bluuebunny/crossref_metadata_2025 huggingface dataset:
Coastal erosion on the north coast of Java: adaptation strategies and coastal management
Authors: Solihuddin T , Husrin S , Salim H L , Kepel T L , Mustikasari E , Heriati A , Ati R N A , Purbani D , Mbay L O N , Indriasari V Y , Berliana B
Published: June 2021

Coastal erosion remains a problem for the socio-economic development of the coastal zone in the north coast of Java. This study aims to determine the coastal characteristics, shoreline changes, and adaptation strategies of the north coast of Java through satellite study and on-ground observations. The analysis covers two decadal periods of satellite data starting from 1998 to 2018. The coastal characteristic of the north coast of Java is typified by sandy, muddy, and gravelly coast. At particular coasts have been extensively modified becoming coastal structure buildings. The shoreline changes are characterized by sectors alternating between erosion and accretion, although in general indicating the erosion processses. The conversion of mangrove ecosystems into fish ponds along with an increase of coastal constructions such as groins, jetties, and seawalls may have strong influences on the coastal erosion at the particular coastal environments. Since traditional hard defense methods used so far have had more damaging than protective effects, there is a need now for the use of soft prevention alternatives and for providing new guidelines for coastal management. A set of permeable breakwater measures, in conjunction with sediment managing schemes, are proposed for the sustainable development of the coastal zone.
Integration of marine spatial objects management to support toward sustainable maritime policy development
Authors: Djunarsjah E , Handayani M
Published: June 2021

Utilization of land and marine potential is an absolute right mandated in Article 33 of the 1945 Constitution. One of the efforts to manage land and marine potential includes the integration of the management of land and marine space objects in the context of sustainable maritime development. However, the implementation of management of marine space objects is overlapping in legal, technical, and institution aspects. Based on ownership of rights and their use, marine space objects are not only limited to the fishery and tourism, but also marine structures, cultivation, underwater treasures, underwater cables and pipes, conservation, customary culture, garbage disposal, shipping, energy and mineral resources, renewable resources, and military. This study will determine maritime policy that can provide assurance of legal, technical, and institutional aspects of management especially for marine space objects. It regulates rights, boundaries, management and an integrated maritime information system. The policy includes management of ownership, use and economic value of marine space. Marine space ownership data consists of the subject and marine space objects. Data on the use of marine space consists of characteristics of marine space, marine spatial use planning and monitoring and evaluation of the implementation of marine space utilization. Meanwhile, data on the economic value of marine space includes information related to the marine space assessment system as well as taxation related to marine space.
Mapping of spatial features model in developing marine ecotourism in Waerole and Nusa Telu, Maluku Province, Indonesia
Authors: Ely A J , Retraubun A S W , Sahetapy D , Papilaya R
Published: June 2021

In the formulation and designation of the ecotourism area, the use of spatial suitability indexes is usually employed. The social, economic, and cultural parameters have almost been ignored in the analysis. These parameters are essential to be included in the development of marine ecotourism to avoid the loss and the impact of these socio-cultural parameters in the development of marine ecotourism. The objective of this research was to construct a conceptual model and thinking perspective and to identify the connectivity of ecology, socio-economy features spatially in designing marine ecotourism areas. Data were collected through observation, participatory mapping, focus group discussion, and interview. Data obtained were then analyzed descriptively and displayed graphically. The conceptual model constructed shows that the marine ecotourism management plan of Waerole and Nuatelu Cape can be categorized into six spatial marine ecotourism explicitly coastal marine e-tourism, snorkeling e-tourism, diving e-tourism, in-shore angling e-tourism, open sea fishing e-tourism, and habitat rehabilitation. The conceptual model for a sustainable management plan for coastal and marine ecotourism suggested the need for holistic and integrated sustainable management comprise of 27 biophysics and socio-economy feature.
Chemical Surface Modification of Oil Palm Fibre: a Case study of developed Oil Palm Fibre-Plastic Composites
Authors: Baffour-Awuah E. , Akinlabi S. A. , Jen T. C. , Okokpujie I. P. , Hassan S. , Ishola F.
Published: June 2021

