bluuebunny/crossref_metadata_2025 huggingface dataset:
Elinvar effect in β-Ti simulated by on-the-fly trained moment tensor potential
Authors: Shapeev Alexander V , Podryabinkin Evgeny V , Gubaev Konstantin , Tasnádi Ferenc , Abrikosov Igor A
Published: October 2020

A combination of quantum mechanics calculations with machine learning techniques can lead to a paradigm shift in our ability to predict materials properties from first principles. Here we show that on-the-fly training of an interatomic potential described through moment tensors provides the same accuracy as state-of-the-art ab initio molecular dynamics in predicting high-temperature elastic properties of materials with two orders of magnitude less computational effort. Using the technique, we investigate high-temperature bcc phase of titanium and predict very weak, Elinvar, temperature dependence of its elastic moduli, similar to the behavior of the so-called GUM Ti-based alloys (Sato et al 2003 Science
300 464). Given the fact that GUM alloys have complex chemical compositions and operate at room temperature, Elinvar properties of elemental bcc-Ti observed in the wide temperature interval 1100–1700 K is unique.
Genetic differences and population structure of spotted barb (cyprinidae) collected from three rivers in Java Island
Authors: Astuti S S , Hariati A M , Kusuma W E , Wiadnya D G R
Published: October 2020

Barbodes binotatus is an endemic species and most dominant freshwater fish in Indonesia. This prelilinary study aimed to calculate genetic differences of the species from three different rivers in Java island. A total of 90 specimens were collected from each river and a total of 26 sequences were analyzed using mitochondrial DNA (mtDNA) region Cytochrome Oxidase Subunit I (COI). BLAST analysis showed > 97 % similarity of B. binotatus with another research. The result of sequence analysis showed that B. binotatus from Central Java were not significantly different from B. binotatus from East Java, and B. binotatus from West Java were significantly different from two others. The genetic differences of B. binotatus from three locations were observed in five basepair (335 bp, 399 bp,449 bp, 497 bp, and 545 bp). The result of population structure analysis showed an FST value of 1.00. It suggested that there was genetic differentiation between populations of Pasuruan, Yogyakarta and Cirebon. Inter-location analysis requires to be done to confirm the genetic differences from another regions.
Factor Analysis of Lipid Profile in Early Adulthood with Inappropriate Food Consumption Habit: Screening Approach Dyslipidemia Induce Atherogenesis Acceleration
Authors: Kumboyono K , Cesa F Y , Wihastuti T A , Nurwidyaningtyas W
Published: October 2020

Dyslipidemia is a risk factor for cardiovascular disease through atherogenesis induction. The productive age of early adulthood today has different eating habits in relation to increasing culinary lifestyles and food hunter habits. In general, dyslipidemia rarely causes early phase symptoms. We suspect that there is an increase in the group with impaired lipid profiles related to dietary habits that do not pay attention to the essential needs of eating. The collected serum was carried out using a venous puncture procedure on 45 early adult subjects (men n = 9; women n = 36) aged 19-27 years in Malang City. The lipids were analysed for lipid profiles including TC, TG, HDL-c, and LDL-c. The results of men respondents showed higher differences in the lipid profiles of TC (p = 0.000), TG (p = 0.001), and LDL (p = 0.000) than women while HDL-c levels (p = 0.010) in women had higher differences than men. Dumpling (contains noodles and beef) has positive correlation with TG, TC, and LDL. At least in this study, we found that men in early adult had a higher lipid profile compared to women. This is of course related to diet have an impact on increasing lipid levels. For this reason, it is advisable to maintain a more productive eating habits to reduce the risk of dyslipidemia.
A Comparative Study on Nutritional Value of Purple Sweet Potatoes from West Java and Central Java, Indonesia
Authors: Kurnianingsih Nia , Ratnawati Retty , Nazwar Tommy Alfandy , Ali Mulyohadi , Fatchiyah Fatchiyah
Published: October 2020

This study aimed to compare the nutritional value of two local cultivars of purple sweet potatoes from West Java and Central Java Indonesia. The proximate analysis was conducted to investigating the percentage of protein, carbohydrate, ash, water, total fat, total energy and energy from fat. Amino acid analysis was conducted using Ultra Performance Liquid Chromatography except the tryptophan by High Performance Liquid Chromatography. West Java cultivar were relatively higher content of carbohydrate, ash, total fat and total energy than Central Java cultivar. Central Java cultivar relatively higher protein and amino acid content. The three highest amino acids in Central Java cultivar were aspartate 2550.2 mg/kg, glutamic acid 1711.9 mg/kg and leucine 1127.8 mg/kg. Meanwhile, the three highest from West Java cultivar were aspartate 1214.8 mg/kg, glutamic acid 1177.8 mg/kg, and phenylalanine 667.9 mg/kg. Methionine was detected as the lowest amino acid in Central Java cultivar and were not detected in West Java cultivar. We assumed that Central Java cultivar have better protein and amino acid content than West Java cultivar. Further study is required to explore the nutrition benefit of both cultivars.
Effect of temperature and pH combination on vegetative cell growth of Bacillus megaterium
Authors: Mahariawan I M D , Kusuma W E , Yuniarti A , Hariati A M
Published: October 2020

