bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon storage in seagrass meadow of Teluk Bakau – Bintan Island
Authors: Nugraha A H , Kawaroe M , Srimariana E S , Jaya I , Apdillah D , Deswati S R 
Published: May 2019

Abstract
Seagrass has the ability to store carbon through photosynthesis. The ability is influenced by environmental factors. This study was aimed to examine the diversity of seagrass and investigate the carbon storage in seagrass’ biomass in two stations at Teluk Bakau Village, Bintan Island. This research was conducted at two stations including Beralas Pasir Island (small island) and Teluk Bakau Village Beach (mainland). Measure of seagrass biomass with dried seagrass sample was carried out at 60°C temperature. The analysis of carbon content was carried out on the biomass of the four dominant seagrass species found in the Teluk Bakau Village namely Cymodocea rotundata, Enhalus acoroides, Syringodium isoetifolium, Thalassia hemprichii. The results show that the carbon storage on seagrass has a correlation with seagrass biomass. Enhalus acoroides has the highest carbon content compared to the other three seagrass species. In general, seagrass located in Teluk Bakau Village Beach have higher biomass than seagrass located in Beralas Pasir Island, and it means that they have high carbon storage. This is expected to occur considering that the area of Teluk Bakau Village Beach is close to the mainland, where there is a high nutrient input support for the growth of seagrass biomass.
Interannual variability of Indonesian throughflow in the Flores Sea
Authors: Putriani P Y , Atmadipoera A S , Nugroho D 
Published: May 2019

AbstractThe main branch of Indonesian Throughflow (ITF) from Makassar Strait passes through Flores Sea. The variance of ITF transport volume was influenced by climate phenomenon such as El Nino Southern Oscillation (ENSO). This research was conducted to describe the relationship between the ENSO and the ITF transport variability. This relationship was explored using data from INDESO model 2008-2015. The variability of transport volume was analyzied using continous wavelet transform and band-pass analysis. Water circulation was analyzed by summing up the average of water current and sea temperatures. The Flores ITF was a portion of Makassar ITF and Eastern ITF that enter via Lifamatola Passage. The flow in the upper layer was intensified during the west monsoon while in the thermocline layer was intensified during the east monsoon. Flores ITF moved along the northern part of Flores Island and was dominated by zonal velocity component.
Endophytic microbes and antioxidant activities of secondary metabolites from mangroves Avicennia marina and Xylocarpus granatum
Authors: Rahmawati S I , Izzati F N , Hapsari Y , Septiana E , Rachman F , Bustanussalam  , Simanjuntak P 
Published: May 2019

Abstract
The utilization of mangrove plants as traditional medicinal ingredients has long been utilized by the community for treatment of various diseases in favour of bioactive components from its secondary metabolites. Secondary metabolites from mangroves could act as an antioxidant to prevent oxidative stress. Mangrove may contain endophytic microbes in its tissues that are capable of producing secondary metabolites. In theory, endophytic microbes isolated from a plant can produce secondary metabolites similar to those of the original plants or even in relatively high numbers. In this research, two mangrove species Avicennia marina and Xylocarpus granatum from Serang, Banten province, samples have been taken to investigate the antioxidant activities of its extracts. Furthermore, isolation of endophytic microbes from both mangroves had been done. This research succeeded to isolate six fungi and three bacteria as endophytic microbes. Meanwhile, the highest extraction yield was obtained by the leaves of A. marina that is approximately 3% (w/w), whereas mangroves’ endophytic microbe highest extract yield was obtained by bacteria from fruits of A. marina 18 mg/100 mL media. For antioxidant activities, the highest activities were obtained by fungi within the stems and the roots of A. marina, also additionally fungi in the leaves of X. granatum.
Phytochemical constituents and antidiabetic activity of edible marine red seaweed (Halymenia durvilae)
Authors: Sanger G , Rarung L K , Damongilala L J , Kaseger B E , Montolalu L A D Y 
Published: May 2019

