bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between shrimps production and mangrove ecosystem in Indramayu Regency
Authors: Dheanisa M R , Handayani T , Susiloningtyas D , Rahatiningtyas N S 
Published: January 2020

Abstract
Shrimp is one of the agricultural commodities which has high economic value with global and increasing market value abroad. Thus, Shrimp production continues to increase. Shrimp production in Indramayu Regency in 2017 was 191,919.41 tons. This makes Indramayu Regency the largest producer of shrimp in West Java (BPS, 2017). Meanwhile, Mangrove is an area that has a high contribution. Mangrove ecosystems have an association with pond productivity. This study aims to analyze the productivity value of shrimp in Indramayu Regency and its effect on the mangrove ecosystem in Indramayu Regency in that particular area. The method that is used to change identify mangrove forests is Landsat 8 image then continued with composite band 564 and NDVI (Normalized Difference Vegetationation Index) with a distance of 1 Km, 2 Km, and 3 Km from the mangroves. Furthermore, the result of the interviews is used to find out the value of shrimp productivity. Analysis of data is calculated through regression methods to see the–relation proximity between shrimp productivity and mangroves. The regression result between the distance of mangroves and productivity yields with the value of R Square equals 71.7%. This result indicates a positive link between shrimp productivity and mangrove ecosystem.
Biodegradation of aliphatic waste components of oil sludge used micro symbiont of Sponge Niphates sp.
Authors: Marzuki I , Chaerul M , Erniati  , Asmeati  , Paserangi I 
Published: January 2020

Abstract
Investigation has been carried out using a sponge Niphates sp. as biodegradation agent of the aliphatic hydrocarbon component of crude oil sludge. The experiment was carried out by colonizing and making suspension of Bacillus pumilus strains GLB197 and Bacillus cohnii strains of DSM 6307, isolated from sponge Niphates sp. Both types of micro symbiont suspension were mixed with sludge waste for 30 days. There are five biodegradation parameters observed, carried out every five days of incubation. Parameters that observed during incubation were pH, gas bubbles and fermentation odor. Meanwhile, the optical density of the media was measured using spectrometer-D20+, Aliphatic components degradation was measured using GC-MS. Observation of biodegradation parameters showed there was a change in pH from 7 to 6, formed gas bubbles, resulting in fermentation odors and showed an increased optical density by an average of 35%. These four parameters occur during the interaction of 10-20 days of interaction in the media. There were 20 types of aliphatic components identified in the crude oil sludge waste. Analysis of four aliphatic components, namely Tridecane, Octadecane, Tricosane, and Nonacosane showed a decrease in the average concentration of 48.11 %.
Productivity and decomposition rate of Rhizophora mucronata and Avicennia alba litter based on environment characteristics in Muara Gembong
Authors: Muliawan R E , Prartono T , Bengen D G 
Published: January 2020

AbstractMangrove forests damage may decrease their function and ecological role in relation to litter production which support the sustenance of aquatic resources. This research aimed to determine and estimate productivity and decomposition rate of mangroveRhizophora mucronataandAvicennia albalitter, and their effect on water nutrients. The research was conducted at three stations in Pantai Mekar Village, Muara Gembong District for 60 days observation during period of April–September 2018. Litter productivity was measured using litter traps and litter decomposition rate was estimated using litter bags. The concentration of water nutrient (nitrate, ammonium and phosphate) was obtained through a laboratory analysis. Litter productivity ofR. mucronataandA. albastands reached 4.68 and 7.11 g m−2day−1respectively with the biggest contributed from leaves litter. Observed different rates of mangrove decomposition was due to the lignin content. The decomposition rate ofR. mucronataandA. albawere Y=12.841e−0.382X(R2=0.97) and Y=11.958e−0.478X(R2=0.91) respectively. The productivity and decomposition rate ofA. albalitter was greater and faster thanR. mucronata. Increased nitrates was indicated of nitrification process, while phosphate and ammonium showed decreased concentration during experiments. Aside from that, water nutrient concentration was affected by dissolved oxygen availability.
Baseline concentration of Polonium-210 (210Po) in several biota from Jakarta Bay
Authors: Makmur M , Prihatiningsih W R , Yahya M N 
Published: January 2020

