bluuebunny/crossref_metadata_2025_split huggingface dataset:
Communities Structure of Fish in Some Mangrove Ecosystem as a Result of the Restoration in Southern Beach of Malang, East Java Indonesia
Authors: Ridlo Irham Ahsanul , Kurniawan Nia , Retnaningdyah Catur 
Published: October 2020

Abstract
The change of function of mangrove ecosystem land for other purposes and logging can affect the community structure of aquatic biota, especially fish. The research objective was to determine the community structure and diversity of fish species in the mangrove ecosystem as result of restoration activity in the southern beach of Malang. Sampling were done in mangrove ecosystem of Bajulmati, Clungup, Kondang Buntung, Tamban, and Sendiki which have different restoration time. Fish sampling methods used net sampling and visual encounters. The results of fish sampling then be used to determined taxa richness, total abundance and indices of dominance, evenness, and diversity. The research results indicated that we found eight fish species in all location with different taxa richness at each location. Total of fish abundance in the range between 51-744 individu/100m2. Periopthalmus and Oryzias javanicus can be found at all of research location. Based on the value of the Diversity Index of fish in the research location, we found that mangrove ecosystem in the southern beach Malang had low diversity index (less than 1) with high dominance index 0.4-0.9 and low of evenness value between 0.03-0.09. It is indicated that restoration of mangrove ecosystem in Malang Southern beach still unsuccessful
Metabolomic Profiles of Curcuma longa L and Cosmos caudatus Extracts and Their In-Silico Anti-cancer Activity
Authors: Safitri Anna , Putri Amila Safira , Octavianty Tri Dewi , Sari Dewi Ratih Tirto 
Published: October 2020

Abstract
The current work intends to analyze Curcuma longa L and Cosmos caudatus extracts using LC-HRMS study, their prospective anti-cancer activity was determined through in silico molecular-docking. Extraction of Curcuma longa L and C. caudatus was carried out first. The resulted extracts were analyzed using LC-HRMS, in the positive ion detection. Using LC-HRMS analysis, many compounds were identified in the both extracts. The target compounds for Curcuma longa L extract was curcumin, and lutein was the target compound for Cosmos caudatus. The 3D molecular structures of curcumin and lutein were downloaded from PubChem database. The protein target was caspase-8 and was retrieved from Protein Data Bank. Caspase-8 protein were docked to curcumin and lutein, performing at HEX 8.0 program and visualized using Discovery Studio v19.1.0.18287. Interaction of curcumin and lutein on caspase-8 showed different patterns. Hydrophobic interactions, formation of hydrogen bonds, and van der Waals forces were shown in the interactions between protein and ligands. The interaction between curcumin, lutein, and the mixture of lutein-curcumin resulted in the LD50 values of 2000 mg/kg, 10 mg/kg, and 2000 mg/kg, respectively. These suggest that not only curcumin and lutein, but also complex of curcumin-lutein might possess capacity as anti-cancer agents.
Effectiveness of The Provision of Snakehead Fish Nuggets and Colored Fruit Extracts to Blood Protein (Total Protein, Albumin, HB) in PLHIV
Authors: Ginta Siahaan 
Published: October 2020

Abstract
The problem of the high prevalence of HIV/ AIDS and its development in the world and in Indonesia is like the iceberg phenomenon. The discovery of HIV / AIDS cases in Dubai reached 1.8 million, of which 940,000 people died of AIDS. Meanwhile, in Indonesia, the discovery of new cases (2016) in Riau Province was around 6,885 cases, Jakarta had 35,947 cases, Papua reached 31,846 cases and North Sumatera had 7,890 cases. This study aims was to determine the effectiveness of the provision of snakehead fish nuggets and colored fruit extracts to blood proteins (total protein, albumin and hemoglobin) in people with HIV (PLHIV). This type of research was Quasi-Experimental with Pre and Post Test Design. This design allowed researchers to measure the differences in total protein, albumin and Hb in PLHIV before and after the intervention of the provision of snakehead fish nuggets and colored fruit extracts. This research was conducted for 22 days, while the sample selection used total sampling technique. The research location was carried out at Bahagia Social Rehabilitation Center of Medan. The results showed that there was an effect of the provision of snakehead fish nuggets and colored fruit extracts on total protein (p = 0.036), albumin levels (p = 0.000) and Hb levels (p = 0.001) in PLHIV. The conclusion of this study that there is a change in blood protein (total protein, albumin, Hb) in PLHIV after being given snakehead fish nuggets and colored fruit extracts.
Analysis of the effect of extracted yellow kepok banana peels (Musa paradisiaca l.) on the size and morphology of Enterococcus faecalis
Authors: Sutanti V , Fuadiyah D , Hidayat LH , Agnizarridlo T , Anggiarta K S 
Published: October 2020

