bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategies for data acquisition using ultrasonic phased arrays
Authors: Velichko A. , Croxford A. J.
Published: October 2018

Ultrasonic phased arrays have produced major benefits in a range of fields, from medical imaging to non-destructive evaluation. The maximum information, which can be measured by an array, corresponds to the Full Matrix Capture (FMC) data acquisition technique and contains all possible combinations of transmitter–receiver signals. However, this method is not fast enough for some applications and can result in a very large volume of data. In this paper, the problem of optimal array data acquisition strategy is considered, that is, how to make the minimum number of array measurements without loss of information. The main result is that under the single scattering assumption the FMC dataset has a specific sparse structure, and this property can be used to design an optimal data acquisition method. An analytical relationship between the minimum number of array firings, maximum steering angle and signal-to-noise ratio is derived, and validated experimentally. An important conclusion is that the optimal number of emissions decreases when the angular aperture of the array increases. It is also shown that plane wave imaging data are equivalent to the FMC dataset, but requires up to an order of magnitude fewer array firings.
The evolution of fungal substrate specificity in a widespread group of crustose lichens
Authors: Resl Philipp , Fernández-Mendoza Fernando , Mayrhofer Helmut , Spribille Toby
Published: October 2018

Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150–200 Mya clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, ‘escape’ from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.
Miocene biome turnover drove conservative body size evolution across Australian vertebrates
Authors: Brennan Ian G. , Keogh J. Scott
Published: October 2018

On deep time scales, changing climatic trends can have a predictable influence on macroevolution. From evidence of mass extinctions, we know that rapid climatic oscillations can indirectly open niche space and precipitate adaptive radiation, changing the course of ecological diversification. These dramatic shifts in the global climate, however, are rare events relative to extended periods of protracted climate change and biome turnover. It remains unclear whether during gradually changing periods, shifting habitats may instead promote non-adaptive speciation by facilitating allopatry and phenotypic conservatism. Using fossil-calibrated, species-level phylogenies for five Australian radiations comprising more than 800 species, we investigated temporal trends in biogeography and body size evolution. Here, we demonstrate that gradual Miocene cooling and aridification correlates with the restricted phenotypic diversification of multiple ecologically diverse vertebrate groups. This probably occurred as species ranges became fractured and isolated during continental biome restructuring, encouraging a shift towards conservatism in body size evolution. Our results provide further evidence that abiotic changes, not only biotic interactions, may act as selective forces influencing phenotypic macroevolution.
A global synthesis of the small-island effect in habitat islands
Authors: Wang Yanping , Chen Chuanwu , Millien Virginie
Published: October 2018

Habitat loss and fragmentation are considered to be the leading drivers of biodiversity loss. The small-island effect (SIE) can be used to predict species extinctions resulting from habitat loss and has important implications for species conservation. However, to date, no study has explicitly evaluated the prevalence of SIEs in habitat islands. Here, we compiled 90 global datasets to systematically investigate the prevalence and underlying factors determining the ubiquity of SIEs in habitat island systems. Among the 90 datasets, SIEs were unambiguously detected in 36 cases. We found significant effects of habitat island types and taxon groups on the threshold area of SIEs. The number of islands, area range, species range, island type and taxon group were key variables that determined the prevalence of SIEs. Our study demonstrates that SIEs occur in 40% of cases and thus are common in habitat islands. We conclude that conservation biologists and applied ecologists should consider the prevalence of SIEs when making management strategies in fragmented landscapes.
Quality characteristics and kimchi processing ability of kimchi cabbage cultivars ‘Cheonjincheongmayeop’ and ‘Chunkwang’
Authors: Park Sang-Un , Chung Young Bae , Park Su-Hyung , Park Hae Woong , Han Eung Soo
Published: October 2018

The quality characteistics and kimchi processing ability of the kimchi cabbage cultivar ‘Cheonjincheongmayup’ (CC) were analyzed and compared with those of the ‘Chunkwang’ (CK) cultivar. The head weight of CC was lower than that of CK, and the head length of CC was larger than that of CK. CC had narrower and longer mid ribs than CK. Furthermore, the head formation index of CC was lower than that of CK. The firmness and soluble solid content were higher in CC than in CK. The salinity of Cheonjincheongmayup kimchi (CCK) was 2.89-3.02%, which was higher than 1.94-2.10% salinity measured in Chunkwang kimchi (CKK). The initial titratable acidity in CCK was higher than that of CKK, but increasd more slowly during storage. CCK was firmer than CKK; lactic acid bacteria in CCK was lower than in CKK initially, but increased more in CKK than in CCK after six weeks of storage. We found that CC was suitable for making Makkimchi because of its long and narrow mid ribs, saltiness, and slow fermentation. CC should be improved as less hot spicy and less hard texture to use a Makkimchi material.
Physicochemical properties and isoflavone content of Chaga Cheonggukjang with Lactobacillus acidophilus KCTC 3925 starter
Authors: Na Ha Gyoon , Jang Eun Ho , Nam Dong Hun , Kim Min-Ah , Kim Mi-Ja , Sohn Eun Hwa , Kim Hyun Dong , Jang Ki-Hyo
Published: October 2018

