bluuebunny/crossref_metadata_2025_split huggingface dataset:
Not such silly sausages: Northern quolls exhibit aversion to toads after training with toad sausages
Authors: Indigo Naomi , Smith James , Webb Jonathan K. , Phillips Ben 
Published: August 2017

AbstractThe invasion of toxic cane toads (Rhinella marina) is a major threat to northern quolls (Dasyurus hallucatus) which are poisoned when they attack this novel prey item. Quolls are now endangered as a consequence of the toad invasion. Conditioned taste aversion can be used to train individual quolls to avoid toads, but we currently lack a training technique that can be used at a landscape scale to buffer entire populations from toad impact. Broad scale deployment requires a bait that can be used for training, but there is no guarantee that such a bait will ultimately elicit aversion to toads. Here we test a manufactured bait—a ‘toad sausage’—for its ability to elicit aversion to toads in northern quolls. To do this, we exposed one group of quolls to a toad sausage and another to a control sausage and compared the quolls’ predatory responses when presented with a dead adult toad. Captive quolls that consumed a single toad sausage showed substantially reduced interest in cane toads, interacting with them for less than half the time of their untrained counterparts and showing substantially reduced attack behaviour. We also quantified bait uptake in the field, by both quolls and non-target species. These field trials showed that wild quolls were the most frequent species attracted to the baits, and that approximately 61% of quolls consumed toad-aversion baits when first encountered. Between 40-68% of these animals developed aversion to further bait consumption. Our results suggest that toad-aversion sausages can be used to train wild quolls to avoid cane toads. This opens the possibility for broad-scale quoll training with toad aversion sausages: a technique that may allow wildlife managers to prevent quoll extinctions at a landscape scale.
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
Authors: Rizzetto Simone , Koppstein David NP , Samir Jerome , Singh Mandeep , Reed Joanne H. , Cai Curtis H. , Lloyd Andrew R. , Eltahla Auda A. , Goodnow Christopher C. , Luciani Fabio 
Published: August 2017

AbstractThe B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. Cell-to-cell variability of BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing (scRNA-seq) presents the opportunity for simultaneous capture of the BCR sequence and transcriptomic signature for a detailed understanding of the dynamics of an immune response.We developed VDJPuzzle 2.0, a bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains. VDJPuzzle successfully reconstructs BCRs from 98.3% (n=117) of human and 96.5% (n=200) from murine B cells. 92.0% of clonotypes and 90.3% of mutations were concordant with single-cell Sanger sequencing of the immunoglobulin chains. VDJPuzzle is available athttps://bitbucket.org/kirbyvisp/vdjpuzzle2
Behavioral and Hematological Response ofClarias gariepinusjuvenile exposed to Acute concentrations of Aqueous Extract of Siam Weed (Chloromolaena odorata) leaf as Anesthetic agent
Authors: Chidi Iheanacho Stanley , Shedrack Nworu 
Published: August 2017

AbstractThis experiment was carried out to investigate the effect of Siam Weed (chloromelena odorata) on the heamatology ofClarias gariepinusjuvenile. A total of one hundred and fifty (150) juvenile ofClarias gariepinuswere randomly assigned to different concentrations ofC. odorataleave aqueous extract in a completely randomize design (CRD). The concentrations were 50mg/l, 100mg/l, 150mg/l, 200mg/l. Distilled water (0.00 mg/l) was used as the control. The fish exhibited stressful behavior which was higher as the concentration ofChromolaena odorataleave extract increased. There was a gradual decrease with time until a state of calmness, which was subsequently followed by death. The effect on 96hr exposed period was recorded and blood samples collected at 24hr and 96hr interval. Result on hematological parameters revealed significant difference (P<0.05) among treatments with increase in exposure time for all the blood parameters.C. odorataat increased concentrations affected the behavior and hematology ofC. gariepinus.
Plant genetic effects on microbial hubs impact fitness across field trials
Authors: Brachi Benjamin , Filiault Daniele , Whitehurst Hannah , Darme Paul , Le Gars Pierre , Le Mentec Marine , Morton Timothy C. , Kerdaffrec Envel , Rabanal Fernando , Anastasio Alison , Box Mathew S. , Duncan Susan , Huang Feng , Leff Riley , Novikova Polina , Perisin Matthew , Tsuchimatsu Takashi , Woolley Roderick , Dean Caroline , Nordborg Magnus , Holm Svante , Bergelson Joy 
Published: August 2017