Abstract
The treatment of pulp and periapical diseases often experience failure due to persistent infections in the pulp and periapical teeth. The dominant bacteria in pulp and periapical infections is Enterococcus faecalis. The use of antimicrobials has shifted to natural materials that have low toxicity, cheaper and have long-lasting properties. Yellow kepok banana peels have many antibacterial compounds such as flavonoids, tannins, alkaloids and easily found in Indonesia. The objective of this research was to determine the description of changes in the morphology and size of Enterococcus faecalis after giving the extract of Yellow kepok banana peels (Musa paradisiaca L) in vitro. The samples of the Yellow kepok banana peels extract with concentrations of 100%, 90%, 80%, 70%, 60% and control treatment were placed on wells with a coverslip. Each well was given BHI-B and Enterococcus faecalis. Coverslips at the 5 concentrations were coated using gold and photographed using a Scanning Electron Microscope (SEM). The photo results were then observed for the bacteria length and morphology. Data were analyzed with descriptive statistics. The average length of the bacteria given the extract increased, compared to the bacteria not given the extract. Meanwhile, the average width of the bacteria given the extract showed an uncertain change. The treated bacteria showed morphological changes in the form of blebs. In conclusion, extract of yellow kepok banana peels (Musa paradisiaca L.) provides an overview of the occurrence of changes in morphology and size of Enterococcus faecalis in vitro.
Synthesis and potential of skipjack tuna bone hydroxyapatite as bone tissue engineering biomaterial
Authors: Wardani S C , Sujuti H , Mustamsir E , Hapsari D N 
Published: October 2020

Abstract
Hydroxyapatite Caio(P04)e(OH)2 is an alloplast material that is used to increase bone regeneration. It can be synthesis by processing natural materials such as fish bones. The purpose of this study was to synthesize hydroxyapatite from natural resources skipjack tuna (Katsuwonus pelamis) bones with precipitation method. Then, characterize hydroxyapatite morfology with FESEM and its biocompatibility using the preosteoblast MC3T3-E1 cell line. Skipjack tuna bone was synthesized into hydroxyapatite through precipitation method. The morphology of hydroxyapatite sample was revealed with field-emission scanning microscope FESEM. While the constituent elements were analyzed using SEM EDAX. Biocompatibility of hydroxyapatite was tested using preosteoblast cell culture. Cells were treated with different hydroxyapatite concentration 200 μglml, 100 μglml and 5 &#x03BC;g/ml. After incubation with C02 5% at 37°C for 24h,48h and 72h the cultore was tested for viability using MTT Cell Viability Assay Kit. Results were reported as optical density. The study showed that skipjack tuna bone produced grain-shaped particles with almost uniform sizes. The surface material appears to be agglomerates and form pores in between. Weight percentages Ca/P ratio for hydroxyapatite from skipjack tuna bones is 1.94. MTT assay showed cell viability after 3 days. These results suggest that skipjack tuna bone hydroxyapatite is has potential as bone engineering biomaterial
Crystallization enhanced thermal-sensitive hydrogels of PCL-PEG-PCL triblock copolymer for 3D printing
Authors: Cui Yuecheng , Jin Ronghua , Zhou Yang , Yu Meirong , Ling Yun , Wang Li-Qun 
Published: October 2020