This study was conducted to investigate the quality characteristics and changes in isoflavone content of Cheonggukjang with added Chaga mushroom by secondary fermentation at 40℃ for 48 h with or without a starter, Lactobacillus acidophilus KCTC 3925. Cheonggukjang samples were divided into three groups: Control (unsterilized Cheonggukjang fermented without a starter), NS (unsterilized Cheonggukjang inoculated with L. acidophilus KCTC 3925), and YS (heat-sterilized Cheonggukjang inoculated with L. acidophilus KCTC 3925). The approximate composition of the three types of Cheonggukjang was 49.79-51.44% moisture, 4.54-4.72% crude ash, 43.21-44.37% crude protein, 11.58-13.65% crude fat, 37.41-40.07% carbohydrate, 31.92-33.82% dietary fiber. The mineral content included 5.43–9.64 mg% Na, 1,792.86–1,824.39 mg% K, 253.69–326.09 mg% Ca, 619.37–691.20 mg% P, 92.59–110.59 mg% Fe, and 0.01–0.02 mg% Cd. Free amino acid contents of NS (2,520.92 mg%) and YS (2,421.94 mg%) were significantly higher than that of the control (2,236.76 mg%). Amino-type nitrogen content for the three types of Cheonggukjang ranged from 837.20-920.27 mg% with no significant difference. Ammonia-type nitrogen content ranged from 137.09-169.36 mg%. Supplement of Cheonggukjang with L. acidophilus KCTC 3925 increased production of aglycone isoflavons compared to that of control. Therefore, our results show that fermenting Chaga Cheonggukjang with L. acidophilus KCTC 3925 leads to improved quality characteristics and increased isoflavone aglycone content.
Preparation of isomaltooligosaccharides using puffed rice flour and evaluation of physicochemical properties
Authors: Lee Eun Byeol , Kim Ha-Yun , Han Gui Jeong , Park Bo-Ram
Published: October 2018

Isomaltooligosaccharides were prepared from puffed rice flour by a One-step processing method under different conditions, and their physicochemical properties were evaluated. Sample was prepared by allowing puffed rice flour to pass through a 50 mesh standard sieve and segregated into experimental groups (PR15-60, PR20-60, PR15-65, and PR20-65) according to the substrate concentrations (15%, 20% w/v) and reaction temperatures (60℃, 65℃). Enzyme reaction of puffed rice flour and water mixture was performed for 0, 1, 6, 24, and 48 h using commercial enzymes (Maltogenic amylase, Promozyme D2 and Transglucosidase; amount: 0.5% (w/v) to obtain the corresponding isomaltooligosaccharides. The reducing sugar content, dextrose equivalent, and total soluble solids of the reactants increased with increasing reaction time. The carbohydrate composition and amount of isomaltooligosaccharides with degree of polymerization (DP) 2 to DP 7 in the rice flour were examined by HPLC with an evaporative light scattering detector. Because of the high carbohydrate composition, the PR20-65 group showed the highest isomaltooligosaccharide content after 6 h of reation (138.47 mg/mL). After 24 h of reaction, the amount of isomaltooligosaccharides (DP2-DP7) and the isomaltooligosaccharides/total carbohydrate ratio in this group were 135.00 mg/mL and 68.04%, respectively.
Analysis of the microbial contamination levels in dried red pepper during production
Authors: Hung Nguyen Bao , Yun Bohyun , Kim Won-Il , Jung Gyusuck , Lee Theresa , Roh Eunjung , Kim Hyun Ju , Lee Seungdon , Kim Se-Ri
Published: October 2018

The purpose of this study was to investigate the main source of contamination of dried red pepper by assessing microbial loads on red peppers, washing water, washing machines, harvesting containers, and worker gloves that had come in contact with the dried red pepper. To estimate microbial loads, indicator bacteria (total bacteria, coliform bacteria and Escherichia coli) and pathogenic bacteria (E. coli O157:H7, Salmonella spp., Listeria monocytogenes, and Clostridium perfringens) were enumerated. The results showed that the numbers of indicator bacteria increased significantly after washing red peppers compared with that before washing (p<0.05). Moreover, E. coli and Listeria spp. were recovered from the red peppers after washing and from the ground water used in the washing process. The number of indicator bacteria on red peppers dried in the green house was lower than that on red peppers dried in a dry oven (p<0.05). However, E. coli O157:H7, Salmonella spp., L. monocytogenes, and C. perfringens were not detected. These results suggested that a disinfection technique may be needed during the washing step in order to prevent potential contamination. In addition, hygienic practices during the drying step using the dry oven, such as establishment of an optimal temperature, should be developed to enhance the safety of dried red pepper.
Quercetin quantification in a Jeju Dendropanax morbifera Lev. extract by varying different parts, harvest times, and extraction solvents
Authors: Lee Ki Hoon , Na Hye Jin , Song Chang Khil , Kang So Young , Kim Sunoh
Published: October 2018