AbstractAlthough complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 A. thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial OTU’s. Host genetics disproportionately influenced hubs within the microbial communities, with their impact then percolating through the community, as evidenced by a decline in the heritability of particular OTUs with their distance to the nearest hub. By simultaneously measuring host performance, we found that host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants grown in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins and the immune system. Using untargeted metabolomics, we corroborate the consistent association of variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host natural variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
Authors: Ryan Corces M. , Trevino Alexandro E. , Hamilton Emily G. , Greenside Peyton G. , Sinnott-Armstrong Nicholas A. , Vesuna Sam , Satpathy Ansuman T. , Rubin Adam J. , Montine Kathleen S. , Wu Beijing , Kathiria Arwa , Cho Seung Woo , Mumbach Maxwell R. , Carter Ava C. , Kasowski Maya , Orloff Lisa A. , Risca Viviana I. , Kundaje Anshul , Khavari Paul A. , Montine Thomas J. , Greenleaf William J. , Chang Howard Y. 
Published: August 2017

ABSTRACTWe present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol enables chromatin accessibility profiling from archival frozen tissue samples and 50 μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.
Type 2 diabetes promotes cell centrosome amplification and the role of AKT-ROS-dependent signalling of ROCK1 and 14-3-3σ
Authors: Wang Pu , Lu Yu Cheng , Wang Jie , Wang Lan , Yu Hanry , Li Yuan Fei , Kong Alice , Chan Juliana , Lee Shao Chin 
Published: August 2017

AbstractType2 diabetes is associated with oxidative stress which can cause cell centrosome amplification. The study investigated centrosome amplification in type 2 diabetes and the underlying mechanisms. We found that centrosome amplification was increased in the peripheral blood mononuclear cells (PBMC) from the type 2 diabetic patients, which correlated with the levels of fasting blood glucose and HbA1c. High glucose, insulin and palmitic acid, alone or in combinations, induced ROS production and centrosome amplification. Together, they increased AKT activation as well as the expression, binding and centrosome translation of ROCK1 and 14-3-3σ. Results from further analyses showed that AKT-ROS-dependent upregulations of expression, binding and centrosome translocation of ROCK1 and 14-3-3σ was the molecular pathway underlying the centrosome amplification induced by high glucose, insulin and palmitic acid. Moreover, the increases in AKT activation and ROS production as well as expression, binding and centrosome distribution of ROCK1 and 14-3-3σ were confirmed in the PBMC from the patients with type 2 diabetes. In conclusion, our results show that type 2 diabetes promotes cell centrosome amplification, and suggest that the diabetic pathophysiological factors-activated AKT-ROS-dependent signalling of ROCK1 and 14-3-3σ is the underlying molecular mechanism.
Identifying genetic determinants of complex phenotypes from whole genome sequence data
Authors: Long George S. , Hussen Mohammed , Dench Jonathan , Aris-Brosou Stéphane 
Published: August 2017

AbstractA critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to identify, the underpinnings of complex phenotypes are harder to predict. While traditional approaches rely on genome-wide association studies based on Single Nucleotide Polymorphism data, the ability of machine learning algorithms to find these determinants in whole proteome data is still not well known. To better understand the applicability of machine learning in this case, we implemented two such algorithms, adaptive boosting (AB) and repeated random forest (RRF), and developed a chunking layer that facilitates the analysis of whole proteome data. We first assessed the performance of these algorithms and tuned them on an influenza data set, for which the determinants of three complex phenotypes (in-fectivity, transmissibility, and pathogenicity) are known based on experimental evidence. This allowed us to show that chunking improves runtimes by an order of magnitude. Based on simulations, we showed that chunking also increases sensitivity of the predictions, reaching 100% with as few as 20 sequences in a small proteome as in the influenza case (5k sites), but may require at least 30 sequences to reach 90% on larger alignments (500k sites). While RRF has less specificity than RF, it was never < 50%, and RRF sensitivity was significantly higher at smaller chunk sizes. We then used these algorithms to predict the determinants of three types of drug resistance (to Ciprofloxacin, Ceftazidime, and Gentamicin) in a bacterium,Pseudomonas aeruginosa. While both algorithms performed well in the case of the influenza data, results were more nuanced in the bacterial case, with RRF making more sensible predictions, with smaller errors rates, than AB. Altogether, we demonstrated that ML algorithms can be used to identify genetic determinants in small proteomes (viruses), even when trained on small numbers of individuals. We further showed that our RRF algorithm may deserve more scrutiny, which should be facilitated by the decreasing costs of both sequencing and phenotyping of large cohorts of individuals.
On the Structure and Mechanism of Two-Pore Channels
Authors: Kintzer Alexander F. , Stroud Robert M. 
Published: August 2017