B. megaterium is a potential bacterial species to be recommended as a probiotic which has been tested to have beneficial effects for fish. Vegetative cells availability is not only influenced by culture media composition but is also affected by environmental conditions such as temperature and pH. The purpose of this study was to determine the effect of temperature and pH combination on vegetative cell production and growth rate of B. megaterium. This study used a combination of temperature treatment (37, 44 and 51 °C) and pH (4, 7 and 10) to produce B. megaterium planted in wheat flour (Triticum aestivum) media. Results showed that the highest vegetative density was found at 37 °C and pH of 10 as much as 11 x 108 cells. mL−1 with a growth rate of 0.65 hour−1. In addition, the morphology of bacteria from this study presented the length and width of B. megaterium at 2.44 – 3.82 µm and 1.11 – 1.31 µm, respectively.
The Two Peptides Fragments of Goat Milk CSN1S2 Protein Blocked Insulin Receptor to Interact Ligand: In Silico Study
Authors: Pertiwi Kadita Octavia , Fatchiyah Fatchiyah
Published: October 2020

Insulin is a hormone that plays important role for tissue development and glucose homeostasis, it has significant implications for many chronic diseases, especially diabetes mellitus (DM). Alpha casein S2 (CSN1S2) isolated from Ethawah goat’s milk has eight peptides residue contain seven to twelve amino acid residues and has multiple functions, such as antimicrobial, immunomodulatory, and anti-oxidant. The purpose of this study is to observe the interaction between CSN1S2 protein peptides and Insulin Receptor. 3-D structure of Insulin Receptor is done by accessing RCSB PDB (ID: 4ZXB), protein was prepared using Discovery Studio BIOVIA 2019 and ligands were prepared using PyRx. Insulin receptor was docked to CSN1S2 protein peptides using HEX 8.0 software and visualized using Discovery Studio BIOVIA 2019. The results of this study showed different binding patterns, most of the chemistry bond were resulted between protein and ligands interaction are hydrogen bonds and electrostatic, the binding energy of CSN1S2 fragment 41-47 and fragment 214-221 to insulin receptor are -186.9 kJ/mol and -172.7 kJ/mol respectively. The caprine CSN1S2 protein peptides have ability to be used as therapeutic agents, such as DM because they can bind to specific sites of the insulin receptor and may reduce the insulin resistance mechanism.
Nutrient content and endemic red fruit oil (Pandanus austrosinensis) fatty acid profile in Papua Indonesia
Authors: Renyaan A. W. A. , Suprayitno E , Aulani’am  , Hariati A M
Published: October 2020

Pandanaceae clan red fruit of the in Papua and West Papua provinces, there are as many as 600 to 700 species. The research location was in the village of Bowi Subur (Settlement Unit VI/SP VI) Masni District Manokwari Regency. This study aims to determine the nutritional content and fatty acid profile found in the Menja cultivar red fruit oil (Pandanus austrosinensis), Edewewits and Mengkin. The nutritional levels of Pandanus austrosinensis, Edewewits, and Mengkin are as follows: the protein is the same at 0.04%, the highest fat in the Menja cultivar (Pandanus austrosinensis) is 99.35%; Mengkin cultivars 98.46%; and Edewewits 98.06%. Consecutive water levels of the Menja cultivars (Pandanus austrosinensis) by 0.71%, Edewewits by 0.46%, and Mengkin by 0.40%. The successive values of the Edewewits cultivar were 4.95 milliequivalents/1000 g, Pandanus austrosinensis were 4.91 mEq/kg, and the Mengkin cultivar was 2.96 milliequivalents/1000 g. The dominant fatty acid content; Menja cultivars (Pandanus austrosinensis): oleic acid 70.55%, palmiticic acid 10.45%; Edewewits cultivar: oalmitic acid 72.00%; Mengkin kutivar: oleic acid 63.76% and palmitic acid 16.56%.
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

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

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

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

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

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 μg/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

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

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

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

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

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

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

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

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.
Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach
Authors: Zhang Weiwei , Wu Hao , Li Ziyi
Published: October 2020

Motivation

It is a common practice in epigenetics research to profile DNA methylation on tissue samples, which is usually a mixture of different cell types. To properly account for the mixture, estimating cell compositions has been recognized as an important first step. Many methods were developed for quantifying cell compositions from DNA methylation data, but they mostly have limited applications due to lack of reference or prior information.