Dendropanax morbifera Leveille (Araliaceae) is an endemic species growing in the south-western part of South Korea that has been used in folk medicine and health functional food. In this study, we investigated an extract of quercetin in Jeju D. morbifera by varying different parts (fruit, sprouts, leaves, sprigs, and branches), harvest times, and extraction solvents. In addition, we aimed to establish a simple and reliable HPLC/UV analytical method to determination of quercetin for the quality control and base line data of the Jeju D. morbifera extract as a health functional food ingredient. The analytical specificity was determined with retention time and photo diode array (PDA) spectrum by analyzing quercetin using HPLC and comparing the results to those of extracts. This analytical method for quercetin was validated for its limit of detection (LOD), limit of quantitation (LOQ), precision, and accuracy. A high linearity in the standard calibration curve was obtained, with a coefficient of determination (R2) of 0.9996. Also, the LOD and LOQ values were found to be 0.28 μg/mL and 0.85 μg/mL, respectively, and the recoveries of quantified compounds ranged from 97.91% to 104.10%. Furthermore, the relative standard deviation (RSD) values of data from the intra- and inter-day precision analyses were less than 1.36% and 3.65%, respectively. As a result, the highest quercetin content among the extracts of Jeju D. morbifera leaves was found to be 20.14 mg/g, which was extracted at harvest in May (cultivation period 10 years) with 60% EtOH. All in all, we believe that the results obtained would be helpful in the development of nutraceutics and natural medicines and for the quality control of D. morbifera.
In vitro antioxidant activity and oxidative stability in bulk oil of coriander seeds ethanol extract
Authors: Kim Min-Ah , Han Chang Hee , Kim Mi-Ja
Published: October 2018

The aim of the study was to confirm whether the coriander seeds ethanol extract (CSEE) exhibited effective antioxidant activity and oxidative stability in corn oil. The results showed that the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) cation radical scavenging activity were 24.4, 55.0, and 81.0, and 8.9, 16.8, and 34.3% at the concentrations of 0.25, 0.5, and 1.0 mg/mL, respectively. The ferric reducing antioxidant power (FRAP) reduction power was 284.1 μM ascorbic acid equivalent/g extract, and the total phenol content (TPC) was 31.9 μM tannic acid equivalent/g extract. Furthermore, the TPC showed positive correlations with the DPPH radical scavenging activity, ABTS cation radical scavenging, and FRAP value (p<0.01). oxygen radical absorbance by fluorescein (ORAC) analysis showed that the antioxidant activities of trolox 50 μM and CSEE 100 μg/mL were 3.1 and 4.4 times higher than those of blank AUC, respectively. In addition, CSEE reduced the amounts of conjugated diene and ρ-anisidine by 8.3 and 40.8%, respectively, in the oxidized corn oil. Thus, the coriander seeds ethanol extract is confirmed to have effective antioxidant activity and oxidative stability in corn oil, and it can be used as a natural antioxidant for preservation in food processing.
Comparison of the antioxidant effects and physiological activities of grape fruit stem extracts derived with different drying methods
Authors: Youn Kwang-Sup
Published: October 2018

This study was conducted to examine the utilization potential of grape stems as nutritional supplements, and the physiological functionalities of 70% ethanol extracts from grape fruit stem (GFS) were investigated. Each experimental group was prepared with different methods and included GFSF (GFS prepared with freeze drying), GFSI (GFS prepared with infrared drying), GFSH (GFS prepared with heat air drying), and GFSS (GFS prepared with sun drying). The respective yields of freeze-dried powders for the GFSF, GFSI, GFSH, and GFSS were 59.27%, 57.13%, 58.57%, and 58.87%, respectively. Total polyphenol contents in the GFSF were significantly greater than those in the other extracts, whereas total flavonoid contents in the GFSI were higher than those in the other extracts. The contents of proanthocyanidin-related substances were ranked in the order of GFSF > GFSI > GFSH > GFSS. The thin layer chromatograph (TLC) analysis of catechin showed that the GFSF, GFSI, GFSH, and GFSS were detected in the same band. The electron donating ability with 500 µg/mL (w/v) solutions of GFSF, GFSI, GFSH, and GFSS amounted to 93.14%, 93.07%, 92.64%, and 86.95%, respectively, and the reducing powers (OD 700) were 1.933, 1.765, 1.455, and 1.200 absorbance units, respectively. Additionally, the ABTS radical scavenging ability showed the same tendency that was observed with the electron donating ability and reducing power. The angiotensin-converting enzyme (ACE) inhibitory activity and tyrosinase inhibitory activity with 500 µg/mL (w/v) solutions of GFSF and GFSI were higher than those of GFSH and GFSS. In conclusion, the infrared drying technique is the superior method for the enhancement of biological activity for by-product utilization.
국내에서 재배된 세계 주요 와인 포도 품종으로 제조된 적포도주 11종의 향기 성분 특성
Authors: Kim Hyun Il , Hur Youn Young , Jung Sung Min , Im Dong Jun , Chung Kyeong Ho , Kim Su Jin
Published: October 2018