AbstractIn eukaryotes, two-pore channels (TPC1-3) comprise a family of ion channels that regulate the conductance of Na+and Ca2+ions across cellular membranes. TPC1-3 form endolysosomal channels, but TPC3 can also function in the plasma membrane. TPC1/3 are voltage-gated channels, but TPC2 opens in response to binding endolysosome-specific lipid phosphatidylinositol-3,5-diphosphate (PI(3,5)P2). Filoviruses, such as Ebola, exploit TPC-mediated ion release as a means of escape from the endolysosome during infection. Antagonists that block TPC1/2 channel conductance abrogate filoviral infections. TPC1/2 form complexes with the mechanistic target of rapamycin complex 1 (mTORC1) at the endolysosomal surface that couple cellular metabolic state and cytosolic nutrient concentrations to the control of membrane potential and pH. We determined the X-ray structure of TPC1 fromArabidopsis thaliana(AtTPC1) to 2.87Å resolution–one of the two first reports of a TPC channel structure. Here we summarize these findings and the implications that the structure may have for understanding endolysosomal control mechanisms and their role in human health.AbbreviationsmTORC1Mechanistic target of rapamycin complex 1TPCTwo-pore channelPI(3,5)P2Phosphatidylinositol-3,5-diphosphateAtTPC1Arabidopsis thalianaTPC1NED19Trans-Ned-19VSDVoltage-sensing domainP1Pore domain in S5-S6P2Pore domain in S11-S12CavVoltage-gated calcium channelNavVoltage-gated sodium channelKvVoltage-gated potassium channelNTDN-terminal domainCTDC-terminal domainEFEF-hand domainNAADPNicotinic acid adenine dinucleotide phosphatePI(4,5)P2Phosphatidylinositol-4,5-diphosphateDHPDihydropyridinePAAPhenylalkylamineBTZBenzothiazepineCaa2+Activating Ca2+-ionCai2+Inhibitory Ca2+-ionfou2Fatty acid oxygenation up-regulated 2SLC38a9Sodium-coupled neutral amino acid transporter 9NPC1Niemann-Pick C1PKAProtein kinase APKCProtein kinase CPKGProtein kinase GH+ATPase - Proton Pump32P– Phosphorus-32
Tetrahydrocannabinolic acid is a potent PPARγ agonist with neuroprotective activity
Authors: Nadal Xavier , del Río Carmen , Casano Salvatore , Palomares Belén , Ferreiro‐Vera Carlos , Navarrete Carmen , Sánchez‐Carnerero Carolina , Cantarero Irene , Bellido Maria Luz , Meyer Stefan , Morello Gaetano , Appendino Giovanni , Muñoz Eduardo 
Published: August 2017

