bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChemInform Abstract: STRUKTUR‐WIRKUNGS‐BEZIEHUNGEN BEI HISTAMINANALOGA 8. MITT. SYNTHESE UND WIRKUNG 2‐SUBSTITUIERTER HISTAMINE
Authors: DZIURON PETER , SCHUNACK WALTER 
Published: March 2016

AbstractDie Titelverbindungen (IVa) bzw. (IVb) werden aus den Iminoestern (I) mit den Dihydroxyketonen (II) bzw. (V) über die Imidazolalkohole (III) bzw. (VI) synthetisiert.
ChemInform Abstract: COMPONENT AMINO ACIDS OF THE ANTIBIOTIC LONGICATENAMYCIN. ISOLATION OF 5‐CHLORO‐D‐ARYPTOPHAN
Authors: SHIBA TETSUO , MUKUNOKI YASUO , AKIYAMA HITOSHI 
Published: March 2016

AbstractLongicatenamycin ist ein Peptid, das nach Berichten von Shoji die‐vier neuen Aminosäuren (I) und (II) enthält.
ChemInform Abstract: DIE HYDROPYROLYSE, EIN NEUER PROZESS ZUR HERST. VON AETHYLEN
Authors: CHAHVEKILIAN E. , DUMON R. 
Published: March 2016

AbstractEine Pilotanlage zur Herstellung von Äthylen nach dem Hydropyrolyse‐Verfahren der Firmen Pierrefitte‐Auby, Heurtey und Naphthachimie wird im nächsten Jahr in Betrieb genommen.
Hollow Zeolite Single‐Crystals Encapsulated Alloy Nanoparticles with Controlled Size and Composition
Authors: Li Shiwen , Tuel Alain , Rousset Jean‐Luc , Morfin Franck , Aouine Mimoun , Burel Laurence , Meunier Frédéric , Farrusseng David 
Published: March 2016

AbstractStandard chemical and physical methods to control the size of supported metallic nanoparticles are generally not compatible with the harsh conditions of applications (high temperature, presence of steam). Sintering of nanoparticles usually occurs, leading to particle growth and eventually to a degradation of physical properties. Here we describe a generic process for synthesizing nanoalloys of controlled size (2–10 nm) and composition encapsulated in zeolite nanoboxes. The originality of the synthesis design is that the nanoboxes act both as nanoreactors in which the bimetallic particles are formed and as protective ultra‐microporous shells, which prevent sintering by coalescence even under harsh conditions. Moreover, the present process allows for control over the size and composition of the NPs, which are factors that ultimately determine the catalytic properties. A series of mono‐ (Au, Pd, Pt) or bi‐ (AuAg, PdAg, PtAg and PdPt) metallic nanoparticles individually encapsulated in hollow silicalite‐1 single crystals have been prepared and characterized. The simultaneous presence of Ag and Au at the surface of Au161Ag22 NPs has been demonstrated by results of the catalytic activity for CO oxidation near room temperature.
Fabrication of Ultrasonic Sensors Using Micro Cantilevers and Characteristic Measurement in Vacuum for Acoustic Emission Sensing
Authors: TAKATA KENGO , SASAKI TAKASHI , TANAKA MITSUYUKI , SAITO HIROSHI , MATSUURA DAISUKE , HANE KAZUHIRO 
Published: March 2016

SUMMARYAcoustic emission (AE) sensors are attractive for the detection of machine fracture in real time. We fabricated AE sensors using the MEMS technology. The AE sensors consisted of silicon cantilevers resonating at frequencies of 50, 100, and 150 kHz. Silicon piezoresistors were installed close to the cantilevers. In order to obtain an ambient pressure appropriate for the operation of the cantilevers, the Q factor of the cantilevers was calculated by analytical models as a function of pressure. The properties of the fabricated sensors were measured in a vacuum chamber. We also tentatively packaged the AE sensor and an amplifier in a vacuum to decrease the influences of air damping and noise.
Single‐breath clinical imaging of hyperpolarized 129xe in the airspaces, barrier, and red blood cells using an interleaved 3D radial 1‐point Dixon acquisition
Authors: Kaushik S. Sivaram , Robertson Scott H. , Freeman Matthew S. , He Mu , Kelly Kevin T. , Roos Justus E. , Rackley Craig R. , Foster W. Michael , McAdams H. Page , Driehuys Bastiaan 
Published: March 2016

