerating size classes of woody vegetation and multidimensional topoclimate at a fine scale. We found a significant effect of topoclimate on both single-species distributions and community composition. Effects of topoclimate were evident in the regenerating size class for all dominant species (four Quercus spp. , Umbellularia californica and Pseudotsuga menziesii ) but only in two dominant species ( Quercus agrifolia and Quercus garryana ) for the adult size class. Adult abundance was correlated with water balance parameters (e.g. climatic water deficit) and recruit abundance was correlated with an interaction between the topoclimate parameters and conspecific adult abundance (likely reflecting local seed dispersal). However, in all cases, the topoclimate signal was weak. The magnitude of environmental variation across our study site may be small relative to the tolerance of long-lived woody species. Dispersal limitations, management practices and patchy disturbance regimes also may interact with topoclimate, weakening its influence on woody vegetation distributions. Our study supports the biological relevance of multidimensional topoclimate for mixed woodland communities, but highlights that this relationship might be mediated by interacting factors at local scales.
GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
Authors: Guðbjartsson Hákon , Georgsson Guðmundur Fr. , Guðjónsson Sigurjón A. , Valdimarsson Ragnar þór , Sigurðsson Jóhann H. , Stefánsson Sigmar K. , Másson Gísli , Magnússon Gísli , Pálmason Vilmundur , Stefánsson Kári 
Published: June 2016

Abstract
Motivation: Our aim was to create a general-purpose relational data format and analysis tools to provide an efficient and coherent framework for working with large volumes of DNA sequence data.
Results: For this purpose we developed the GORpipe software system. It is based on a genomic ordered architecture and uses a declarative query language that combines features from SQL and shell pipe syntax in a novel manner. The system can for instance be used to annotate sequence variants, find genomic spatial overlap between various types of genomic features, filter and aggregate them in various ways.
Availability and Implementation: The GORpipe software is freely available for non-commercial academic usage and can be downloaded from www.nextcode.com/gorpipe.
Contact: hakon@wuxinextcode.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Revealing aperiodic aspects of solenoid proteins from sequence information
Authors: Hrabe Thomas , Jaroszewski Lukasz , Godzik Adam 
Published: June 2016

Abstract
Motivation: Repeat proteins, which contain multiple repeats of short sequence motifs, form a large but seldom-studied group of proteins. Methods focusing on the analysis of 3D structures of such proteins identified many subtle effects in length distribution of individual motifs that are important for their functions. However, similar analysis was yet not applied to the vast majority of repeat proteins with unknown 3D structures, mostly because of the extreme diversity of the underlying motifs and the resulting difficulty to detect those.
Results: We developed FAIT, a sequence-based algorithm for the precise assignment of individual repeats in repeat proteins and introduced a framework to classify and compare aperiodicity patterns for large protein families. FAIT extracts repeat positions by post-processing FFAS alignment matrices with image processing methods. On examples of proteins with Leucine Rich Repeat (LRR) domains and other solenoids like proteins, we show that the automated analysis with FAIT correctly identifies exact lengths of individual repeats based entirely on sequence information.
Availability and Implementation: https://github.com/GodzikLab/FAIT.
Contact: adam@godziklab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs
Authors: Arenillas David J. , Forrest Alistair R. R. , Kawaji Hideya , Lassmann Timo ,   The FANTOM Consortium, Wasserman Wyeth W. , Mathelier Anthony 
Published: June 2016

Abstract
With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions.
Availability and Implementation: The CAGEd-oPOSUM web tool is implemented in Perl, MySQL and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM.
Contacts: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
iPTM-mLys: identifying multiple lysine PTM sites and their different types
Authors: Qiu Wang-Ren , Sun Bi-Qian , Xiao Xuan , Xu Zhao-Chun , Chou Kuo-Chen 
Published: June 2016

AbstractMotivation: Post-translational modification, abbreviated as PTM, refers to the change of the amino acid side chains of a protein after its biosynthesis. Owing to its significance for in-depth understanding various biological processes and developing effective drugs, prediction of PTM sites in proteins have currently become a hot topic in bioinformatics. Although many computational methods were established to identify various single-label PTM types and their occurrence sites in proteins, no method has ever been developed for multi-label PTM types. As one of the most frequently observed PTMs, the K-PTM, namely, the modification occurring at lysine (K), can be usually accommodated with many different types, such as ‘acetylation’, ‘crotonylation’, ‘methylation’ and ‘succinylation’. Now we are facing an interesting challenge: given an uncharacterized protein sequence containing many K residues, which ones can accommodate two or more types of PTM, which ones only one, and which ones none?Results: To address this problem, a multi-label predictor called iPTM-mLys has been developed. It represents the first multi-label PTM predictor ever established. The novel predictor is featured by incorporating the sequence-coupled effects into the general PseAAC, and by fusing an array of basic random forest classifiers into an ensemble system. Rigorous cross-validations via a set of multi-label metrics indicate that the first multi-label PTM predictor is very promising and encouraging.Availability and Implementation: For the convenience of most experimental scientists, a user-friendly web-server for iPTM-mLys has been established at http://www.jci-bioinfo.cn/iPTM-mLys, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.Contact: wqiu@gordonlifescience.org, xxiao@gordonlifescience.org, kcchou@gordonlifescience.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Reducing bycatch in beam trawls and electrotrawls with (electrified) benthos release panels
Authors: Soetaert Maarten , Lenoir Heleen , Verschueren Bart 
Published: June 2016

Abstract
Benthos release panels (BRPs) are known for their capacity to release large amounts of unwanted benthos and debris, which can decrease mortality on these animals and eases the on board sorting process aboard demersal beam trawlers. They can reduce the bycatch of undersized fish, which is desired once the European discard ban is implemented. However, unacceptable commercial losses of sole (Solea solea L.) and damage to the BRP as a consequence of suboptimal and unsuitable rigging in the traditional beam trawl with chain mat, is hampering a successful introduction in commercial beam-trawl fisheries. To eliminate these drawbacks, square-meshed BRPs with different mesh sizes (150, 200, and 240 mm) were rigged in a trawl with square net design as used in electrotrawls and tested for selectivity. In addition to this, the effect of electric stimulation at the height of the BRP to eliminate the loss of commercial sole was examined. According to our observations, no abrasion of the net attributable to suboptimal rigging occurred in any of the BRPs tested. The catch comparisons showed significant release of benthos and undersized fish in all panel mesh sizes, but there was always a significant loss of marketable sole in the 150, 200, and 240 mm BRPs. Adding a 80 Hz electric cramp stimulus to the BRP, resulted in equal catches of sole larger than 25 cm as the standard net, without negatively affecting the release of benthos and most undersized commercial fish. This clearly demonstrates the promising potential of electrified BRPs (eBRPs), but further optimization by using smaller BRP mesh sizes or optimized electric stimuli is warranted to retain all marketable sole.