Abstract
Seaweeds have bioactive compounds with enormous health prospective which interests the pharmaceutical industries. The isolated bioactive compounds of seaweeds have been utilized as drug and food in the world. Phytochemical constituents of seaweeds have an assortment of prospective biological activity, such as antidiabetes. In worldwide the appearance of type two diabetes mellitus (T2DM) as the greatest non-transmittable disease has motivated search for new antidiabetic approaches. The purpose of the research was to determine the phytochemical properties and antidiabetic effect using α-glukosidase on methanol extract, n-hexane, chloroform, and water fraction of marine red algae Halymenia durvilae. The result of this study showed the phyto-constituent of H.durvilae includes steroids, flavonoids and triterpenoids are present in all extracts. Saponins and hyquinones showed their presence only in methanol extract. Alkaloid and tannin were not present in methanol extract and its fractions. H.durvilae on the extract and its fractions had antidiabetic activity. Water fraction had the highest activity to inhibit α-glukosidase (IC50 4.34±0.32 mg mL) followed by chloroform, hexane and methanol extract. Therefore, it can be concluded that H.durvilae could be used as a dietary food source of bioactive compound especially natural antidiabetic compounds.
Exploring human-nature interaction on the coastal floodplain in the Ganges-Brahmaputra delta through the lens of Ostrom’s social-ecological systems framework
Authors: Gain Animesh K , Ashik-Ur-Rahman Md. , Vafeidis Athanasios 
Published: May 2019

Abstract
This study diagnoses temporal and spatial variations in the performance of different social-ecological systems (SES) in coastal floodplain management in the Ganges-Brahmaputra delta. We go beyond common pool resource management problems and address the management of local public goods. In the assessment, we consider recent developments in the framework initially developed by Elinor Ostrom. The main variables of the framework that we use are resource systems, the environment, the governance system and actors. The focal SES is defined based on guiding questions relating to the definition of the key problem, system boundaries, and action situations. According to our results, the performance of resource systems and the environment deteriorated in 1960–79 compared to the performance prior to 1960. The condition reached a low point during 1980–1999 but improved slightly after 1999. The horizontal network structure of local governance was active until 1960. Due to the introduction of the ‘tidal river management’ approach in the 90 s, the performance of the resource system and the environment has slightly improved, as has the involvement of government and non-government organizations. Our results also show that overall SES performance is comparatively better <in the case of locally managed floodplains than it is for those managed by government agencies. Our new approaches, such as the recent development of the diagnostic framework, the guiding questions for defining focal SES, and application of the framework to local public goods can potentially be used in the fields of sustainability science and SES science. The qualitative performance of each of the selected indicators is useful for identifying intervention options to achieve a sustainable outcome for the coastal floodplain SES.
Assessing concordance among human, in silico predictions and functional assays on genetic variant classification
Authors: Luo Jiaqi , Zhou Tianliangwen , You Xiaobin , Zi Yi , Li Xiaoting , Wu Yangming , Lan Zhaoji , Zhi Qihuan , Yi Dandan , Xu Lei , Li Ang , Zhong Zaixuan , Zhu Mei , Sun Gang , Zhu Tao , Rao Jianmei , Lin Luhua , Sang Jianfeng , Shi Yujian 
Published: May 2019

Abstract

Motivation
A variety of in silico tools have been developed and frequently used to aid high-throughput rapid variant classification, but their performances vary, and their ability to classify variants of uncertain significance were not systemically assessed previously due to lack of validation data. This has been changed recently by advances of functional assays, where functional impact of genetic changes can be measured in single-nucleotide resolution using saturation genome editing (SGE) assay.

Results
We demonstrated the neural network model AIVAR (Artificial Intelligent VARiant classifier) was highly comparable to human experts on multiple verified datasets. Although highly accurate on known variants, AIVAR together with CADD and PhyloP showed non-significant concordance with SGE function scores. Moreover, our results indicated that neural network model trained from functional assay data may not produce accurate prediction on known variants.

Availability and implementation
All source code of AIVAR is deposited and freely available at https://github.com/TopGene/AIvar.