Application of chemicals to treat the surface of oil palm fibre could have effects on the characteristics of plastics when oil palm fibre and plastic composites are developed. Identification, sampling, and review of literature relating to oil palm fibre (OPF) chemical surface treatment, vis-avis the formation of OPF-plastic composites were done in this study. Chemicals relating to oil palm fibre surface treatment and their effects on OPF-plastic composite characteristics were analyzed. Some surface chemical modifiers influence specific characteristics of composites positively and better than others, while the same chemical may have influence negatively on other traits. Thus, the degree of effect of chemical treatment of OPF-plastic composite could depend on the interesting characteristics, type of chemical, the quantity of chemical and type of plastic.
Impact of Specific Number of Air to Clinker on Clinker Cooling Process in Grate Coolers in a Cement Plant
Authors: Oyepata J. S. , Akintunde M. A. , Dahunsi O. A. , Yaru S. S. , Idowu E. T.
Published: June 2021

The impact of specific number of airs to clinker on a clinker cooling process in grate coolers in a cement plant was investigated. Clinker cooling process is a complex process due to the vast number of interacting operating parameters such as: clinker cooler length, ambient temperature, clinker cooler width, clinker cooler drives speed, clinker cooler fan speed, clinker and air mass flow rates, and clinker density and air densities. This research examines heat transfer and multiphase fluid flow analysis as relating to specific number of air to clinker in a clinker cooling system. It employs a physical “dimensionally scaled-down” model. A 3D model of the clinker bed was developed using SolidWorks 2014 based on geometric parameters adopted in the scaled conceptual design after an existing running clinker cooler. The designed model was scaled down by ratio 25:1, that is, existing cooler being twenty-five times higher than the modelled with length 1.3 m, width 0.3 m and variable clinker bed height of 0.3 m, 0.4m and 0.6m as geometric dimensions. Numerical experimentation done involved high temperature clinker entering the clinker cooler from the heating-up furnace (HUF) at 1350 °C, specific numbers of 2.2041 and 1.7959 Nm3/kg clk, air inlet temperature of 32 °C, inlet mass flow rate of air at 0.45 kg/s at clinker 0.15 kg/s. It was observed that at a specific number of 2.2041 Nm3/kg clk at a bed height 0.6 m an optimal energy recoverable efficiency of 70% was recovered into the system and with an improved lower outlet clinker temperature of 68 °C. While, at a specific number of 1.7959 Nm3/kg clk and at a clinker bed height of 0.3 m, the lowest recoverable efficiency of 57.52% was recovered into the modelled clinker cooler and with highest outlet clinker temperature of 168.7 °C. Hence, specific number of airs to clinker also plays a significant role in clinker cooler performance.
Decentralized Electricity Generation Can Revive Nigeria Dying Critical Sectors
Authors: Towoju O.A. , Ishola F. A. , Elomien E.
Published: June 2021

The growth and industrial advancement of any nation are hampered on constant and sufficient electricity supplies, as there exists a correlation between electricity per capita consumption and the standard of living. The manufacturing industries of Nigeria are in a state of comatose, just as research activities in her ivory towers of learning is at a low state because of the epileptic electricity supply. There are approved licenses for electricity generation to the tune of 26,000 MW as of 2015, and the current available capacity is in excess of 6000 MW of the installed generation capacity of about 12,000 MW. An average of about 4000 MW is what get distributed to the populace partly due to the constraints on the transmission and the distribution network, however, the manufacturing industries demand stands in excess of 13,000 MW. Decentralized generation in line with some of the windows of opportunity provided by the National Electric Regulatory Commission will allow for the supply of the excess generated electricity to the manufacturing industries and higher institutions of learning and encourage generation at full capacity and commissioning of new plants with the provision of conducive environment. The country’s moribund industries will certainly come back to life, and newer ones come into play with constant and adequate supply of electricity, and foster research collaboration with our higher institutions with the attendant positive effect on the nation’s economy.
Central Composite Design for Solvent Extraction of Oil from Neem (Azadirachta indica) seed
Authors: Ojewumi M. E. , Ehinmowo A.B. , Ekanem G.P. , Nsionu J.U. , Bolujo E.O.
Published: June 2021

