bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge
Authors: Ettinger Cassandra L. , Voerman Sofie E. , Lang Jenna M. , Stachowicz John J. , Eisen Jonathan A. 
Published: April 2017

Background
Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA.

Methods
We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites.

Results
Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism).

Discussion
Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.
A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome
Authors: Walsh Calum J. , Guinane Caitriona M. , O’ Toole Paul W. , Cotter Paul D. 
Published: April 2017

Background
The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM).

Methods
The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins. This approach was compared with two existing methods to screen both genomic and metagenomic datasets obtained from the Human Microbiome Project (HMP).

Results
Of the methods evaluated, the new profile HMM identified the greatest number of putative LanB proteins in the stool and oral metagenome data while BlastP identified the fewest. In addition, the model identified more LanB proteins than a pre-existing Pfam lanthionine dehydratase model. Searching the gastrointestinal tract subset of the HMP reference genome database with the new HMM identified seven putative subclass I lantibiotic producers, including two members of the Coprobacillus genus.

Conclusions
These findings establish custom profile HMMs as a potentially powerful tool in the search for novel bioactive producers with the power to benefit human health, and reinforce the repertoire of apparent bacteriocin-encoding gene clusters that may have been overlooked by culture-dependent mining efforts to date.
Territorial black-capped chickadee males respond faster to high- than to low-frequency songs in experimentally elevated noise conditions
Authors: LaZerte Stefanie E. , Slabbekoorn Hans , Otter Ken A. 
Published: April 2017

Low-frequency urban noise can interfere with avian communication through masking. Some species are able to shift the frequency of their vocalizations upwards in noisy conditions, which may reduce the effects of masking. However, results from playback studies investigating whether or not such vocal changes improve audibility in noisy conditions are not clear; the responses of free-ranging individuals to shifted signals are potentially confounded by functional trade-offs between masking-related audibility and frequency-dependent signal quality. Black-capped chickadees (Poecile atricapillus) naturally sing their songs at several different frequencies as they pitch-shift to match conspecifics during song-matching contests. They are also known to switch to higher song frequencies in response to experimental noise exposure. Each male produces both high- and low-frequency songs and absolute frequency is not a signal of aggression or dominance, making this an interesting species in which to test whether higher-frequency songs are more audible than lower-frequency songs in noisy conditions. We conducted playback studies across southern and central British Columbia, Canada, using paired song stimuli (high- vs low-frequency songs, n = 24 pairs) embedded in synthetic background noise created to match typical urban sound profiles. Over the course of each playback, the signal-to-noise ratio of the song stimuli was gradually increased by raising the amplitude of the song stimuli while maintaining background noise at a constant amplitude. We evaluated variation in how quickly and aggressively territorial males reacted to each of the paired stimuli. We found that males responded more quickly to playbacks of high- than low-frequency songs when high-frequency songs were presented first, but not when low-frequency songs were first. This difference may be explained by high-frequency songs being more audible combined with a carry-over effect resulting in slower responses to the second stimulus due to habituation. We observed no difference in overall aggression between stimuli. These results suggest that high-frequency songs may be more audible under noisy conditions.
Evolution of developmental sequences in lepidosaurs
Authors: Skawiński Tomasz , Borczyk Bartosz 
Published: April 2017

Background
Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny.

Methods
We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular).

Results
Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies.

Discussion
Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.
South Asian summer monsoon breaks: Process‐based diagnostics in HIRHAM5
Authors: Hanf Franziska S. , Annamalai H. , Rinke Annette , Dethloff Klaus 
Published: April 2017