Supplementary information
Supplementary data are available at Bioinformatics online.
Trust in the Court: The Role of the Registry of the European Court of Human Rights
Authors: Creamer Cosette D , Godzimirska Zuzanna 
Published: May 2019

Abstract
The growing impact of European institutions on the daily lives of citizens has stimulated greater attention to the public’s trust in these bodies. Existing research on trust in the European Court of Human Rights (ECtHR) tends to focus on the role of judges and their rulings. In contrast, this article examines the role of the ECtHR’s Registry. We argue that the civil servants of the ECtHR serve a critical function for the court’s operation and have the potential to play an indispensable trust-building role. Drawing on interviews with court officials and survey responses from government agents, we identify and discuss the practices and features of the Registry that contribute to, or undermine, member states’ estimations of trust in the ECtHR. In light of repeated and mounting criticism by member governments, our findings have important implications for the continued relevance of, and political support for, the Court moving forward.
Conservation Genomics in the Sagebrush Sea: Population Divergence, Demographic History, and Local Adaptation in Sage-Grouse (Centrocercus spp.)
Authors: Oh Kevin P , Aldridge Cameron L , Forbey Jennifer S , Dadabay Carolyn Y , Oyler-McCance Sara J 
Published: May 2019

AbstractSage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several populations on the periphery of the species ranges. Population genomic analyses reaffirmed genome-wide differentiation between greater and Gunnison sage-grouse, revealed pronounced intraspecific population structure, and highlighted important differentiation of a small isolated population of greater sage-grouse in the northwest of the range. Patterns of genome-wide differentiation were largely consistent with a hypothesized role of genetic drift due to limited gene flow among populations. Inferred ancient population demography suggested persistent declines in effective population sizes that have likely contributed to differentiation within and among species. Several genomic regions with single-nucleotide polymorphisms exhibiting extreme population differentiation were associated with candidate genes linked to metabolism of xenobiotic compounds. In vitro activity of enzymes isolated from sage-grouse livers supported a role for these genes in detoxification of sagebrush, suggesting that the observed interpopulation variation may underlie important local dietary adaptations, warranting close consideration for conservation strategies that link sage-grouse to the chemistry of local sagebrush.
Fundamental Flaws with the Fundamental Niche
Authors: Angilletta Michael J , Sears Michael W , Levy Ofir , Youngblood Jacob P , VandenBrooks John M 
Published: May 2019

AbstractFor more than 70 years, Hutchinson’s concept of the fundamental niche has guided ecological research. Hutchinson envisioned the niche as a multidimensional hypervolume relating the fitness of an organism to relevant environmental factors. Here, we challenge the utility of the concept to modern ecologists, based on its inability to account for environmental variation and phenotypic plasticity. We have ample evidence that the frequency, duration, and sequence of abiotic stress influence the survivorship and performance of organisms. Recent work shows that organisms also respond to the spatial configuration of abiotic conditions. Spatiotemporal variation of the environment interacts with the genotype to generate a unique phenotype at each life stage. These dynamics cannot be captured adequately by a multidimensional hypervolume. Therefore, we recommend that ecologists abandon the niche as a tool for predicting the persistence of species and embrace mechanistic models of population growth that incorporate spatiotemporal dynamics.
Is Amphistomy an Adaptation to High Light? Optimality Models of Stomatal Traits along Light Gradients
Authors: Muir Christopher D 
Published: May 2019

AbstractStomata regulate the supply of CO2 for photosynthesis and the rate of water loss out of the leaf. The presence of stomata on both leaf surfaces, termed amphistomy, increases photosynthetic rate, is common in plants from high light habitats, and rare otherwise. In this study I use optimality models based on leaf energy budget and photosynthetic models to ask why amphistomy is common in high light habitats. I developed an R package leafoptimizer to solve for stomatal traits that optimally balance carbon gain with water loss in a given environment. The model predicts that amphistomy is common in high light because its marginal effect on carbon gain is greater than in the shade, but only if the costs of amphistomy are also lower under high light than in the shade. More generally, covariation between costs and benefits may explain why stomatal and other traits form discrete phenotypic clusters.
Device exchange from HeartMate II to HeartMate 3 left ventricular assist device
Authors: Takeda Koji , Takayama Hiroo , Sanchez Joseph , Cevasco Marisa , Yuzefpolskaya Melana , Colombo Paolo C , Naka Yoshifumi 
Published: May 2019