The aroma compounds of 11 red wines grown and produced in Wanju region were characterized by headspace-solid phase microextraction combined with gas chromatography-mass spectrometry. Seventy-five aroma compounds were identified in the 11 red wines. The aroma compounds were grouped into five aroma series and their odor activity values were calculated to determine the aroma impact compounds in 11 wines. Alcohols, esters and C6compounds were the main contributors to the aroma in the 11 wines. Isoamyl alcohol and phenylethyl alcohol obtained from the 11 red wines contributed to the floral, sweet, and fatty odorants in the wine. Octanoic acid ethyl ester, and hexanoic acid ethyl ester contributed to the fruity, floral, and sweet odorants of all the red wines. 1-Hexanol was detected all the wines, which contributed to the green odorant. The major aroma contribution of Chanceller, Malbec, Marchel, Narsha, Pinot Meunier, and Sangiovetto wines were the fruity series. The green series was the major contribution of the Cabernet Franc, Cabernet Sauvignon, and Sauvignon Vert wines. The floral series was the major contribution of the MBA and Narsha wines. Based on the results of these studies, aroma component analysis could be used as a selection criterion for developing wine cultivars.
Antioxidant and anti-inflammatory activities of Opuntia ficus-indica and Opuntia humifusa fruits ethanol extracts
Authors: Kim Dong-Gyu , Shin Jung-Hye , Kang Min-Jung
Published: October 2018

Opuntia species have been used for centuries as food resources and in traditional folk medicine for their nutritional properties and their benefit in chronic diseases, particularly diabetes, obesity, cardiovascular diseases, and cancer. The aim of this study was to evaluate the antioxidant activities and anti-inflammatory effects of 75% ethanol extracts from Opuntia ficus-indica fruits (OFFE) and Opuntia humifusa fruits (OHFE). The total polyphenol and total flavonoid contents of OFFE were 17.07±0.08 and 8.65±0.08 mgQE/g, respectively, whereas those of OHFE were 9.41±0.14 and 2.03±0.08 mgQE/g, respectively. The antioxidant activities of OFFE and OHFE were determined based on various radical scavenging activities using 1,1-diphenyl-2-dipicrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging assays. The DPPH and ABTS radical scavenging activities of OFFE were significantly higher than those of OHFE. In addition, the release of nitric oxide (NO) and reactive oxygen species (ROS) were ameliorated by pretreatment with OFFE and OHFE in a dose-dependent manner. OFFE also suppressed the secretion of pro-inflammatory cytokines, including interleukin-1β (IL-1β) and interleukin-6(IL-6) but not tumor necrosis factor-α (TNF-α) from lipopolysaccharide (LPS)-stimulated RAW 264.7 cells, but the OHFE did not decrease cytokine expression. These results suggest that OFFE exhibits strong antioxidant activity and anti-inflammatory effects and can be developed as a potential therapeutic candidate for diseases involving oxidative stress and inflammation.
Evolutionarily conserved anatomical and physiological properties of olfactory pathway till fourth order neurons in a species of grasshopper(Hieroglyphus banian)
Authors: Singh Shilpi , Joseph Joby
Published: October 2018

Olfactory systems of different species show variations in structure and physiology despite some conserved characteristics. We characterized the olfactory circuit of the grasshopperHieroglyphus banianof family Acrididae (subfamily: Hemiacridinae) and compared it to a well-studied species of locust,Schistocerca americana(subfamily: Cyrtacanthacridinae), also belonging to family Acrididae. We used in vivo electrophysiological, immunohistochemical and anatomical (bulk tract tracing) methods to elucidate the olfactory pathway from the second order neurons in antennal lobe to the fourth order neurons in β-lobe ofH. banian.

We observe highly conserved anatomical and physiological characteristics till the fourth order neurons in the olfactory circuit ofH. banianandS. americana, though they are evolutionarily divergent (~57 million years ago). However, we found one major difference between the two species-there are four antennal lobe tracts inH. banianwhile only one is reported inS. americana. Besides, we are reporting for the first time, a new class of bilateral neurons which respond weakly to olfactory stimuli even though they innervate densely downstream of Kenyon cells.
The first draft genomes of the antFormica exsecta, and itsWolbachiaendosymbiont reveal extensive gene transfer from endosymbiont to host
Authors: Dhaygude Kishor , Nair Abhilash , Johansson Helena , Wurm Yannick , Sundström Liselotte
Published: October 2018