AbstractThis study assesses the ability of a high‐resolution downscaling simulation with the regional climate model (RCM) HIRHAM5 in capturing the monsoon basic state and boreal summer intraseasonal variability (BSISV) over South Asia with focus on moist and radiative processes during 1979–2012. A process‐based vertically integrated moist static energy (MSE) budget is performed to understand the model's fidelity in representing leading processes that govern the monsoon breaks over continental India. In the climatology (June–September) HIRHAM5 simulates a dry bias over central India in association with descent throughout the free troposphere. Sources of dry bias are interpreted as (i) near‐equatorial Rossby wave response forced by excess rainfall over the southern Bay of Bengal promotes anomalous descent to its northwest and (ii) excessive rainfall over near‐equatorial Arabian Sea and Bay of Bengal anchor a “local Hadley‐type” circulation with descent anomalies over continental India. Compared with observations HIRHAM5 captures the leading processes that account for breaks, although with generally reduced amplitudes over central India. In the model too, anomalous dry advection and net radiative cooling are responsible for the initiation and maintenance of breaks, respectively. However, weaker contributions of all adiabatic MSE budget terms, and an inconsistent relationship between negative rainfall anomalies and radiative cooling reveals shortcomings in HIRHAM5's moisture‐radiation interaction. Our study directly implies that process‐based budget diagnostics are necessary, apart from just checking the northward propagation feature to examine RCM's fidelity to simulate BSISV.
Semi‐Latin Squares
Authors: Bailey R. A. 
Published: April 2017

AbstractSemi‐Latin squares are generalizations of Latin squares with more than one letter in each cell. Various names given to them in the twentieth century are reviewed, along with their applications in several different areas. Methods of constructing them are given, as are the proper methods of randomization and data analysis. Some results are presented about which semi‐Latin squares are optimal when considered as incomplete‐block designs.
Incomplete Data in Astrostatistics
Authors: Chattopadhyay Asis K. 
Published: April 2017

AbstractDuring the past two decades, the interdisciplinary field of astrostatistics has newly emerged in order to study important astrophysical issues through appropriate statistical analysis. Statistical analysis with missing data is an important problem as the problem of incomplete information is very common in many situations. Missing values occur for a variety of reasons, from recording problems to instrument limitations. In particular, when data are combined from multiple archives or instruments, it is virtually certain that some objects will not be present in all of the contributing sources. Standard techniques of missing data analysis may not be equally applicable for astronomical data analysis as the concept of “missing at random” is not likely to be true for such type of data. In the present study, a review of the papers related to missing information in astronomical data and techniques for analysis of missing data have been considered. A new method developed by Deet al. (2016) has also been discussed.
Adaptive neural control for nonstrict‐feedback stochastic nonlinear time‐delay systems with input and output constraints
Authors: Si Wen‐Jie 
Published: April 2017

SummaryThis paper investigates an adaptive neural tracking control for a class of nonstrict‐feedback stochastic nonlinear time‐delay systems with input saturation and output constraint. First, the Gaussian error function is used to represent a continuous differentiable asymmetric saturation model. Second, the appropriate Lyapunov‐Krasovskii functional and the property of hyperbolic tangent functions are used to compensate the time‐delay effects, the neural network is used to approximate the unknown nonlinearities, and a barrier Lyapunov function is designed to ensure that the output parameters are restricted. At last, based on Lyapunov stability theory, a robust adaptive neural control method is proposed, and the designed controller decreases the number of learning parameters and thus reduces the computational burden. It is shown that the designed neural controller can ensure that all the signals in the closed‐loop system are 4‐Moment (or 2 Moment) semi‐globally uniformly ultimately bounded and the tracking error converges to a small neighborhood of the origin. Two examples are given to further verify the effectiveness of the proposed approach.
Das Distortion/Interaction‐Activation‐Strain‐Modell zur Analyse von Reaktionsgeschwindigkeiten
Authors: Bickelhaupt F. Matthias , Houk Kendall N. 
Published: April 2017

AbstractDas Activation‐Strain‐ oder Distortion/Interaction‐Modell ist ein Instrument zur Analyse von Aktivierungsbarrieren und damit von Reaktionsgeschwindigkeiten. Für eine bimolekulare Reaktion ergibt sich die Aktivierungsenergie aus der Summe der Energien, die für die Deformation der Grundzustandsgeometrie der Reaktanten benötigt wird, um die Geometrie des Übergangszustands anzunehmen, plus der Wechselwirkungsenergie zwischen diesen deformierten Reaktanten. Die mit der Deformation assoziierte Energie wird “activation strain” (Aktivierungsspannung) oder “distortion energy” (Deformationsenergie) genannt. Diese Energie bildet den Hauptbeitrag zur Aktivierungsbarriere. Der Übergangszustand wird erreicht, wenn die stabilisierende Wechselwirkung die Aktivierungsspannung überwindet. Die Verlaufsanalyse dieser Energien gibt Einblicke in die reaktivitätsbestimmenden physikalischen Faktoren. Anwendungsbeispiele für das Modell sind die Analyse von Substitutions‐ und Eliminierungsreaktionen sowie Cycloadditionen.
Multivalente Peptid‐Nanopartikel‐Konjugate zur Hemmung des Influenzavirus
Authors: Lauster Daniel , Glanz Maria , Bardua Markus , Ludwig Kai , Hellmund Markus , Hoffmann Ute , Hamann Alf , Böttcher Christoph , Haag Rainer , Hackenberger Christian P. R. , Herrmann Andreas 
Published: April 2017