PurposeWe sought to develop and test a clinically feasible 1‐point Dixon, three‐dimensional (3D) radial acquisition strategy to create isotropic 3D MR images of 129Xe in the airspaces, barrier, and red blood cells (RBCs) in a single breath. The approach was evaluated in healthy volunteers and subjects with idiopathic pulmonary fibrosis (IPF).MethodsA calibration scan determined the echo time at which 129Xe in RBCs and barrier were 90° out of phase. At this TE, interleaved dissolved and gas‐phase images were acquired using a 3D radial acquisition and were reconstructed separately using the NUFFT algorithm. The dissolved‐phase image was phase‐shifted to cast RBC and barrier signal into the real and imaginary channels such that the image‐derived RBC:barrier ratio matched that from spectroscopy. The RBC and barrier images were further corrected for regional field inhomogeneity using a phase map created from the gas‐phase 129Xe image.ResultsHealthy volunteers exhibited largely uniform 129Xe‐barrier and 129Xe‐RBC images. By contrast, 129Xe‐RBC images in IPF subjects exhibited significant signal voids. These voids correlated qualitatively with regions of fibrosis visible on CT.ConclusionsThis study illustrates the feasibility of acquiring single‐breath, 3D isotropic images of 129Xe in the airspaces, barrier, and RBCs using a 1‐point Dixon 3D radial acquisition. Magn Reson Med 75:1434–1443, 2016. © 2015 Wiley Periodicals, Inc.
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks
Authors: Blatti Charles , Sinha Saurabh 
Published: March 2016

Abstract
Motivation: Analysis of co-expressed gene sets typically involves testing for enrichment of different annotations or ‘properties’ such as biological processes, pathways, transcription factor binding sites, etc., one property at a time. This common approach ignores any known relationships among the properties or the genes themselves. It is believed that known biological relationships among genes and their many properties may be exploited to more accurately reveal commonalities of a gene set. Previous work has sought to achieve this by building biological networks that combine multiple types of gene–gene or gene–property relationships, and performing network analysis to identify other genes and properties most relevant to a given gene set. Most existing network-based approaches for recognizing genes or annotations relevant to a given gene set collapse information about different properties to simplify (homogenize) the networks.
Results: We present a network-based method for ranking genes or properties related to a given gene set. Such related genes or properties are identified from among the nodes of a large, heterogeneous network of biological information. Our method involves a random walk with restarts, performed on an initial network with multiple node and edge types that preserve more of the original, specific property information than current methods that operate on homogeneous networks. In this first stage of our algorithm, we find the properties that are the most relevant to the given gene set and extract a subnetwork of the original network, comprising only these relevant properties. We then re-rank genes by their similarity to the given gene set, based on a second random walk with restarts, performed on the above subnetwork. We demonstrate the effectiveness of this algorithm for ranking genes related to Drosophila embryonic development and aggressive responses in the brains of social animals.
Availability and Implementation: DRaWR was implemented as an R package available at veda.cs.illinois.edu/DRaWR.
Contact: blatti@illinois.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Authors: Li Heng 
Published: March 2016

Abstract
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10–15%. Complex and computationally intensive pipelines are required to assemble such reads.
Results: We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools.
Availability and implementation: https://github.com/lh3/minimap and https://github.com/lh3/miniasm
Contact: hengli@broadinstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Detecting critical state before phase transition of complex biological systems by hidden Markov model
Authors: Chen Pei , Liu Rui , Li Yongjun , Chen Luonan 
Published: March 2016