The wood antFormica exsecta(Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well established model for studies of ecological characteristics and evolutionary conflict. In this study, we sequenced and assembled draft genomes forFormica exsectaand its endosymbiontWolbachia. The draftF. exsectagenome is 277.7 Mb long; we identify 13,767 protein coding genes for which we provide gene ontology, and protein domain annotations. This is also the first report of aWolbachiagenome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) fromWolbachiatoF. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes. We expect that theF. exsectagenome will be valuable resource in further exploration of the molecular basis of the evolution of social organization.
Excitatory-inhibitory windows shape coherent neuronal dynamics driven by optogenetic stimulation in the primate brain
Authors: Shewcraft Ryan A. , Dean Heather L. , Fabiszak Margaret M. , Hagan Maureen A. , Wong Yan T. , Pesaran Bijan
Published: October 2018

Coherent neuronal dynamics play an important role in complex cognitive functions. Optogenetic stimulation promises to provide new ways to test the functional significance of coherent neural activity. However, the mechanisms by which optogenetic stimulation drives coherent dynamics remain unclear, especially in the non-human primate brain. Here, we perform computational modeling and experiments to study the mechanisms of optogenetic-stimulation-driven coherent neuronal dynamics in non-human primates. Neural responses arise from stimulation-evoked temporal windows of excitatory and inhibitory activity. The temporal properties of the E-I windows generate coherent neuronal dynamics at varied frequencies and depend on optogenetic stimulation parameters. Experimental results agree with parameter dependent predictions from the computational models. These results demonstrate that responses to optogenetic stimulation are governed by local circuit properties that alter the timing of E-I activity. Transient imbalances in excitatory and inhibitory activity may provide a general mechanism for generating coherent neuronal dynamics.
Differentiating Genomic SNPs Using Allele Depth and Predicted Genotype
Authors: Hasan Saam
Published: October 2018

Differentiating between genomic SNPs and other types of single nucleotide variants becomes a key issue in research aimed at studying the importance of these variants of a particular type in biological processes. Here we present an R based method for differentiating between genomic single nucleotide polymorphisms (SNPs) and RNA editing sites. We use data from an earlier study of ours and target only the known dbsnp SNPs that we found in our study. Our method involves calculating the ratio of allele depth for ref and alt alleles and comparing that to the predicted genotype. We use the concept that editing levels should be different for each allele and thus should not reflect the ratio predicted by the genotype. The study yielded an accuracy rate ranging from 86 to over 90 percent at successfully predicted dbsnp entries as SNPs. Albeit this is in the absence of known RNA editing site vcf data to compare as a reference.
An averaging strategy to reduce variability in target-decoy estimates of false discovery rate
Authors: Keich Uri , Tamura Kaipo , Stafford Noble William
Published: October 2018

Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed dataset analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, datasets or databases. In such cases, the nominal FDR might be 1% but the true proportion of false discoveries might be 10%. The averaged TDC protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.
Brain responses to anticipating and receiving beer: Comparing light, at-risk, and dependent alcohol users
Authors: Groefsema Martine M. , Engels Rutger C.M.E. , Voon Valerie , Schellekens Arnt F.A. , Luijten Maartje , Sescousse Guillaume
Published: October 2018

Background

Impaired brain processing of alcohol-related rewards has been suggested to play a central role in alcohol use disorder. Yet, evidence remains inconsistent, and mainly originates from studies in which participants passively observe alcohol cues or taste alcohol. Here we designed a protocol in which beer consumption was predicted by incentive cues and contingent on instrumental action, closer to real life situations. We predicted that anticipating and receiving beer (compared with water) would elicit activity in the brain reward network, and that this activity would correlate with drinking level across participants.

Methods

The sample consisted of 150 beer-drinking males, aged 18-25 years. Three groups were defined based on AUDIT scores: light drinkers (n=40), at-risk drinkers (n=63), and dependent drinkers (n=47). fMRI measures were obtained while participants engaged in the Beer Incentive Delay task involving beer- and water-predicting cues, followed by real sips of beer or water.

Results

During anticipation, outcome notification and delivery of beer compared with water, higher activity was found in a reward-related brain network including the medial prefrontal cortex, orbitofrontal cortex and amygdala. Yet, no activity was observed in the striatum, and no differences were found between the groups.

Conclusions

Our results reveal that anticipating, obtaining and tasting beer activates parts of the brain reward network, but that these brain responses do not differentiate between different drinking levels. We speculate that other factors, such as cognitive control or sensitivity to social context, may be more discriminant predictors of drinking behaviour in young adults.
Sample-based regulatory intervention for managing risk within heterogeneous populations, with phytosanitary inspection of mixed consignments as a case study
Authors: Lane Stephen E. , Cannon Rob M. , Arthur Anthony D. , Robinson Andrew P.
Published: October 2018

Inspection of consignments of imported goods is commonly undertaken at national borders in order to prevent incursions of pests and diseases and deter malefactors. Inspection of the whole consignment is usually either impossible or inefficient, so inspection of a random sample is used instead.

The size of the random sample for plant products is justified by appeal to International Standards for Phytosanitary Measures No. 31, “Methodologies for Sampling of Consignments”. ISPM 31 notes that “A lot to be sampled should be a number of units of a single commodity identifiable by its homogeneity […]” and “Treating multiple commodities as a single lot for convenience may mean that statistical inferences can not be drawn from the results of the sampling.”