Abstract
Nuclide 210Po is the main contributor to internal doses due to ingestion of radionuclide in humans, and enters the human body through the consumption of food, including seafood. The research aim is to analyse the activity of the 210Po, in several species of biota that commonly available in the Jakarta Bay. The sample consist of tuna, tenggiri (mackerel), kakap merah (red snapper), Shrimp and green mussel were collected in 2017. The activity of 210Po in the edible part of that biota ranged from 9.05 ± 3.05 to 137.37±37 Bq/kg of fresh biota, and the highest activity in the green mussel and the lowest for tuna. This result were comparable to those presented by other study from several regions of the world and the UNSCEAR data. The daily intake of 210Po from these biota varied between 0.24 and 14.27 Bq year–1. The estimated dose of 210Po intake ranged from 0.03 – 3.6 μSv year–1 are lower than the average natural radiation received by humans globally. This study contributes to the Indonesia baseline data of 210Po in marine biota.
The vulnerability of fish, crabs and prawns resources in the Mahakam Estuary
Authors: Aisyah  , Triharyuni S 
Published: January 2020

Abstract
River estuary in coastal areas, is highly affected by inland water conditions such as freshwater and sediment flows, ocean water such as tides, waves, and the substitution of saltwater to land. Large ecological and economic potential causes logical consequences for ecosystem changes, including the condition of fish resources that have habitat and life cycles directly related to conditions that occur upstream. The purpose of this study was to examine ecological stresses and fishing activity in Mahakam Estuary represented by mangrove crabs, cat fish and giant prawns. The main analysis in this study was the calculation of vulnerability values with concepts and approaches to vulnerability of catfish populations, giant prawns and mangrove crabs, based on two functions of vulnerability, namely exposure and sensitivity. The vulnerability analysis of three types of fisheries commodities refers to the method used by NOAA with some modifications to the assessment component. It is known that catfish are in a low level of vulnerability, giant prawns are at a high level of vulnerability, mangrove crabs are in a very high level of vulnerability or very vulnerable.
Phytoplankton communities of the Barents Sea frontal zone during the early spring period
Authors: Vodopyanova V , Larionov V , Makarevich P , Vashenko P , Bulavina A 
Published: January 2020

Abstract
In April 2018, complex studies of phytoplankton communities were carried out in the northwestern Barents Sea in the region of the Polar Front (74.8°-76.2° N) in a layer of 0-50 m. The region under study encompassed surface Arctic water and Atlantic water of the Fram branch (which conditionally corresponds to the Arctic water mass) divided from the Atlantic water mass by the Polar Front. Phytoplankton community on both sides of the front were represented by early spring complex, 90% of biomass was formed by diatoms (Achnanthes taeniata, Nitzschia grunowii, Thalassiosira antarctica). In water of Atlantic origin Phaeocystis pouchetii were found among the dominants. However, the level of development of microplankton was significantly higher in water from the Arctic Basin. The highest chlorophyll-a concentrations referred to surface Arctic water (3.13±0.43 mg/m3) and Atlantic Fram water (2.04±0.29 mg/m3). The concentration of chlorophyll-a at the stations performed in the Atlantic water mass was an order of magnitude lower - 0.50±0.26 mg/m3. Thus, during the early-spring period, the Polar Front is a powerful boundary that limits exclusively the level of development and quantitative indicators of the early spring microphytoplankton complex. The front line separates the more productive Arctic water, with average chlorophyll-a concentrations of 2-3 mg/m3, from the Atlantic water, in which concentrations of this pigment are an order of magnitude lower.
Analysis of antioxidation activity for the small molecular biomass extracted from the waste of resources
Authors: Chung T-W , Wang M-Y , Chen M-T 
Published: January 2020