Abstract
Motivation: Identifying the critical state or pre-transition state just before the occurrence of a phase transition is a challenging task, because the state of the system may show little apparent change before this critical transition during the gradual parameter variations. Such dynamics of phase transition is generally composed of three stages, i.e. before-transition state, pre-transition state and after-transition state, which can be considered as three different Markov processes.
Results: By exploring the rich dynamical information provided by high-throughput data, we present a novel computational method, i.e. hidden Markov model (HMM) based approach, to detect the switching point of the two Markov processes from the before-transition state (a stationary Markov process) to the pre-transition state (a time-varying Markov process), thereby identifying the pre-transition state or early-warning signals of the phase transition. To validate the effectiveness, we apply this method to detect the signals of the imminent phase transitions of complex systems based on the simulated datasets, and further identify the pre-transition states as well as their critical modules for three real datasets, i.e. the acute lung injury triggered by phosgene inhalation, MCF-7 human breast cancer caused by heregulin and HCV-induced dysplasia and hepatocellular carcinoma. Both functional and pathway enrichment analyses validate the computational results.
Availability and implementation: The source code and some supporting files are available at https://github.com/rabbitpei/HMM_based-method.
Contacts: lnchen@sibs.ac.cn or liyj@scut.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees
Authors: Martínez-Aquino Andrés 
Published: March 2016

AbstractPhylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host–parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a “compass” when “walking” through jungles of tangled phylogenetic trees.
Describing the evolution of mobile technology usage for Latino patients and comparing findings to national mHealth estimates
Authors: Arora Sanjay , Ford Kelsey , Terp Sophie , Abramson Tiffany , Ruiz Ryan , Camilon Marissa , Coyne Christopher J , Lam Chun Nok , Menchine Michael , Burner Elizabeth 
Published: March 2016

Abstract
Objectives Describe the change in mobile technology used by an urban Latino population between 2011 and 2014, and compare findings with national estimates.
Materials and Methods Patients were surveyed on medical history and mobile technology use. We analyzed specific areas of mobile health capacity stratified by chronic disease, age, language preference, and educational attainment.
Results Of 2144 Latino patients, the percentage that owned a cell phone and texted were in-line with Pew estimates, but app usage was not. Patients with chronic disease had reduced access to mobile devices ( P  &lt; .001) and lower use of mobile phone functionalities.
Discussion Prior research suggests that Latinos can access mHealth; however, we observed lower rates among Latino patients actively seeking heath care.
Conclusion Published national estimates do not accurately reflect the mobile technology use of Latino patients served by our public safety-net facility. The difference is greater for older, less educated patients with chronic disease.
Zika Virus Disease: A Simple Model Approach to Rapid Impact Assessment
Authors: Wilson James M. , Malone Robert W. , Smith-Gagen Julie , Pabayo Roman ,   Zika Response Working Group
Published: March 2016

AbstractThere has been substantial media attention regarding Zika infection as a threat to pregnancy, prompted by WHO’s declaration of a Public Health Event of International Concern (PHEIC). Here we present a simple risk assessment model for two states within the continental United States at-risk for autochthonous transmission of Zika virus, Texas and Florida. Our simple impact assessment model is partially validating at this early interval in the crisis.
Effects of Unleaded Petroleum on the Macrophage Aggregates (MA) formation in Red King tilapia (Oreochromis sp.) Fingerlings
Authors: Beso Ancel Jeff G. , Candelaria Veronica Y. , Dela Cruz Jennifer G. , Tolentino Margie S. , Tameta Anna Danica C , Espinosa Allen A. 
Published: March 2016