However, commonly consignments are heterogeneous, either because the same commodities have multiple sources or because there are several different commodities. The ISPM 31 prescription creates a substantial impost on border inspection because it suggests that heterogeneous populations must be split into homogeneous sub-populations from which separate samples of nominal size must be taken.

We demonstrate that if consignments with known heterogeneity are treated as stratified populations and the random sample of units is allocated proportionally based on the number of units in each stratum, then the nominal sensitivity at the consignment level is achieved if our concern is the level of contamination in the entire consignment taken as a whole. We argue that unknown heterogeneity is no impediment to appropriate statistical inference. We conclude that the international standard is unnecessarily restrictive.
Diffusion Tensor Model links to Neurite Orientation Dispersion and Density Imaging at high b-value in Cerebral Cortical Gray Matter
Authors: Fukutomi Hikaru , Glasser Matthew F. , Murata Katsutoshi , Akasaka Thai , Fujimoto Koji , Yamamoto Takayuki , Autio Joonas A. , Okada Tomohisa , Togashi Kaori , Zhang Hui , Van Essen David C. , Hayashi Takuya
Published: October 2018

Diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) are widely used models to infer microstructural features in the brain from diffusion-weighted MRI. Several studies have recently applied both models to increase sensitivity to biological changes, however, it remains uncertain how these measures are associated. Here we show that cortical distributions of DTI and NODDI are associated depending on the choice of b-value, a factor reflecting strength of diffusion weighting gradient. We analyzed a combination of high, intermediate and low b-value data of multi-shell diffusion-weighted MRI (dMRI) in healthy 456 subjects of the Human Connectome Project using NODDI, DTI and a mathematical conversion from DTI to NODDI. Cortical distributions of DTI and DTI-derived NODDI metrics were remarkably associated with those in NODDI, particularly when applied highly diffusion-weighted data (b-value =3000 sec/mm2). This was supported by simulation analysis, which revealed that DTI-derived parameters with lower b-value datasets suffered from errors due to heterogeneity of cerebrospinal fluid fraction and partial volume. These findings suggest that high b-value DTI redundantly parallels with NODDI-based cortical neurite measures, but the conventional low b-value DTI does not reasonably characterize cortical microarchitecture.
Defoliation estimation of forest trees from ground-level images
Authors: Kälin Ursula , Lang Nico , Hug Christian , Gessler Arthur , Wegner Jan Dirk
Published: October 2018

In this paper, we propose to estimate tree defoliation from ground-level RGB photos with convolutional neural networks (CNN). Tree defoliation is usually assessed with field campaigns, where experts estimate multiple tree health indicators per sample site. Campaigns span entire countries to come up with a holistic, nation-wide picture of forest health. Surveys are very laborious, expensive, time-consuming and need a large number of experts. We aim at making the monitoring process more efficient by casting tree defoliation estimation as an image interpretation problem. What makes this task challenging is strong variance in lighting, viewpoint, scale, tree species, and defoliation types. Instead of accounting for each factor separately through explicit modelling, we learn a joint distribution directly from a large set of annotated training images following the end-to-end learning paradigm of deep learning. The proposed workflow works as follows: (i) Human experts visit individual trees in forests distributed all over Switzerland, (ii) acquire one photo per tree with an off-the-shelf, hand-held RGB camera and (iii) assign a defoliation value. The CNN approach is (iv) trained on a subset of the images with expert defoliation assessments and (v) tested on a hold-out part to check predicted values against ground truth. We evaluate our supervised method on three data sets with different level of difficulty acquired in Swiss forests and achieve an average mean absolute error (avgMAE) of 7.6% for the joint data set after cross-validation. Comparison to a group of human experts on one of the data sets shows that our CNN approach performs only 0.9 percent points worse. We show that tree defoliation estimation from ground-level RGB images with a CNN works well and achieves performance close to human experts.
A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)
Authors: Louro Bruno , De Moro Gianluca , Garcia Carlos , Cox Cymon J. , Veríssimo Ana , Sabatino Stephen J. , Santos António M. , Canário Adelino V. M.
Published: October 2018

Background

The European sardine (Sardina pilchardus Walbaum, 1792) has a high cultural and economic importance throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Consequently, there is an urgent need to better understand the causal factors of this continuing decrease in the sardine stock. Important biological and ecological features such as levels of population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.

Findings

The sardine genome of a single female individual was sequenced using Illumina HiSeq X Ten 10X Genomics linked-reads generating 113.8 Gb of data. Three draft genomes were assembled: two haploid genomes with a total size of 935 Mbp (N50 103Kb) each, and a consensus genome with a total size of 950 Mbp (N50 97Kb). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of eleven tissues were sequenced and used to aid the functional annotation of the genome, resulting in 40 777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of more than 2.3 million phased SNPs with heterozygous loci.