Abstract
The waste of peanut press cake from oil mill was powdered and used as the feedstock to extract the protein and the extract solution was further hydrolysed by using an enzyme mixture of alcalase and flavourzyme. The peanut protein was become the smaller molecules after enzymatic hydrolysis and the antioxidation activities were analysed by using experimental design. The response surface methodology was applied to analyse the parameters and the interaction between parameters of the enzymatic hydrolysis process for the variation of antioxidation activities of the small molecular protein. On the basis of the experimental results, the optimum responses of antioxidation activities were obtained as the DPPH free radical scavenging ability of 76.85%, reducing power (absorbance value) of 0.1 Abs, and Ferrous ion (Fe2+) chelating ability of 17.19% under the operating parameters in solid-liquid ratio of 1:10, enzyme concentration of 10%, and hydrolysis time of 8 hr.
Co-sorption of sulfamethoxazole and Cu onto several soils with different properties and their binding mechanism
Authors: Shao Yifei , Liu Xijuan , Liu Aiju , Dong Yuanpeng , Hu Xinxin 
Published: January 2020

Abstract
The present study aims to investigate the co-sorption characteristic of Sulfamethoxazole (SMX) and Cu(II) onto two typical soils with different properties in China. The sorption of SMX and Cu(II) onto soil is carried out by batch method. The results indicated that Cu(II) co-presence significantly increased SMX adsorption on Black soils, but decreased SMX adsorption on Brown soils. The further kinetic models fitting found, however, that Cu(II) co-presence had little effect on the sorption process of SMX onto soils. The co-sorption of SMX and Cu(II) on soil mineral surface was confirmed by the X-ray photoelectron spectroscopy and Energy Spectrum Analysis based on the variation of elemental bonding energy after adsorption. The further Infrared Spectrometric Analysis proved that SMX and Cu(II) were bonded on soil mineral surface by coordination of Cu(II) with the N reactive groups of SMX. Finally, in view of the different sorption of SMX on Brown and Black soils after Cu(II) addition, it could conclude that the coordination is not favourable to SMX adsorption onto soil mineral phases.
Research on building energy efficiency based on energyplus software
Authors: Zhang Junxue 
Published: January 2020

Abstract
Energyplus is an important software in the field of building energy efficiency, which can accurately simulate building energy consumption. By comparing simulated situation of building energy consumption with actual usage of energy, the energy consumption can be shown in some buildings so as to optimize the building energy efficiency, especially for promoting the thermal performance of buildings. This paper utilizes the building energy simulated software-EnergyPlus to simulate the energy consumption of the dormitory of Southeast University so as to verify the key factors of building energy consumption.
Impact of Lymphovascular Invasion on Survival Outcome in Patients With Gastric Cancer
Authors: Mei Di , Zhao Bochao , Zhang Jiale , Luo Rui , Lu Huiwen , Xu Huimian , Huang Baojun 
Published: January 2020

Abstract

Objectives
To evaluate the prognostic significance of lymphovascular invasion (LVI) for patients with gastric cancer (GC).

Methods
A total of 1,720 consecutive patients who underwent curative gastrectomy were retrospectively identified. The association between LVI and clinicopathologic characteristics was determined and its impact on survival outcome was evaluated.

Results
LVI was detected in 21.3% of GC patients, 5.9% of patients with early GC, 24.0% of patients with advanced GC, and 6.7% of node-negative patients using H&E staining. Tumor size (odds ratio [OR], 1.509; 95% confidence interval [CI], 1.159-1.965; P &lt; .01), differentiated type (OR, 1.817; 95% CI, 1.377-2.398; P &lt; .001), and the depth of tumor invasion (OR, 3.011; 95% CI, 2.174-4.171; P &lt; .001) were independent predictive factors for LVI. LVI-positive patients have a poorer prognosis than LVI-negative patients, irrespective of tumor stage or lymph node metastasis. LVI was an independent prognostic factor for patients with GC (hazard ratio, 1.299; 95% CI, 1.112-1.518; P &lt; .001).

Conclusions
LVI provided additional prognostic information for GC patients, and LVI-positive patients should be considered candidates for adjuvant chemotherapy.
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
Authors: Czech Lucas , Barbera Pierre , Stamatakis Alexandros 
Published: January 2020

Abstract

Summary
We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven.