ABSTRACTThe Philippines is one of the major producers of tilapia, the most cultured fish and widely consumed in the world. Although fishes in general is said to be adapted to various stressful conditions, the effect on several cellular immune parameters may be of interest to determine the capacity of the organism to withstand stressors. In this paper, the effect of unleaded petroleum on the splenic macrophage aggregate (MA) formation was studied. This was done to have an overview of the immune response of Tilapia or fishes in general when an oil spill, which almost occur annually at different parts of the world, happen. Histological analysis assessed the area occupied by splenic MA 24 hours after introduction of unleaded petroleum to the aquatic system. To determine whether Mabuhay balls, a technology that claims to be beneficial in terms of improving water quality, was added to one tank (T1) to be able to compare it with another tank (T2). There is a strong statistically significant difference between the groups at day1 (p=0.000) opposite the result of day 6 (p=0.155). Thus, unleaded petroleum increased MA formation, a sign that may indicate a high immune activity as an initial positive response to stress. Mabuhay ball have lessen the mortality but has no effect on splenic MA formation.
An atypical role for the myeloid receptor Mincle in CNS injury
Authors: Arumugam Thiruma V. , Manzanero Silvia , Furtado Milena , Biggins Patrick J. , Hsieh Yu-Hsuan , Gelderblom Mathias , MacDonald Kelli PA , Salimova Ekaterina , Li Yu-I , Korn Othmar , Dewar Deborah , Macrae I Mhairi , Ashman Robert B. , Tang Sung-Chun , Rosenthal Nadia A. , Ruitenberg Marc J. , Magnus Tim , Wells Christine A. 
Published: March 2016

AbstractMincle is a C-type lectin known to play a role in innate immune responses to sterile inflammation, but its contribution to pathologies following an ischemic or traumatic injury is not well understood. In the current study we demonstrate a key role for Mincle in ischemic (i.e. transient middle cerebral artery occlusion) but not traumatic central nervous system injury; absence of Mincle also did not significantly alter the extent of tissue damage or functional outcome in peripheral models of ischemic tissue injury. In the stroke model mice lacking Mincle displayed significantly improved functional outcome from focal cerebral ischemia. The functional improvements in Mincle KO animals were accompanied by reduced infiltration of neutrophils and lower levels of proinflammatory cytokines in recruited peripheral blood cells. Bone marrow chimera experiments revealed that presence of Mincle in the central nervous system, but not peripheral immune cells, was the critical regulator of a poor outcome following transient focal cerebral ischemia, however we exclude a direct role for Mincle in microglia or neural activation. We demonstrate that Mincle lacks widespread expression in the brain, but is specifically associated with macrophages resident in the perivascular niche. These findings implicate Mincle in the initiation, extent and severity of local responses to ischemic injury in the brain, but not peripheral tissues. Mincle signalling therefore offers a novel therapeutic target in the quest to limit damage after stroke.Sources of support:Australian National Health & Medical Research Council [1057846, 1060538 and Fellowship to NAR], SpinalCure Australia (Career Development Fellowship to MJR), the Australian Research Council, the State Government of Victoria, the Australian Government and The University of Queensland.
Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels
Authors: McDowell Ian C. , Pai Athma A. , Guo Cong , Vockley Christopher M. , Brown Christopher D. , Reddy Timothy E. , Engelhardt Barbara E. 
Published: March 2016