Abstract
The HeartMate II (HMII) left ventricular assist device can be exchanged to HeartMate 3 (HM3) to reduce the risk of device thrombosis and stroke. However, data of this procedure are still limited. We reviewed early and mid-term outcomes of 9 patients who received a HMII to HM3 exchange at our institution. The median age of the cohort was 58 years [interquartile range (IQR) 53–61], and 7 (78%) patients were men. The median duration of HMII support was 608 days (IQR 493–1116). Indications for device exchange include device thrombosis (n = 8.89%) and driveline injury (n = 1.11%). Procedures were performed through a lateral thoracotomy in all patients. The median cardiopulmonary bypass time was 117 min (IQR 97–133). In-hospital mortality was 0%. One patient required repositioning of the HM3 pump through full sternotomy due to inflow malposition. During 486 days (IQR 235–712) of follow-up, 3 patients (33%) developed late HMII pump pocket infection after discharge. Five patients had a successful heart transplant and 1 patient died due to unknown reason. HMII to HM3 exchange can be performed via lateral thoracotomy. However, there is a risk of inflow malposition and previous pump pocket infection.
Antifungal susceptibility profiles of rare ascomycetous yeasts
Authors: Pérez-Hansen Antonio , Lass-Flörl Cornelia , Lackner Michaela ,   Rare Yeast Study Group, Aigner M , Alastruey-Izquierdo A , Arikan-Akdagli S , Bader O , Becker K , Boekhout T , Buzina W , Cornely O A , Hamal P , Kidd S E , Kurzai O , Lagrou K , Lopes Colombo A , Mares M , Masoud H , Meis J F , Oliveri S , Rodloff A C , Orth-Höller D , Guerrero-Lozano I , Sanguinetti M , Segal E , Taj-Aldeen S J , Tortorano A M , Trovato L , Walther G , Willinger B 
Published: May 2019

AbstractObjectivesTo generate antifungal susceptibility patterns for Trichomonascus ciferrii (Candida ciferrii), Candida inconspicua (Torulopsis inconspicua) and Diutina rugosa species complex (Candida rugosa species complex), and to provide key parameters such as MIC50, MIC90 and tentative epidemiological cut-off values (TECOFFs).MethodsOur strain set included isolates of clinical origin: C. inconspicua (n = 168), D. rugosa species complex (n = 90) [Candida pararugosa (n = 60), D. rugosa (n = 26) and Candida mesorugosa (n = 4)], Pichia norvegensis (Candida norvegensis) (n = 15) and T. ciferrii (n = 8). Identification was performed by MALDI-TOF MS or internal transcribed spacer sequencing. Antifungal susceptibility patterns were generated for azoles, echinocandins and amphotericin B using commercial Etest and the EUCAST broth microdilution method v7.3.1. Essential agreement (EA) was calculated for Etest and EUCAST.ResultsC. inconspicua, C. pararugosa and P. norvegensis showed elevated azole MICs (MIC50 ≥0.06 mg/L), and D. rugosa and C. pararugosa elevated echinocandin MICs (MIC50 ≥0.06 mg/L). EA between methods was generally low (<90%); EA averaged 77.45%. TECOFFs were suggested for C. inconspicua and D. rugosa species complex.ConclusionsRare yeast species tested shared high fluconazole MICs. D. rugosa species complex displayed high echinocandin MICs, while C. inconspicua and P. norvegensis were found to have high azole MICs. Overall, the agreement between EUCAST and Etest was poor and therefore MIC values generated with Etest cannot be directly compared with EUCAST results.
Structural and environmental predictors of presence and abundance of tri-colored bats in Texas culverts
Authors: Meierhofer Melissa B , Leivers Samantha J , Fern Rachel R , Wolf Lilianna K , Young John H , Pierce Brian L , Evans Jonah W , Morrison Michael L 
Published: May 2019