Availability and implementation
Both genesis and gappa are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa.

Supplementary information
Supplementary data are available at Bioinformatics online.
FTIP: an accurate and efficient method for global protein surface comparison
Authors: Zhang Yuan , Sui Xing , Stagg Scott , Zhang Jinfeng 
Published: January 2020

Abstract

Motivation
Global protein surface comparison (GPSC) studies have been limited compared to other research works on protein structure alignment/comparison due to lack of real applications associated with GPSC. However, the technology advances in cryo-electron tomography (CET) have made methods to identify proteins from their surface shapes extremely useful.

Results
In this study, we developed a new method called Farthest point sampling (FPS)-enhanced Triangulation-based Iterative-closest-Point (ICP) (FTIP) for GPSC. We applied it to protein classification using only surface shape information. Our method first extracts a set of feature points from protein surfaces using FPS and then uses a triangulation-based efficient ICP algorithm to align the feature points of the two proteins to be compared. Tested on a benchmark dataset with 2329 proteins using nearest-neighbor classification, FTIP outperformed the state-of-the-art method for GPSC based on 3D Zernike descriptors. Using real and simulated cryo-EM data, we show that FTIP could be applied in the future to address problems in protein identification in CET experiments.

Availability and implementation
Programs/scripts we developed/used in the study are available at http://ani.stat.fsu.edu/∼yuan/index.fld/FTIP.tar.bz2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Unifying the Basic Models of Ecology to Be More Complete and Easier to Teach
Authors: Lehman Clarence , Loberg Shelby , Clark Adam T , Schmitter Daniel 
Published: January 2020

Abstract
Population and basic community ecology are commonly presented to students through a set of distinct models, such as those for exponential growth, logistic growth, competition, predation, and so forth. This approach mirrors the historical development of the field, but it has several shortcomings as a way to present ecological theory. First, the classical equations can appear disconnected from one another. Second, differences in the parameters and styles of the equations do not lend themselves to comparison in a common graphical form. And third, the set of equations as they are commonly presented provides no easy way to see whether any concepts are left out. In fact, something is left out that is not commonly taught: the concept of faster-than-exponential growth approaching a singularity, which is important for understanding rapidly growing systems. In the present article, we demonstrate a unified approach that simplifies the traditional equations of ecology, expands their scope, and emphasizes their interconnections.
Impaired theta phase coupling underlies frontotemporal dysconnectivity in schizophrenia
Authors: Adams Rick A , Bush Daniel , Zheng Fanfan , Meyer Sofie S , Kaplan Raphael , Orfanos Stelios , Marques Tiago Reis , Howes Oliver D , Burgess Neil 
Published: January 2020

AbstractFrontotemporal dysconnectivity is a key pathology in schizophrenia. The specific nature of this dysconnectivity is unknown, but animal models imply dysfunctional theta phase coupling between hippocampus and medial prefrontal cortex (mPFC). We tested this hypothesis by examining neural dynamics in 18 participants with a schizophrenia diagnosis, both medicated and unmedicated; and 26 age, sex and IQ matched control subjects. All participants completed two tasks known to elicit hippocampal-prefrontal theta coupling: a spatial memory task (during magnetoencephalography) and a memory integration task. In addition, an overlapping group of 33 schizophrenia and 29 control subjects underwent PET to measure the availability of GABAARs expressing the α5 subunit (concentrated on hippocampal somatostatin interneurons). We demonstrate—in the spatial memory task, during memory recall—that theta power increases in left medial temporal lobe (mTL) are impaired in schizophrenia, as is theta phase coupling between mPFC and mTL. Importantly, the latter cannot be explained by theta power changes, head movement, antipsychotics, cannabis use, or IQ, and is not found in other frequency bands. Moreover, mPFC-mTL theta coupling correlated strongly with performance in controls, but not in subjects with schizophrenia, who were mildly impaired at the spatial memory task and no better than chance on the memory integration task. Finally, mTL regions showing reduced phase coupling in schizophrenia magnetoencephalography participants overlapped substantially with areas of diminished α5-GABAAR availability in the wider schizophrenia PET sample. These results indicate that mPFC-mTL dysconnectivity in schizophrenia is due to a loss of theta phase coupling, and imply α5-GABAARs (and the cells that express them) have a role in this process.
Stable Encoding of Visual Cues in the Mouse Retrosplenial Cortex
Authors: Powell Anna , Connelly William M , Vasalauskaite Asta , Nelson Andrew J D , Vann Seralynne D , Aggleton John P , Sengpiel Frank , Ranson Adam 
Published: January 2020