AbstractLong intergenic non-coding RNAs (lincRNA) are members of a class of non-protein-coding RNA transcript that has recently been shown to contribute to gene regulatory processes and disease etiology. It has been hypothesized that lincRNAs influence disease risk through the regulation of mRNA transcription [88], possibly by interacting with regulatory proteins such as chromatin-modifying complexes [37, 50]. The hypothesis of the regulation of mRNA by lincRNAs is based on a small number of specific lincRNAs analyses; the cellular roles of lincRNAs regulation have not been catalogued genome-wide. Relative to mRNAs, lincRNAs tend to be expressed at lower levels and in more tissue-specific patterns, making genome-wide studies of their regulatory capabilities difficult [15]. Here we develop a method for Mendelian randomization leveraging expression quantitative trait loci (eQTLs) that regulate the expression levels of lincRNAs (linc-eQTLs) to perform such a study across four primary tissues. We find that linc-eQTLs are largely similar to protein-coding eQTLs (pc-eQTLs) in cis-regulatory element enrichment, which supports the hypothesis that lincRNAs are regulated by the same transcriptional machinery as protein-coding RNAs [15, 80] and validates our linc-eQTLs. We catalog 74 lincRNAs with linc-eQTLs that are in linkage disequilibrium with TASs and are in protein-coding gene deserts; the putative lincRNA-regulated traits are highly enriched for adipose-related traits relative to mRNA-regulated traits.
UnderstandingWolbachiaacquisition and co-divergence of hosts and their associated bacteria:Wolbachiainfection in theChorthippus parallelushybrid zone
Authors: Martinez-Rodriguez Paloma , Arroyo-Yebras Francisca , Bella Jose Luis 
Published: March 2016

AbstractWolbachiais one of the best known bacterial endosymbionts affecting insects and nematodes. It is estimated that it infects 40% of insect species, so epidemiologically it may be considered a pandemic species. However, the mechanisms by which it is acquired from other species (horizontal transmission) or by which it coevolves with its hosts as a result of vertical transmission across generations are not known in detail. In fact, there are few systems in which the codivergence between host and bacterium has been described.This study goes in deep in theWolbachiainfection in the grasshopperChorthippus parallelus. This well-known system allows us to investigate the mechanism of acquisition of variousWolbachiastrains in a new host, and the bacterial genomic changes during bacterial-host codivergence: We describe the genetic diversity ofWolbachiastrains infecting both subspecies ofC. parallelusand analyse their phylogenetic relationship. We also show the emergence of new bacterial alleles resulting from recombination events inWolbachiainfecting hybrid hosts. Our data suggest that F strains detected in this grasshopper have co-diverged with its host,versusa more recent horizontal transmission of B strains. According with this, we discuss the potential role ofWolbachiain the dynamics of the grasshopper hybrid zone and in the divergence of the two grasshopper subspecies since the origin of their hybrid zone.
A comparative analysis of host feeding and life‐history traits in parasitoid wasps
Authors: Fischbein Deborah , Jofré Nélida , Corley Juan C. 
Published: March 2016

AbstractFeeding in insect parasitoids can have significant implications from behavioral and evolutionary ecology standpoints. Females of many species not only search for hosts to lay their eggs on, but also may use them as a food source. Host‐feeding, as this behavior is known, occurs mostly in the Hymenoptera. There is some evidence of benefits of host feeding at the intraspecific level, but there are only few studies of the potential association between host feeding behavior and life‐history traits across hymenopteran parasitoids. The main goal of this paper is to test for correlated evolution of host feeding and various other life‐history traits, aiming for an understanding of the diversity of parasitoid life histories. For this, we performed a comparative analysis based mainly on phylogenetically independent contrasts (PIC), using data for 187 species of hymenopteran parasitoids, and (1) examined whether host‐feeding behavior is correlated with life span, lifetime potential fecundity, and maximum egg load, (2) re‐tested the potential evolutionary correlation suggested by Jervis et al. [Journal of Animal Ecology 70 (2001) 442] between host feeding and the ovigeny index (OI), and (3) re‐tested the possible correlation between lifetime potential fecundity and life span across species and examined whether host feeding affects this relationship. Results indicate a positive evolutionary correlation between host feeding and both life span and maximum egg load, and a negative evolutionary correlation between host feeding and OI. Lifetime potential fecundity does not correlate with host feeding but correlates positively with life span. The effect of the interaction between host feeding and life span on potential fecundity was not significant. As has been noted in the past, the array of correlations between traits suggests the existence of adaptive suites of life‐history traits involving trade‐offs based on resource allocation patterns.