Conclusions

A draft genome was obtained with the 10X Genomics linked-reads technology, despite a high level of sequence repeats and heterozygosity that are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data are a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.
Increased Epstein-Barr virus C-promoter activity with CTCF-binding site deletion is associated with elevated EBNA2 recruitment
Authors: Groves Ian J , Allday Martin J
Published: October 2018

The regulation of transcription from Epstein-Barr virus promoters is known to involve the association of the host CCCTC-binding factor (CTCF) protein. This control involves direct binding of CTCF across the EBV genome and the formation of three-dimensional loops between virus promoters and enhancers. We sought to address how the deletion of a CTCF binding site upstream of the C-promoter (Cp) affected viral transcription in infected lymphoblastoid cell lines (LCLs) and how binding of the EBV trans-activating protein EBNA2 was changed across this promoter. Transcript level from Cp was up-regulated with CTCF binding site deletion, and transcription from other promoters (Wp and Qp) was decreased, while transcript levels were largely unchanged by independent mutation of a Cp-RBPJκ binding site. In turn, expression of EBNA2 protein was also increased, likely driven by increases in polycistronic EBNA2-encoding transcripts. Finally, Cp up-regulation was associated with an 8-fold increase in EBNA2 enrichment across Cp, concomitant with increased association of the associated cellular factor RBPJκ, probably due to a more accessible three-dimensional chromatin conformation upstream of Cp. Overall, the data presented here confirm that binding of CTCF directly upstream of Cp is important for the regulation of transcription from this and other EBV promoters.
High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
Authors: Johnston Michael J , Nikolic Ana , Ninkovic Nicoletta , Guilhamon Paul , Cavalli Florence MG , Seaman Steven , Zemp Franz J , Lee John , Abdelkareem Aly , Ellestad Katrina , Murison Alex , Kushida Michelle M , Coutinho Fiona J , Ma Yussanne , Mungall Andrew J , Moore Richard , Marra Marco A , Taylor Michael D , Dirks Peter B , Pugh Trevor J , Morrissy Sorana , Croix Bradley St , Mahoney Douglas J , Lupien Mathieu , Gallo Marco
Published: October 2018

We investigated the role of 3D genome architecture in instructing functional properties of glioblastoma stem cells (GSCs) by generating the highest-resolution 3D genome maps to-date for this cancer. Integration of DNA contact maps with chromatin and transcriptional profiles identified specific mechanisms of gene regulation, including individual physical interactions between regulatory regions and their target genes. Residing in structurally conserved regions in GSCs was CD276, a gene known to play a role in immuno-modulation. We show that, unexpectedly, CD276 is part of a stemness network in GSCs and can be targeted with an antibody-drug conjugate to curb self-renewal, a key stemness property. Our results demonstrate that integrated structural genomics datasets can be employed to rationally identify therapeutic vulnerabilities in self-renewing cells.

SIGNIFICANCE

In adult GBM, GSCs act as therapy-resistant reservoirs to nucleate tumor recurrence. New therapeutic approaches that target these cell populations hold the potential of significantly improving patient care and overall prognosis for this always-lethal cancer. Our work describes new links between 3D genome architecture and stemness properties in GSCs. In particular, through integration of multiple genomics and structural genomics datasets, we found an unexpected connection between immune-related genes and self-renewal programs in GBM. Among these, we show that targeting CD276 with knockdown strategies or specific antibody-drug conjugates achieve suppression of self-renewal. Strategies to target CD276+ cells are currently in clinical trials for solid tumors. Our results indicate that CD276-targeting agents could be deployed in GBM to specifically target GSC populations.

HIGHLIGHTS

We generated high (sub-5 kb) resolution Hi-C maps for stem-like cells from GBM patients.

Integration of Hi-C and genomics datasets dissects mechanisms of gene regulation.

3D genomes poise immune-related genes, including CD276, for expression.

Targeting CD276 curbs self-renewal properties of GBM cells.
Centrosome-nuclear envelope tethering and microtubule motor-based pulling forces collaborate in centrosome positioning during mitotic entry
Authors: Boudreau Vincent , Chen Richard , Edwards Alan , Sulaimain Muhammad , Maddox Paul S.
Published: October 2018