Abstract
Temperature-sensitive hydrogels with mild gel-forming process, good biocompatibility and biodegradability have been widely studied as bioinks and biomaterial inks for 3D bioprinting. However, the hydrogels synthesized via copolymerization of aliphatic polyesters and polyethylene glycols have low mechanical strength and cannot meet the needs of 3D printing. In this paper, we propose a strategy of enhancing the strength of hydrogels by introducing crystallization between blocks to meet the requirements of 3D bioprinting inks. A series of polycaprolactone-polyethylene glycol-polycaprolactone (PCL-PEG-PCL) triblock polymers were prepared by ring-opening polymerization, of which the strong crystallinity of polycaprolactone blocks improved the printability and enhanced the mechanical properties of the ink. It was found that the resulted hydrogels were temperature-responsive, and the PCL blocks could form a crystalline phase in the state of the hydrogel, thereby significantly increasing the modulus of the hydrogel. Moreover, the mechanical strength of the hydrogel could be adjusted by changing the composition ratio of each block of the copolymer. The 3D printing results showed that the PCL-PEG-PCL hydrogel with crystallinity can not only be extruded and printed via temperature adjustment, but also the three-dimensional structure can be effectively maintained after 3D printing. The gels demonstrated good cell compatibility, and the cell survival rate was maintained at a high level.
Corrigendum: The Study of Primary Tin Mineralization in Tsk. Pengarem, Southern Bangka Island. (IOP Conf. Series: Earth and Environmental Science 375 (2019) 012008)
Authors: Franto  , Pramumijoyo Subagyo , Setijadji Lucas Donny 
Published: October 2020

Published on October 20, 2020

The revision I proposed is just adding a reference that missing:

1. In the Abstract section, the following text appears:

“The typical tin mineralization in this site was mineralization in gozzan unit, and was the result of supergene process carried by mineral cassiterite that associated with minerals iron oxide such as ilmenite and goethite”.

2. In type of alteration, point 7:

“Muscovitization is hydrothermal alteration process that characterized by the presence of the mica mineral accumulation such as muscovite that associated with minerals that compiling the intrusion body such as biotite, feldspar, and plagioclase”.

3. In the typical deposits, point h. metasomatism:

“This deposit is formed by precipation process that comes from sodium chloride liquid that is rich with metal elements (syssedimentary) that formed in the edge of the alteredgranitoidafter hydrothermal alteration”.

This should read:

1. In the Abstract section:

“The typical tin mineralization in this site was mineralization in gozzan unit, and was the result of supergene process carried by mineral cassiterite that associated with minerals iron oxide such as ilmenite and goethite” [1].
2. In type of alteration, point 7:

“Muscovitization is hydrothermal alteration process that characterized by the presence of the mica mineral accumulation such as muscovite that associated with minerals that compiling the intrusion body such as biotite, feldspar, and plagioclase” [1].
3. In the typical deposits, point h. metasomatism:

“This deposit is formed by precipation process that comes from sodium chloride liquid that is rich with metal elements (syssedimentary) that formed in the edge of the alteredgranitoidafter hydrothermal alteration” [1].
Thus, I just add one reference that I missed:
[1] Rahman, M.F.A., 2016, Studi Geologi, Alterasi dan Tipe Mineralisasi Pada Endapan Timah Primer Daerah Paku, Air Semut Dan Payung, Kecamatan Payung, Kabupaten Bangka Selatan, Skripsi, Fakultas Teknik, Departemen Teknik Geologi, Universitas Gadjah Mada, Yogyakarta.
3D printed micro-chambers carrying stem cell spheroids and pro-proliferative growth factors for bone tissue regeneration
Authors: Lee Jinkyu , Seok Ji Min , Huh Seung Jae , Byun Hayeon , Lee Sangmin , Park Su A , Shin Heungsoo 
Published: October 2020

Abstract
Three-dimensional (3D)-printed scaffolds have proved to be effective tools for delivering growth factors and cells in bone-tissue engineering. However, delivering spheroids that enhance cellular function remains challenging because the spheroids tend to suffer from low viability, which limits bone regeneration in vivo. Here, we describe a 3D-printed polycaprolactone micro-chamber that can deliver human adipose-derived stem cell spheroids. An in vitro culture of cells from spheroids in the micro-chamber exhibited greater viability and proliferation compared with cells cultured without the chamber. We coated the surface of the chamber with 500 ng of platelet-derived growth factors (PDGFs), and immobilized 50 ng of bone morphogenetic protein 2 (BMP-2) on fragmented fibers, which were incorporated within the spheroids as a new platform for a dual-growth-factor delivery system. The PDGF detached from the chamber within 8 h and the remains were retained on the surface of chamber while the BMP-2 was entrapped by the spheroid. In vitro osteogenic differentiation of the cells from the spheroids in the micro-chamber with dual growth factors enhanced alkaline phosphatase and collagen type 1A expression by factors of 126.7 ± 19.6 and 89.7 ± 0.3, respectively, compared with expression in a micro-chamber with no growth factors. In vivo transplantation of the chambers with dual growth factors into mouse calvarial defects resulted in a 77.0 ± 15.9% of regenerated bone area, while the chamber without growth factors and a defect-only group achieved 7.6 ± 3.9% and 5.0 ± 1.9% of regenerated bone areas, respectively. These findings indicate that a spheroid-loaded micro-chamber supplied with dual growth factors can serve as an effective protein-delivery platform that increases stem-cell functioning and bone regeneration.
Induced anisotropic superconductivity in ionic liquid cation intercalated 1T-SnSe2
Authors: Rousuli Awabaikeli , Zhang Haoxiong , Zhang Kenan , Zhong Haoyuan , Feng Runfa , Wu Yang , Yu Pu , Zhou Shuyun 
Published: October 2020