AbstractZur Inhibition der Bindung von Influenza‐A‐Virus an die Wirtzellglykokalyx haben wir multivalente Peptid‐Polymer‐Nanopartikel entwickelt, die mit nanomolarer Affinität an das Virus über dessen Spikeprotein Hämagglutinin binden. Die dafür gewählten dendritischen Polyglycerolgerüste sind äußerst biokompatibel und eignen sich gut für eine multivalente Präsentation. Wir konnten in In‐vitro‐Experimenten zeigen, dass durch eine Vergrößerung des Polymergerüsts und durch Anpassung der Peptiddichte eine Virusinfektion drastisch reduziert wird. Solch ein Peptid‐Polymer‐Konjugat eignete sich auch für ein In‐vivo‐Szenario. Mit dieser Studie stellen wir den ersten nicht Kohlenhydrat‐basierten, kovalent verknüpften, multivalenten Virusinhibitor im nano‐ bis pikomolaren Bereich vor, unter Wahrung einer geringen Peptidligandendichte auf großen dendritischen Gerüsten.
Designed Heme‐Cage β‐Sheet Miniproteins
Authors: D'Souza Areetha , Wu Xiangyang , Yeow Edwin Kok Lee , Bhattacharjya Surajit 
Published: April 2017

AbstractThe structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β‐sheet proteins remains challenging. Herein, we describe the construction and characterization of four‐stranded β‐sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or “heme cage” by bis‐histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic‐resolution structures confirmed the presence of a four‐stranded β‐sheet fold. The heme–protein complexes also exhibited high stability against thermal and chaotrope‐induced unfolding.
Analysis of toldimfos in porcine muscle and bovine milk using liquid chromatography–triple quadrupole mass spectrometry
Authors: Zhang Dan , Park Jin‐A , Abd El‐Aty A. M. , Kim Seong‐Kwan , Cho Sang‐Hyun , Zheng Weijia , Choi Jeong‐min , Shim Jae‐Han , Chang Byung‐Joon , Kim Jin‐Suk , Shin Ho‐Chul 
Published: April 2017

AbstractAn analytical method was developed for the detection of toldimfos sodium residues in porcine muscle and bovine milk using liquid chromatography–triple quadrupole tandem mass spectrometry (LC–MS/MS) analysis. The drug was extracted from muscle and milk using 10 mm ammonium formate in acetonitrile and then purified using n‐hexane. The drug was well separated on a Luna C18 column using a mixture of 10 mm ammonium formate in ultrapure water (A) and acetonitrile (B) as the mobile phase. Good linearity was achieved over the tested concentration range (0.005–0.03 mg/kg) in matrix‐matched standard calibration. The determination coefficients (R2) were 0.9942 and 0.9898 for muscle and milk, respectively. Fortified porcine muscle and bovine milk contained concentrations equivalent to and twice the limit of quantification (0.005 mg/kg) yielded recoveries in the range of 75.58–89.74% and relative standard deviations of ≤8.87%. Samples collected from large markets located in Seoul, Republic of Korea, tested negative for toldimfos sodium residue. In conclusion, ammonium formate in acetonitrile can effectively extract toldimfos sodium from porcine muscle and bovine milk without solid‐phase extraction, which is usually required for cleanup before analysis. This method can be applied for the routine analysis of toldimfos in foods of animal origins.
Performance evaluation of prototype‐based clustering algorithms combined MDL index
Authors: Aljobouri Hadeel K. , Jaber Hussain A. , Çankaya Ilyas 
Published: April 2017