Optimization of neem oil extraction using Central Composite Design (CCD) was evaluated in this research. The effects of two factors: sample weight and extraction duration on the response which is neem oil volume extracted, were investigated. The CCD employed resulted in 13 experimental runs. Extraction was carried out in a 250 ml Soxhlet extractor. Hexane was used as solvent with thermostated heating mantle at temperature 60°C. Results obtained shows the optimized values of 54.69% of neem oil was obtained with 25 g weight of sample with extraction time of 12hours. Ther2andr2adjvalues were close to 1 which indicates that the regression model was a good one.
A Comprehensive Review of Thermal Power Plants Reliability Using Stochastic Methods
Authors: Shopeju O. O , Oyedepo S. O
Published: June 2021

Adequate and reliable electricity supplies are essential for socio-economic transformation of any nation. Therefore, in the current competitive market, the major focus of any power utility should be to provide consumers with electrical energy in the most economical way, with a high quality and reliability level. On a global scale, reliable electric power availability has been observed as effective and indispensable machinery for the rapid industrial and economic growth of any nation. Efficient and quality energy supply continuity has become one of the more relevant factors of development both in Industrialized and in Developing Countries; therefore, a suitable analysis is recommended to reach a sound compromise between service quality and cost. The analysis of reliability has increasingly been accepted as a basic tool for designing, operation scheduling and maintenance of any system. A power system is expected to supply electrical energy as economical as possible and with a high level of quality and reliability. The reliability of a power system can be evaluated deterministically or probabilistically. The use of deterministic reliability indices in terms of generating reserve capacity is now considered obsolete. Hence, in this study, reliability assessments using probabilistic indices to estimate the operational reliability of thermal power plants have been comprehensively reviewed. This paper concludes that a probabilistic approach of assessing thermal power plants is more result-oriented than deterministic approach.
The Possibility of Biogas production in Nigeria from Organic Waste Material: A Review
Authors: Biodun M.B. , Fayomi O.S.I. , Okeniyi J. O.
Published: June 2021

Biogas waste initiative is one big solution to Nigeria’s growing solid waste problem. This study explores the potential biogas processing of organic waste materials and their benefits to the areas where the excess of such organic waste is located. Based on this review, researchers were noted to be proposing lots of distinctive ways to contain generating solid waste and discoveries have been highlighted to show the importance of converting these organic wastes to biogas. Processing is a well-established technology mainly for sustainable energy use generation in addition to the valorization of organic residues. Through this analysis, these wastes were described as enormous sources of biogas that can assist to solve some of the electricity problems in the country.
Slurry-Phase Bioremediation of Ogoni Land Crude Oil Contaminated Soil
Authors: Babalola R. , Efeovbokhan V.E. , Atiku Y. O. , Usoro U.E. , Ibeh M. A. , Alagbe E.E. , Omoleye J. A. , Abatan O. G.
Published: June 2021

The contamination of soil originated from evolutional activities such as transportation and spillage, as in the case of Ogoni land in the Niger Delta area of Nigeria, and it is a well-known environmental problem in Nigeria. This study examined the capacity of two indigenous bacteria, Pseudomonas aeruginosa, and Bacillus subtilis to remediate the hydrocarbon contaminated soil. The focus of the work was to isolate, identify, and determine the extent of bioremediation achieved in the soil contaminated with crude oil in Ogoni land, which was used as a case study for the slurry-phase bioremediation process. These organisms earlier mentioned were identified based on their morphological and biochemical characteristics. The bacteria species were considered separately and in combination in a Laboratory-scale slurry-phase in a 14-day treatment period using 30 g of soil for each case. The performance of each batch bioreactor was compared to the sterile control. The slurry phase bio-reactor, RA, treated with Pseudomonas sp., had an actual degradation of 31%, the slurry phase bio-reactor, RB, treated with Bacillus sp., had a real degradation of 35%. The slurry phase bio-reactor Rc, which contain both microorganisms had an actual degradation of 36%, the slurry phase bio-reactor RD had a real degradation of 0%. The results obtained confirm that the isolated bacterial from the soil can effectively utilize contaminating crude oil as a source of carbon and energy. The decrease of hydrocarbon in the sterile control was used as a basis for comparison of the petroleum hydrocarbons lost through the extraction process as microbiological activity was not possible. Results from the study have shown that P. aeruginosa and B. subtilis strains were effective for the slurry-phase bioremediation of hydrocarbon contaminated soil.
Investigation of Fracture behaviour of API X70 Pipeline Steel
Authors: Egene M. S. , Adedipe O. , Okoro U.G. , Obanimomo K. T.
Published: June 2021