Abstract
The rodent retrosplenial cortex (RSC) functions as an integrative hub for sensory and motor signals, serving roles in both navigation and memory. While RSC is reciprocally connected with the sensory cortex, the form in which sensory information is represented in the RSC and how it interacts with motor feedback is unclear and likely to be critical to computations involved in navigation such as path integration. Here, we used 2-photon cellular imaging of neural activity of putative excitatory (CaMKII expressing) and inhibitory (parvalbumin expressing) neurons to measure visual and locomotion evoked activity in RSC and compare it to primary visual cortex (V1). We observed stimulus position and orientation tuning, and a retinotopic organization. Locomotion modulation of activity of single neurons, both in darkness and light, was more pronounced in RSC than V1, and while locomotion modulation was strongest in RSC parvalbumin-positive neurons, visual-locomotion integration was found to be more supralinear in CaMKII neurons. Longitudinal measurements showed that response properties were stably maintained over many weeks. These data provide evidence for stable representations of visual cues in RSC that are spatially selective. These may provide sensory data to contribute to the formation of memories of spatial information.
Clinical Features of Human Metapneumovirus-Associated Community-acquired Pneumonia Hospitalizations
Authors: Howard Leigh M , Edwards Kathryn M , Zhu Yuwei , Grijalva Carlos G , Self Wesley H , Jain Seema , Ampofo Krow , Pavia Andrew T , Arnold Sandra R , McCullers Jonathan A , Anderson Evan J , Wunderink Richard G , Williams Derek J 
Published: January 2020

Abstract

Background
Human metapneumovirus (HMPV) is a leading cause of respiratory tract infections. Few studies have compared the clinical characteristics and severity of HMPV-associated pneumonia with other pathogens.

Methods
Active, population-based surveillance was previously conducted for radiographically confirmed, community-acquired pneumonia hospitalizations among children and adults in 8 United States hospitals. Clinical data and specimens for pathogen detection were systematically collected. We described clinical features of all HMPV-associated pneumonia and, after excluding codetections with other pathogen types, we compared features of HMPV-associated pneumonia with other viral, atypical, and bacterial pneumonia and modeled the severity (mild, moderate, and severe) and length of stay using multivariable proportional odds regression.

Results
HMPV was detected in 298/2358 (12.6%) children and 88/2320 (3.8%) adults hospitalized with pneumonia and was commonly codetected with other pathogens (125/298 [42%] children and 21/88 [24%] adults). Fever and cough were the most common presenting symptoms of HMPV-associated pneumonia and were also common symptoms of other pathogens. After excluding codetections in children (n = 1778), compared to HMPV (reference), bacterial pneumonia exhibited increased severity (odds ratio [OR], 3.66; 95% confidence interval [CI], 1.43–9.40), respiratory syncytial virus (RSV; OR, 0.76; 95% CI, .59–.99) and atypical (OR, 0.39; 95% CI, .19–.81) infections exhibited decreased severity, and other viral pneumonia exhibited similar severity (OR, 0.88; 95% CI, .55–1.39). In adults (n = 2145), bacterial (OR, 3.74; 95% CI, 1.87–7.47) and RSV pneumonia (OR, 1.82; 95% CI, 1.32–2.50) were more severe than HMPV (reference), but all other pathogens had similar severity.

Conclusions
Clinical features did not reliably distinguish HMPV-associated pneumonia from other pathogens. HMPV-associated pneumonia was less severe than bacterial and adult RSV pneumonia, but was otherwise as or more severe than other common pathogens.