Results

We develop Tsisal, a novel complete deconvolution method which accurately estimate cell compositions from DNA methylation data without any prior knowledge of cell types or their proportions. Tsisal is a full pipeline to estimate number of cell types, cell compositions and identify cell-type-specific CpG sites. It can also assign cell type labels when (full or part of) reference panel is available. Extensive simulation studies and analyses of seven real datasets demonstrate the favorable performance of our proposed method compared with existing deconvolution methods serving similar purpose.

Availability and implementation

The proposed method Tsisal is implemented as part of the R/Bioconductor package TOAST at https://bioconductor.org/packages/TOAST.

Supplementary information

Supplementary data are available at Bioinformatics online.
SNHG5 inhibits the progression of EMT through the ubiquitin-degradation of MTA2 in oesophageal cancer
Authors: Wei Sisi , Sun Shiping , Zhou Xinliang , Zhang Cong , Li Xiaoya , Dai Suli , Wang Yaojie , Zhao Lianmei , Shan Baoen
Published: October 2020

A substantial fraction of transcripts are known as long noncoding RNAs (lncRNAs), and these transcripts play pivotal roles in the development of cancer. However, little information has been published regarding the functions of lncRNAs in oesophageal squamous cell carcinoma (ESCC) and the underlying mechanisms. In our previous studies, we demonstrated that small nucleolar RNA host gene 5 (SNHG5), a known lncRNA, is dysregulated in gastric cancer (GC). In this study, we explored the expression and function of SNHG5 in development of ESCC. SNHG5 was found to be downregulated in human ESCC tissues and cell lines, and this downregulation was associated with cancer progression, clinical outcomes and survival rates of ESCC patients. Furthermore, we also found that overexpression of SNHG5 significantly inhibited the proliferation, migration and invasion of ESCC cells in vivo and in vitro. Notably, we found that metastasis-associated protein 2 (MTA2) was pulled down by SNHG5 in ESCC cells using RNA pulldown assay. We also found that SNHG5 reversed the epithelial–mesenchymal transition by interacting with MTA2. In addition, overexpression of SNHG5 downregulated the transcription of MTA2 and caused its ubiquitin-mediated degradation. Thus, overexpression of MTA2 partially abrogated the effect of SNHG5 in ESCC cell lines. Furthermore, we found that MTA2 mRNA expression was significantly elevated in ESCC specimens, and a negative correlation between SNHG5 and MTA2 expression was detected. Overall, this study demonstrated, for the first time, that SNHG5-regulated MTA2 functions as an important player in the progression of ESCC and provide a new potential therapeutic strategy for ESCC.
Left brachial artery: one more way to percutaneous insertion of IMPELLA 2.5L circulatory support for high-risk percutaneous coronary intervention – a case report
Authors: Sganzerla Paolo , Cinelli Francesco , Capoferri Andrea , Rondi Mauro
Published: October 2020

Background

Percutaneous circulatory support allows the performance of coronary interventions in ever more complex anatomic and clinical situations. The large-bore systems currently available need a suitable vascular calibre to be inserted restricting percutaneous access mainly to the common femoral artery.

Case summary

We present the case of a 64-year-old man, admitted with an acute coronary syndrome and congestive heart failure, due to triple-vessel coronary artery disease with left main involvement and left ventricular dysfunction. He was successfully treated with percutaneous coronary intervention (PCI) supported through an IMPELLA 2.5L circulatory system. Concomitant severe and diffuse peripheral vascular disease did not allow femoral insertion of the circulatory support which was therefore successfully introduced through a left brachial percutaneous approach.

Discussion

To the best of our knowledge, this is the first report of a brachial, percutaneous placement of the IMPELLA 2.5L system to support a high-risk PCI procedure. In appropriately selected patients, this approach could be an option when common vascular accesses are not available.
Case report of severe PCR-confirmed COVID-19 myocarditis in a European patient manifesting in mid January 2020
Authors: Hudowenz Ole , Klemm Philipp , Lange Uwe , Rolf Andreas , Schultheiss Heinz-Peter , Hamm Christian , Müller-Ladner Ulf , Wegner Franz
Published: October 2020

Background

Viral genesis is the most common cause of myocarditis. COVID-19-associated myocarditis seems to be a notable extrapulmonary manifestation, which may result in the need for a different treatment. There has been no positive polymerase chain reaction (PCR) testing of SARS-CoV-2 in heart specimens, thus far.