Background and PurposePhytocannabinoids are produced in Cannabis sativa L. in acidic form and are decarboxylated upon heating, processing and storage. While the biological effects of decarboxylated cannabinoids such as Δ9‐tetrahydrocannabinol have been extensively investigated, the bioactivity of Δ9‐tetahydrocannabinol acid (Δ9‐THCA) is largely unknown, despite its occurrence in different Cannabis preparations. Here we have assessed possible neuroprotective actions of Δ9‐THCA through modulation of PPARγ pathways.Experimental ApproachThe effects of six phytocannabinoids on PPARγ binding and transcriptional activity were investigated. The effect of Δ9‐THCA on mitochondrial biogenesis and PPARγ coactivator 1‐α expression was investigated in Neuro‐2a (N2a) cells. The neuroprotective effect was analysed in STHdhQ111/Q111 cells expressing a mutated form of the huntingtin protein and in N2a cells infected with an adenovirus carrying human huntingtin containing 94 polyQ repeats (mHtt‐q94). The in vivo neuroprotective activity of Δ9‐THCA was investigated in mice intoxicated with the mitochondrial toxin 3‐nitropropionic acid (3‐NPA).Key ResultsCannabinoid acids bind and activate PPARγ with higher potency than their decarboxylated products. Δ9‐THCA increased mitochondrial mass in neuroblastoma N2a cells and prevented cytotoxicity induced by serum deprivation in STHdhQ111/Q111 cells and by mutHtt‐q94 in N2a cells. Δ9‐THCA, through a PPARγ‐dependent pathway, was neuroprotective in mice treated with 3‐NPA, improving motor deficits and preventing striatal degeneration. In addition, Δ9‐THCA attenuated microgliosis, astrogliosis and up‐regulation of proinflammatory markers induced by 3‐NPA.Conclusions and ImplicationsΔ9‐THCA shows potent neuroprotective activity, which is worth considering for the treatment of Huntington's disease and possibly other neurodegenerative and neuroinflammatory diseases.
Variation in chick‐a‐dee calls of bridled titmice (Baeolophus wollweberi): Frequent use of non‐combinatorial calls in a combinatorial calling system
Authors: Jung Hwayoung , Freeberg Todd M. 
Published: August 2017

AbstractChick‐a‐dee calls of Poecile (chickadee) and Baeolophus (titmouse) species are complex in terms of the structural composition of note types and the diversity of messages. Studies so far have mainly focused on the calls of various chickadee and just one titmouse species—the tufted titmouse (B. bicolor). To begin to address this lack of titmouse data, our study investigated variation in note composition of calls of bridled titmice (B. wollweberi). We obtained calls from 26 flocks in the Chiricahua Mountains of Arizona in the overwintering flocking period. Bridled titmice produce proportionally more non‐combinatorial call variants than combinatorial call variants. The number of the single noted calls furthermore exceeded the number of multinote calls. In general, structural variation in the combinatorial calls appears to be comparable to calls of better‐studied chickadees and of tufted titmice, although bridled titmice appear to have a unique call length distribution. We also analyzed some behavioral associations with call variation and found that flight behavior and close interactions between individuals were associated with use of specific note types. Finally, we found microgeographic variation in note type use in these calls. We discuss some possible explanations for call complexity in this species.
Remote sensing as a tool to assess botanical composition, structure, quantity and quality of temperate grasslands
Authors: Wachendorf M. , Fricke T. , Möckel T. 
Published: August 2017

AbstractGrassland systems frequently exhibit small‐scale botanical and structural heterogeneity with pronounced spatio‐temporal dynamics. These features present particular challenges for sensor applications, in addition to limitations posed by the high cost and low spatial resolution of many available remote‐sensing (RS) systems. There has been little commercial application ofRSfor practical grassland farming. This article considers the developments in sensor performance, data analysis and modelling over recent decades, identifies significant advances inRSfor grassland research and practice and reviews the most important sensor types and corresponding findings in research. Beside improvements of single sensor types, the development of systems with complementary sensors is seen as a very promising research area, and one that will help to overcome the limitations of single sensors and provide better information about grassland composition, yield and quality. From an agronomic point of view, thematic maps of farm fields are suggested as the central outcome ofRSand data analysis. These maps could represent the relevant grassland features and constitute the basis for various farm management decisions at strategic, tactical and operational levels. The overarching goal will be to generate low cost, appropriate and timely information that can be provided to farmers to support their decision‐making.
Diagnostic accuracy of instantaneous wave free‐ratio in clinical practice
Authors: Ding Wern Yew , Nair Satheesh , Appleby Clare 
Published: August 2017