AbstractClustering algorithms are used to group data depending on a distance. Best clustering analysis should be resisting the presence of outliers, less sensitive to initialization as well as the input sequence ordering. This article compares the performance among three of prototype‐based unsupervised clustering algorithms: Neural Gas (NG), Growing Neural Gas (GNG) and Robust Growing Neural Gas (RGNG). Based on NG and GNG, there are different clustering algorithms proposed and suggested in different literatures. So, in this work a comparison between the two basic clustering algorithms NG and GNG have presented using the performance evaluation of these techniques, in contrast to the RGNG which was proposed within the GNG. Another comparison due to the MDL criterion between RGNG that used MDL value as the clustering validity index, versus GNG and NG combined with MDL. Statistical estimations are applied to explain the meaning of the output results when these algorithms fed to the synthetic 2D dataset. Moreover, a simple software package is designed and implemented as an automatic clustering model for any dataset to use as a part of the neural network course. NG, GNG and RGNG algorithms are performed in the same package using a MATLAB‐based Graphical User Interface (GUI) tool. This visual tool lets the students/ researchers visualize the desired results using plots also clicking a few buttons.
Thienylquinonoidal Porphyrins and Hexaphyrins with Singlet Diradical Ground States
Authors: Naoda Koji , Shimizu Daiki , Kim Jun Oh , Furukawa Ko , Kim Dongho , Osuka Atsuhiro 
Published: April 2017

AbstractTo explore stable organic diradicaloids, meso‐thienylquinonoid‐substituted porphyrins Pn and hexaphyrins Hn, where “n” denotes the number of thienyl units in the meso‐substituents, were synthesized. P0 was identified as a closed‐shell quinonoid, whereas P1 was shown to possess significant diradical character with diradical character index (y) of 0.99 and quite small singlet‐triplet energy gap (ΔES‐T) of −0.13 kcal mol−1. P1 was certainly stable, allowing its isolation, but decomposed gradually in solution. In the hexaphyrin series, it was shown that H0 and H1 were closed‐shell quinonoids, but H2 was a highly stable diradicaloid with y=0.85 and ΔES‐T of −3.72 kcal mol−1. The high stability of H2 was ascribed to effective spin delocalization over the entire conjugated network. Characteristically, H2 displays an intense absorption band in NIR region at λmax=1175 nm with molar absorption coefficient (ϵ) of 8.81×104 mol−1 L cm−1, a narrow HOMO–LUMO gap of 0.69 eV, and nine reversible redox potential waves.
Radical Arylation of Anilines and Pyrroles via Aryldiazotates
Authors: Hofmann Josefa , Gans Eva , Clark Timothy , Heinrich Markus R. 
Published: April 2017

AbstractThe radical arylation of anilines and pyrroles can be achieved under transition‐metal‐ and catalyst‐free conditions by using aryldiazotates in strongly alkaline aqueous solutions. The aryldiazotates act as protected diazonium ions, which do not undergo azo coupling with electron‐rich aromatic substrates, but can still serve as an aryl radical source at slightly elevated temperatures. Based on an improved preparation of aryldiazotates in aqueous solution, homolytic aromatic substitutions of anilines and pyrroles were conducted with good overall yields and high regioselectivity. Moreover, DFT calculations provided further mechanistic insights.
Nonparametric and semiparametric estimation of quantile residual lifetime for length‐biased and right‐censored data
Authors: Wang Yixin , Zhou Zhefang , Zhou Xiao‐Hua , Zhou Yong 
Published: April 2017

AbstractQuantile residual lifetime models are often of concern in survival analysis, especially when studying a chronic or irreversible disease like dementia. In the past several decades residual life models have been studied extensively with right‐censored survival data. However these methods are not suitable to analyze the length‐biased and right‐censored data from the prevalent cohort sampling. In this article we propose nonparametric and semiparametric model‐based procedures to estimate the quantile residual lifetime with censored length‐biased data. Two test statistics are established for comparing the quantile residual lifetimes of two groups, evaluated, respectively, on ratio and difference in terms of type I error probabilities and powers. Some simulations are conducted to compare the proposed method with existing approaches. Real dementia data from the National Alzheimer's Coordinating Center are used to illustrate the proposed estimation methods by estimating the quantile residual lifetimes of the dementia patients. The Canadian Journal of Statistics 45: 220–250; 2017 © 2017 Statistical Society of Canada