Abstract
The weak van der Waals interaction between adjacent layers of quasi-two-dimensional materials provides opportunities for inserting intercalants to induce novel properties distinct from the host materials. Here we report induced superconductivity in an intercalated SnSe2 crystal by using a new type of intercalants—organic cations from ionic liquids, [C2MIm]+ and [DEMB]+. The intercalation of both cations increases the interlayer spacing and leads to induced superconductivity with T

c
of 7.1 and 6.9 K and a large superconducting anisotropy. Angle-resolved photoemission spectroscopy and Hall measurements reveal the importance of electron doping by the cations in the induced superconductivity, and the interlayer expansion and electric polarization of the cations in the large anisotropy. Our work reports induced superconductivity in an intercalated material with new intercalants which contribute both charge carriers and interlayer expansion, and provides a new pathway to the manipulation of superconductivity in layered materials.
Breakdown signatures of the phenomenological Lindblad master equation in the strong optomechanical coupling regime
Authors: Betzholz Ralf , Taketani Bruno G , Torres Juan Mauricio 
Published: October 2020

Abstract
The Lindblad form of the master equation has proven to be one of the most convenient ways to describe the impact of an environment interacting with a quantum system of interest. For single systems the jump operators characterizing these interactions usually take simple forms with a clear interpretation. However, for coupled systems these operators take significantly different forms and the full dynamics cannot be described by jump operators acting on the individual subsystems only. In this work, we investigate the differences between a common phenomenological model for the master equation and the more rigorous dressed-state master equation for optomechanical systems. We provide an analytical method to obtain the absorption spectrum of the system for both models and show the breakdown of the phenomenological model in both the bad cavity and the ultra-strong coupling limit. We present a careful discussion of the indirect dephasing of the optical cavity in both models and its role in the differences of their predicted absorption spectra. Our work provides a simple experimental test to determine whether the simpler phenomenological model can be used to describe the system and is a step forward toward a better understanding of the role of the coupling between subsystems for open-quantum-system dynamics.
Neighbourhood walkability and physical activity: moderating role of a physical activity intervention in overweight and obese older adults with metabolic syndrome
Authors: Colom Antoni , Mavoa Suzanne , Ruiz Maurici , Wärnberg Julia , Muncunill Josep , Konieczna Jadwiga , Vich Guillem , Barón-López Francisco Javier , Fitó Montserrat , Salas-Salvadó Jordi , Romaguera Dora 
Published: October 2020

Abstract

Background
While urban built environments might promote active ageing, an infrequently studied question is how the neighbourhood walkability modulates physical activity changes during a physical activity intervention programme in older adults. We assessed the influence of objectively assessed neighbourhood walkability on the change in physical activity during the intervention programme used in the ongoing PREvención con DIeta MEDiterránea (PREDIMED)-Plus trial.

Method
The present study involved 228 PREDIMED-Plus senior participants aged between 55 and 75, recruited in Palma de Mallorca (Spain). Overweight/obese older adults with metabolic syndrome were randomised to an intensive weight-loss lifestyle intervention or a control group. A walkability index (residential density, land use mix, intersections density) was calculated using geographic information systems (1 km sausage-network buffer). Physical activity was assessed using accelerometer and a validated questionnaire, at baseline and two follow-up visits (6-months and 1-year later). Generalised additive mixed models were fitted to estimate the association between the neighbourhood walkability index and changes in physical activity during follow-up.