AbstractThe tri-colored bat (Perimyotis subflavus) is being reviewed for listing under the Endangered Species Act by the United States Fish and Wildlife Service. It is also listed as a species of greatest conservation need by the Texas Parks and Wildlife Department due to its susceptibility to white-nose syndrome (WNS) in other states. Several colonies of hibernating tri-colored bats have been documented roosting in culverts. Culverts are widespread in Texas as part of roadway infrastructure; thus, our objective was to understand and quantify which structural and environmental factors best explain culvert use and abundance of hibernating tri-colored bats in Texas. We selected and surveyed 207 culverts for presence of tri-colored bats using the Generalized Random Tessellation Stratified (GRTS) design and opportunistic sampling across 10 of 12 Texas level III ecoregions during the winters of 2016–2017 and 2017–2018. We recorded environmental and structural features of culverts at each site. We used a zero-inflated Poisson regression to identify which culvert features best explained presence and abundance of hibernating tri-colored bats. We found that number of culvert sections predicted presence of tri-colored bats. We also found that abundance of tri-colored bats was influenced by length of culvert, elevation, number of sections, portal height, portal obstruction, aspect, external VPD, external temperature, and NDVI. With the current threats to tri-colored bat populations, there is a need to consider management of culvert roosts. In addition, it is imperative to further investigate the potential susceptibility to WNS of culvert-roosting bats at more southern latitudes for local and regional planning efforts.
The 2019 Taurid resonant swarm: prospects for ground detection of small NEOs
Authors: Clark David L , Wiegert Paul , Brown Peter G 
Published: May 2019

Abstract
In June 2019 the Earth will approach within 5° mean anomaly of the centre of the Taurid resonant swarm, its closest post-perihelion encounter with Earth since 1975. This will be the best viewing geometry to detect and place limits on the number of NEOs proposed to reside at the swarm centre until the early 2030s. We present an analysis of the optimal times and pointing locations to image NEOs associated with the swarm.
Cyclotron emission, absorption, and the two faces of X-ray pulsar A 0535+262
Authors: Tsygankov Sergey S , Doroshenko Victor , Mushtukov Alexander A , Suleimanov Valery F , Lutovinov Alexander A , Poutanen Juri 
Published: May 2019

Abstract
Deep NuSTAR observation of X-ray pulsar A 0535+262, performed at a very low luminosity of ∼7 × 1034 erg s−1, revealed the presence of two spectral components. We argue that the high-energy component is associated with cyclotron emission from recombination of electrons collisionally excited to the upper Landau levels. The cyclotron line energy of Ecyc = 47.7 ± 0.8 keV was measured at the luminosity of almost an order of magnitude lower than what was achieved before. The data firmly exclude a positive correlation of the cyclotron energy with the mass accretion rate in this source.
Defining EGFR amplification status for clinical trial inclusion
Authors: French Pim J , Eoli Marica , Sepulveda Juan Manuel , de Heer Iris , Kros Johan M , Walenkamp Annemiek , Frenel Jean-Sebastien , Franceschi Enrico , Clement Paul M , Weller Michael , Ansell Peter , Looman Jim , Bain Earle , Morfouace Marie , Gorlia Thierry , van den Bent Martin 
Published: May 2019

Abstract

Background
Precision medicine trials targeting the epidermal growth factor receptor (EGFR) in glioblastoma patients require selection for EGFR-amplified tumors. However, there is currently no gold standard in determining the amplification status of EGFR or variant III (EGFRvIII) expression. Here, we aimed to determine which technique and which cutoffs are suitable to determine EGFR amplification status.

Methods
We compared fluorescence in-situ hybridization (FISH) and real-time quantitative (RT-q)PCR data from patients screened for trial inclusion into the Intellance 2 clinical trial, with data from a panel-based next generation sequencing (NGS) platform (both DNA and RNA).

Results
By using data from >1000 samples, we show that at least 50% of EGFR amplified nuclei should be present to define EGFR gene amplification by FISH. Gene amplification (as determined by FISH) correlates with EGFR expression levels (as determined by RT-qPCR) with receiver operating characteristics analysis showing an area under the curve of up to 0.902. EGFR expression as assessed by RT-qPCR therefore may function as a surrogate marker for EGFR amplification. Our NGS data show that EGFR copy numbers can strongly vary between tumors, with levels ranging from 2 to more than 100 copies per cell. Levels exceeding 5 gene copies can be used to define EGFR-amplification by NGS; below this level, FISH detects very few (if any) EGFR amplified nuclei and none of the samples express EGFRvIII.

Conclusion
Our data from central laboratories and diagnostic sequencing facilities, using material from patients eligible for clinical trial inclusion, help define the optimal cutoff for various techniques to determine EGFR amplification for diagnostic purposes.