Centrosome positioning relative to the nucleus and cell shape is highly regulated across cell types, during cell migration and during spindle formation in cell division. Across most sexually reproducing animals, centrosomes are provided to the oocyte through fertilization and must be positioned properly to establish the zygotic mitotic spindle. How centrosomes are positioned in space and time through the concerted action of key mitotic entry biochemical regulators including Protein Phosphatase 2A (PP2A-B55/SUR-6), biophysical regulators including Dynein and the nuclear lamina is unclear. Here, we uncover a role for PP2A-B55/SUR-6 in regulating centrosome positioning. Mechanistically, PP2A-B55/SUR-6 regulates nuclear size prior to mitotic entry, in turn affecting nuclear envelope-based Dynein density and motor capacity. Using computational simulations, PP2A-B55/ SUR-6 regulation of nuclear size and nuclear envelope Dynein density were both predicted to be required for proper centrosome positioning. Conversely, compromising nuclear lamina integrity led to centrosome detachment from the nuclear envelope and migration defects. Removal of PP2A-B55/SUR-6 and the nuclear lamina simultaneously further disrupted centrosome positioning, leading to unseparated centrosome pairs dissociated from the nuclear envelope. Taken together, we propose a model in which centrosomes migrate and are positioned through the concerted action of nuclear envelope-based Dynein pulling forces and cen-trosome-nuclear envelope tethering.
Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert
Authors: Uritskiy Gherman , Getsin Samantha , Munn Adam , Gomez-Silva Benito , Davila Alfonso , Glass Brian , Taylor James , DiRuggiero Jocelyne
Published: October 2018

Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth’s ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize and de-convolute the temporal response of a highly specialized community to a major disturbance. With shotgun metagenomic sequencing, we investigated the halite microbiome taxonomic composition and functional potential over a 4-year longitudinal study, uncovering the dynamics of the initial response and of the recovery of the community after a rainfall event. The observed changes can be recapitulated by two general modes of community shifts – a rapidType 1shift and a more gradualType 2adjustment. In the initial response, the community entered an unstable intermediate state after stochastic niche re-colonization, resulting in broad predicted protein adaptations to increased water availability. In contrast, during recovery, the community returned to its former functional potential by a gradual shift in abundances of the newly acquired taxa. The general characterization and proposed quantitation of these two modes of community response could potentially be applied to other ecosystems, providing a theoretical framework for prediction of taxonomic and functional flux following environmental changes.
A prognostic signature for lower-grade gliomas based on expression of long noncoding RNAs
Authors: Kiran Manjari , Chatrath Ajay , Tang Xiwei , Keenan Daniel Macrae , Dutta Anindya
Published: October 2018

Diffuse low-grade and intermediate-grade gliomas (together known as lower-grade gliomas, WHO grade II and III) develop in the supporting glial cells of brain and are the most common types of primary brain tumor. Despite a better prognosis for lower-grade gliomas, 70% of patients undergo high-grade transformation within 10 years, stressing the importance of better prognosis. Long non-coding RNAs (lncRNAs) are gaining attention as potential biomarkers for cancer diagnosis and prognosis. We have developed a computational model, UVA8, for prognosis of lower-grade gliomas by combining lncRNA expression, Cox regression and L1-LASSO penalization. The model was trained on a subset of patients in TCGA. Patients in TCGA, as well as a completely independent validation set (CGGA) could be dichotomized based on their risk score, a linear combination of the level of each prognostic lncRNA weighted by its multivariable cox regression coefficient. UVA8 is an independent predictor of survival and outperforms standard epidemiological approaches and previous published lncRNA-based predictors as a survival model. Guilt-by-association studies of the lncRNAs in UVA8, all of which predict good outcome, suggest they have a role in suppressing interferon stimulated response and epithelial to mesenchymal transition. The expression levels of 8 lncRNAs can be combined to produce a prognostic tool applicable to diverse populations of glioma patients. The 8 lncRNA (UVA8) based score can identify grade II and grade III glioma patients with poor outcome and thus identify patients who should receive more aggressive therapy at the outset.
The History, Advocacy and Efficacy of Data Management Plans
Authors: Smale Nicholas , Unsworth Kathryn , Denyer Gareth , Barr Daniel
Published: October 2018

Data management plans (DMPs) have increasingly been encouraged as a key component of institutional and funding body policy. Although DMPs necessarily place administrative burden on researchers, proponents claim that DMPs have myriad benefits, including enhanced research data quality, increased rates of data sharing, and institutional planning and compliance benefits.

In this manuscript, we explore the international history of DMPs and describe institutional and funding body DMP policy. We find that economic and societal benefits from presumed increased rates of data sharing was the original driver of mandating DMPs by funding bodies. Today, 86% of UK Research Councils and 63% of US funding bodies require submission of a DMP with funding applications. Given that no major Australian funding bodies require DMP submission, it is of note that 37% of Australian universities have taken the initiative to internally mandate DMPs.

Institutions both within Australia and internationally frequently promote the professional benefits of DMP use, and endorse DMPs as ‘best practice’. We analyse one such typical DMP implementation at a major Australian institution, finding that DMPs have low levels of apparent translational value. Indeed, an extensive literature review suggests there is very limited published systematic evidence that DMP use has any tangible benefit for researchers, institutions or funding bodies.

We are therefore led to question why DMPs have become the go-to tool for research data professionals and advocates of good data practice. By delineating multiple use-cases and highlighting the need for DMPs to be fit for intended purpose, we question the view that a good DMP is necessarily that which encompasses the entire data lifecycle of a project. Finally, we summarise recent developments in the DMP landscape, and note a positive shift towards evidence-based research management through more researcher-centric, educative, and integrated DMP services.