AimsTo evaluate the correlation between iFR and FFR in real‐world clinical practice.Methods and ResultsRetrospective, single‐centre study of 229 consecutive pressure‐wire studies (np = 158). Real‐time iFR and FFR measurements were performed for angiographically borderline stenoses. Functionally significant stenoses were defined as iFR <0.86 or FFR ≤0.80. An iFR between 0.86 and 0.93 was considered within the grey zone (Hybrid approach). Median iFR and FFR (IQR) were 0.92 (0.87‐0.95) and 0.83 (0.76‐0.89), respectively. Pearson's correlation coefficient was 0.75 (P < 0.001). Bland‐Altman plot showed a mean difference between iFR and FFR that remained consistent throughout the range of values. The optimal iFR cutoff was 0.91—sensitivity 80%, specificity 82% with ROC area under curve of 89%. Using the Hybrid iFR‐FFR strategy, we demonstrated high accuracy of iFR results—sensitivity 95%, specificity 96%, PPV 95%, and NPV 96%. In addition, this method would have avoided adenosine in 56% of patients. Mean follow‐up period was 17.2 (±3.4) months. All‐cause mortality was 3.2% (np = 5) and repeat intervention was required in six lesions (2.6%).ConclusionsThis study demonstrates that iFR is a valuable adjunct to FFR using the Hybrid iFR‐FFR strategy in a real‐world population. The use of adenosine may be avoided in about half the cases.
THE EFFECT OF EXTERNAL SUCTION AT THE DUST OUTLET OF A CYCLONE
Authors: Dewika M. , Rashid M. , Hasyimah N. 
Published: August 2017

Cyclone is one of the most commonly used particulate dust collectors in industries. It employs centrifugal force generated by a spinning gas stream to separate the particulate matter from the carrier gas. However, cyclone is efficient to collect coarse rather than fine particulate size fraction. In this regard, a study was carried out to determine the effect of creating more negative pressure at the storage hopper of a 100 mm diameter laboratory scale cyclone. The negative pressure was created by drawing out a small portion of the gas stream by means of an air pump attached to the storage hopper. Results showed that there was exponentially related between the pressure drop (ΔP) and the amount of gas stream drawn at the storage hopper, but with an increment of 2.6% with suction compared to without. Interestingly, it was observed that more of the fine particulate matter was drawn from the gas stream as the suction flow rate increases. This is due to the suction velocity which exceeds the terminal falling velocities of the fine particles size range. There was a reduction by weight in the fine particle emitted from the cyclone ranging between 14% to 52% by introduction of the suction. The finding serves as a basis for future work in reducing fine particulates from a cyclone separator.
Motion Video-Based Quantitative Analysis of the ‘lifting-Thrusting— Method: A Comparison between Teachers and Students of Acupuncture
Authors: Tang Wen-Chao , Yang Hua-Yuan , Liu Tang-Yi , Gao Ming , Xu Gang 
Published: August 2017

Objective To compare objective measures of needle manipulation between students and teachers of acupuncture using motion video analysis technology, to help support instructional acupuncture education. Methods A total of 30 teachers and 60 students participated in this study. Acupuncture needles were inserted at LI11 and motion videos were recorded for three subtypes of ‘lifting-thrusting’ manipulation: (1) ‘mild reinforcing-attenuating’; (2) ‘reinforcing’; and (3) ‘attenuating’. The videos were analysed using Simi Motion 3D software to acquire the movement parameters of four trace marks: ‘thumb tip’; ‘forefinger tip’; ‘forefinger middle joint’; and ‘forefinger base joint’. Differences between the two groups were compared using t-tests, X2 tests and/or rank-sum tests. Results Changes in the near-end interphalangeal joint were positively associated with a range of movement along the X axis. Motion parameters for the thumb tip, the proximal interphalangeal (PIP) joint of the forefinger and the X axis shaft swing near the end of the forefinger in the teacher group were higher than those in the student group. The teacher group featured smaller trough dispersion and smaller crest dispersion during ‘reinforcing’ and ‘attenuating’ manipulations, respectively. Conclusions The ‘lifting-thrusting’ manipulation could be simplified as a fixed-axis rotation using metacarpophalangeal joints in the thumb and forefinger as the shaft centre. Teachers opened at a larger angular variation for the PIP during the lifting and thrusting processes with better spatial control. Temporal control was similar between groups and therefore appears easier to grasp. Repetitive training might be helpful for improving athletic and spatial stability during needle manipulation.