Case summary

A 48-year-old male patient presented with fever, dyspnoea, and haemoptysis. Laboratory findings showed highly elevated inflammatory and cardiac damage markers. Thoracic computed tomography (CT) revealed bilateral, patchy peripheral ground-glass opacities with a crazy-paving pattern, focal consolidations, and mild pleural effusions. Cardiac imaging with echocardiography and magnetic resonance imaging (MRI) detected a reduced biventricular function. MRI additionally showed myocardial oedema and late gadolinium enhancement. Lung and heart biopsies were performed, revealing alveolitis with necrosis and acute lymphocytic myocarditis. Testing for usual cardiotropic viruses was negative, and no aspects of vasculitis or granuloma could be found. Due to fulfilling the criteria, the patient was diagnosed with rheumatic vasculitis. Treatment with cyclophosphamide and steroids was initiated. Later, the patient reported a history of travel to Tyrol in mid January. Consequently, PCR testing for SARS-CoV-2 was performed, which was positive in the heart specimen. Immunosuppressive treatment was discontinued. During a follow-up visit at the end of April, the patient’s recovery was stable.

Discussion

In COVID-19 infections, myocardial inflammation can be present as an extrapulmonary manifestation. Positive PCR testing confirms myocardial invasion of the virus. Imaging and laboratory studies correlate with the histopathological findings, and thus should be performed in COVID-19 patients who are suspicious for myocarditis. Supportive treatment with steroids may be useful in these patients.
A simple technique of artificial chordae implantation in robotic cardiac surgery using a novel tube device supporting expanded polytetrafluoroethylene chordae ligation
Authors: Tedoriya Takeo , Okano Ryoi , Fukuzumi Masaomi , Miyauchi Tadamasa
Published: October 2020

Artificial chordae implantation is an important technique for treating leaflet lesions in mitral valve repair. Considering that the expanded polytetrafluoroethylene (ePTFE) suture is slippery on the surface, adequate ligation without laxity should be critically considered, especially in robotic surgery. To resolve this issue, we applied a novel device that controls the length of an ePTFE suture (Chordarizer) for artificial chordae implantation in robotic mitral valve repair. After assessing the mitral valve via the right side of the left atrium, we stitched a CV-4 ePTFE suture to the target papillary muscle. Using a calliper, we measured the length of the artificial chordae and passed the CV-4 through the appropriate Chordarizer. Then, we stitched the CV-4 to the tip of the leaflet from the left ventricle side and tied it using da Vinci arms. Finally, the Chordarizer was peeled away. Chordarizer ensured safe and reliable artificial chordae implantation procedures with robotic mitral surgery, by maintaining the desired CV4 length.
In-hospital mortality and organ failure after open and endovascular thoraco-abdominal aortic surgery can be predicted by increased levels of circulating dipeptidyl peptidase 3
Authors: Gombert Alexander , Barbati Mohammad , Kotelis Drosos , Simon Tim-Philipp , Breuer Thomas , Hartmann Oliver , Santos Karine , Bergmann Deborah , Schulte Janin , Marx Gernot , Jacobs Michael , Stoppe Christian
Published: October 2020

OBJECTIVES

Endovascular and open thoraco-abdominal aortic aneurysm (TAAA) repair is associated with specific complications. Circulating dipeptidyl peptidase 3 (cDPP3) is a novel biomarker that shows a strong association with organ failure which has not been assessed in surgical settings. Therefore, the objective of this study was to assess the prognostic capabilities of cDPP3 for predicting patient survival and organ failure following open and endovascular TAAA repair.

METHODS

Thirty-three patients undergoing TAAA repair were assessed in this prospective observational single-centre study. cDPP3 levels were serially measured perioperatively until 72 h after admission to the intensive care unit (ICU). In-hospital mortality and any organ failure were the clinical end points.

RESULTS

Postoperative organ failure was detected in 17 patients (51.5%), and 6 patients died after surgery (18.2%). At 12 h after admission to the ICU, cDPP3 levels were significantly increased in patients who died or developed organ failure (P < 0.001). cDPP3 levels after surgery demonstrated a remarkable predictive accuracy for in-hospital mortality [12 h area under the receiver operating characteristic curve (AUC): 0.907 (P < 0.001), 24 h AUC: 0.815 (P = 0.016), 48 h AUC: 0.914 (P = 0.003)] and the development of organ failure [12 h AUC: 0.882 (P < 0.001), 24 h AUC: 0.850 (P < 0.001), 48 h AUC: 0.846 (P < 0.001)]. Additionally, a significant correlation between cDPP3, the sequential organ failure assessment score and procalcitonin, C-reactive protein and interleukin-6 levels (P < 0.001, P < 0.001, P = 0.011, P = 0.007, respectively) based on all available measurements and time points was observed.