Results
Higher neighbourhood walkability (1 z-score increment) was associated with moderate-to-vigorous accelerometer assessed physical activity duration, (β = 3.44; 95% CI = 0.52; 6.36 min/day). When analyses were stratified by intervention arm, the association was only observed in the intervention group (β = 6.357; 95% CI = 2.07;10.64 min/day) (P for interaction = 0.055).

Conclusions
The results indicate that the walkability of the neighbourhood could support a physical activity intervention, helping to maintain or increase older adults’ physical activity.
Parallel Assessment Challenges in Nutritional and Sleep Epidemiology
Authors: Dunietz Galit Levi , Jansen Erica C , Hershner Shelley , O’Brien Louise M , Peterson Karen E , Baylin Ana 
Published: October 2020

Abstract
Sleep has been consistently linked to health outcomes in clinical studies, but only in recent years has sleep become a focus in epidemiologic studies and public health. In particular, the sizable prevalence of insufficient sleep in the population warrants well-designed epidemiologic studies to examine its impact on public health. As a developing field, sleep epidemiology encounters methodological challenges similar to those faced by nutritional epidemiology research. In this article, we describe a few central challenges related to assessment of sleep duration in population-based studies in comparison with measurement challenges in nutritional epidemiology. In addition, we highlight 3 strategies applied in nutritional epidemiology to address measurement challenges and suggest ways these strategies could be implemented in large-scale sleep investigations.
Associations Between Self- and Informant-Reported Abilities of Instrumental Activities of Daily Living and Cognitive Functions in Older Adults With Mild Cognitive Impairment
Authors: Zhao Xin , Liang Wenjia , Maes Joseph H R 
Published: October 2020

Abstract

Objective
Older adults (OAs) with mild cognitive impairment (MCI) show disabilities in instrumental activities of daily living (IADLs), which have been linked to compromised cognitive functioning. However, it is unclear which cognitive functions are primarily involved. The present study sought to identify the cognitive function(s) most strongly associated with the IADL limitations in MCI.

Method
OAs with MCI (N = 120) completed cognitive tasks measuring general cognitive processing speed, working memory (WM) maintenance and updating, inhibition, and shifting ability. IADL abilities were assessed through both self- and informant reports.

Results
Self-reported IADL abilities were positively associated with both cognitive processing speed and WM updating capacity. Informant-reported IADL abilities were also positively associated with processing speed and WM updating, in addition to cognitive shifting ability.

Conclusion
Both general processing speed and WM updating capacity were consistently predictive of IADL abilities. These results might inform the design of training programs aimed at maintaining or improving functional independence in individuals with MCI to focus more on these cognitive functions. However, the strength of the association between specific cognitive functions and IADL abilities in OAs with MCI depends on the source of the information about the IADL abilities, which highlights the need for gathering data from both the examinee and informants.
TreeMap: a structured approach to fine mapping of eQTL variants
Authors: Liu Li , Chandrashekar Pramod , Zeng Biao , Sanderford Maxwell D , Kumar Sudhir , Gibson Greg 
Published: October 2020

Abstract

Motivation
Expression quantitative trait loci (eQTL) harbor genetic variants modulating gene transcription. Fine mapping of regulatory variants at these loci is a daunting task due to the juxtaposition of causal and linked variants at a locus as well as the likelihood of interactions among multiple variants. This problem is exacerbated in genes with multiple cis-acting eQTL, where superimposed effects of adjacent loci further distort the association signals.

Results
We developed a novel algorithm, TreeMap, that identifies putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. Guided by the hierarchical structure of linkage disequilibrium, TreeMap performs an organized search for individual and multiple causal variants. Via extensive simulations, we show that TreeMap detects co-regulating variants more accurately than current methods. Furthermore, its high computational efficiency enables genome-wide analysis of long-range eQTL. We applied TreeMap to GTEx data of brain hippocampus samples and transverse colon samples to search for eQTL in gene bodies and in 4 Mbps gene-flanking regions, discovering numerous distal eQTL. Furthermore, we found concordant distal eQTL that were present in both brain and colon samples, implying long-range regulation of gene expression.

Availability and implementation
TreeMap is available as an R package enabled for parallel processing at https://github.com/liliulab/treemap.

Supplementary information
Supplementary data are available at Bioinformatics online.