CONCLUSIONS

The present findings highlight the role of cDPP3 as an early, highly specific postoperative biomarker for prediction of in-hospital mortality and organ failure after TAAA repair.
Cephalometry without complex dedicated postprocessing in an oriented magnetic resonance imaging dataset: a pilot study
Authors: März Karoline , Chepura Taras , Plewig Blanka , Haddad Daniel , Weber Daniel , Schmid Matthias , Hirschfelder Ursula , Gölz Lina
Published: October 2020

Objectives

Magnetic resonance imaging (MRI) enables a 3D-volume-imaging without ionizing radiation. Therefore, it was the aim of this study to present a post-processing-free method for cephalometric analysis of a MRI-dataset and to examine whether there is a significant difference between cephalometric analysis of conventional 2D cephalograms and MRI scans.

Methods

One MRI scan each was performed on three cadaver heads using a 3T-MR-scanner. Cephalometric analysis was conducted directly on the 3D dataset. All reference points were projected onto a virtual sagittal plane that was perpendicular to the Frankfort horizontal plane. Double-sided points were averaged. Cephalometric angles were measured from the projected points. Results were compared with cephalometric measurements on conventional lateral cephalometric radiographs (LCRs). The cephalometric analysis was performed by five raters.

Results

390-angle measurements were obtained. The inter-rater reliability was high [intraclass correlation coefficients (ICCs) ≥ 0.74 for all angles]. Differences between the measurements on the cephalograms and MRI scans ranged between –0.91° (–1.88°, 0.07°) and 0.97° (–0.63°, 2.57°) on average and were equivalent with respect to a margin of [–2°, 2°] in all angles except L1—Me-Tgo (Bonferroni-Holm-corrected P < 0.05 in all angles except L1—Me-Tgo). The best match was found for the SNA angle.

Conclusion

The clinical comparability of the MRI- and LCR-based cephalometry could be stated. Using MRI in orthodontics would reduce radiation exposure and the risk of stochastic radiation damage, which is of importance especially in younger patients.
Reducing Ageism With Brief Videos About Aging Education, Ageism, and Intergenerational Contact
Authors: Lytle Ashley , Macdonald Jamie , Apriceno MaryBeth , Levy Sheri R
Published: October 2020

Background and Objectives

With an increasing older population, ageism continues to be a significant social issue. Interventions to reduce ageism and improve intergenerational contact are needed.

Research Design and Methods

Building on the Positive Education about Aging and Contact Experiences (PEACE) model, undergraduates in an online experiment were randomly assigned to watch videos that provided education about aging, ageism, and positive intergenerational contact (experimental condition) or education about wallpaper (control condition).

Results

In Part 1, 845 undergraduates in the experimental condition (vs. control condition) reported lower levels of ageism, less negative age stereotypes, more positive age stereotypes, and more aging knowledge in an immediate post-test. In Part 2 (1–6 weeks later), undergraduates in the experimental condition (vs. control condition) reported more positive age stereotypes in a delayed post-test.

Discussion and Implications

These findings highlight the promise of providing information about aging and positive intergenerational contact to reduce ageism. Brief online educational videos based on the PEACE model hold promise as an effective tool to reach a wide audience and reduce ageism.
Pyntacle: a parallel computing-enabled framework for large-scale network biology analysis
Authors: Parca Luca , Truglio Mauro , Biagini Tommaso , Castellana Stefano , Petrizzelli Francesco , Capocefalo Daniele , Jordán Ferenc , Carella Massimo , Mazza Tommaso
Published: October 2020

Background

Some natural systems are big in size, complex, and often characterized by convoluted mechanisms of interaction, such as epistasis, pleiotropy, and trophism, which cannot be immediately ascribed to individual natural events or biological entities but that are often derived from group effects. However, the determination of important groups of entities, such as genes or proteins, in complex systems is considered a computationally hard task.

Results

We present Pyntacle, a high-performance framework designed to exploit parallel computing and graph theory to efficiently identify critical groups in big networks and in scenarios that cannot be tackled with traditional network analysis approaches.

Conclusions

We showcase potential applications of Pyntacle with transcriptomics and structural biology data, thereby highlighting the outstanding improvement in terms of computational resources over existing tools.