Oil and gas production has significantly increased over the years in order to meet future demands for oil and gas products, regardless of the unstable price being experienced by producing nations. The use of pipelines for the transportation of these products has been the globally recognized solution. These pipelines are fabricated by welding and their fracture properties depend on a number of factors which include temperature, particularly for pipelines operating in cold environment such as deeper water depths. Therefore, information of fracture behaviour of welded pipelines located in cold regions is therefore important for reliable design for service. In this paper, fracture behaviour of welded x70 pipeline steel was investigated using charpy v-notch specimens. Impact tests were carried out on weld and parent materials at temperatures -10°C, -20°C, -40°C, -60°C, -80°C, -100°C, -120°C, -160°C, 0°C, 10°C and 20°C. Results revealed that higher energy was absorbed in the weld than in parent materials regardless of the test temperature used. results implied that the fracture behaviour of the material could be significantly influenced by temperature, welding and the notch sensitivity of the materials.
Development of Heat sink from Aluminium Silicon Carbide for Electrical and Electronic Applications
Authors: Olaoluwayinka O. , Inegbenebor A.O. , Fayomi O. S. I. , Udoye N.E. , Babalola P. O.
Published: June 2021

Heat sinks play a vital role in dissipating heat in electrical and electronic equipment. The heat sink device influences the overall efficiency, cost, and size of this equipment. Due to the development of the ever-evolving electronics market, new materials with a good thermal conductivity that can absorb and disperse heat away from high temperature and lightweight are sought for. As a result of this, searching for new materials with the tended properties to replace the traditional material is the focus of this work. The candidate materials choosing is aluminium silicon carbide composite because of its properties similar to the one needed for the heat sink. The aluminium silicon carbide composite was processed with different grits silicon carbide. Thereafter, additives with different oxide composition of calcium, zinc and chromium through the processing of stir and mechanical casting were used for the production of the samples. Nine samples in all were produced for the analysis and properties testing. The results show that density, electrical conductivity and thermal conductivity of produced samples are closely similar to the control sample. This preliminary result indicated that the developed heat sink sample could replace the traditional one.
Design and construction of a manual food grinder
Authors: Kilanko O. , Leramo R.O. , Fayomi O.S.I. , Oyedepo S.O. , Babalola P.O. , Ilori T.A. , Mozea K.P. , Patrick P.N.
Published: June 2021

In this study, a light weight portable manual food grinder for domestic use was designed and fabricated to meet food grinding needs that arise from erratic power supply in Nigeria. The design analysis for crank lever parameters and conveyor shaft diameter were done. To make the grinder light weight, the body of the machine, the front cover that house the grinding mechanisms and the support stand were printed with Fused deposition modelling 3D printer. The crank lever, conveyour shaft, grinding discs and the adjustment lever were made of cast alumimum metal. The design analysis revealed that an effort force of 600N on the crank lever will inflict maximum twisting moment of 72000 N-mm and 45000 N-mm on the conveyor shaft of the grinder. For the design of crank lever arm, the minimum boss diameter, boss length, boss thickness, lever thickness, lever width, and crank lever diameter were 18.24 mm, 22.9 mm, 3.42 mm, 8.58 mm, 17.36 mm and 14.94 mm respectively. The minimum conveyor shaft diameter was 25.02 mm while the machine required minimum power of 301.59W.
Mechanical Ventilator for Respiratory Impaired Persons: A Review
Authors: Owodolu T. , Bolu C. A. , Azeta J. , Okokpujie I. P. , O. Kilanko S.
Published: June 2021

Mechanical ventilator is one of the most important devices used in anesthesia and intensive care units for generating a regulated flow of gas into a patient’s lungs. Oxygen is required by every human to stay alive and in cases where a patient is undergoing an acute respiratory distress, a mechanical ventilator is used to deliver external ventilation which could be generated from a hospital’s built in supply system or from a portable oxygen generator. The ventilator is connected to the patient’s lungs through an endotracheal tube (ETT) to deliver air by compressing a conventional bag-valve mask (BVM) with a pivoting cam arm, thereby eliminating the need for a human operator. The device also operates by setting some parameters which can be predetermined by clinicians as well as an assist control mode and an alarm to determine when the system is over pressured. The paper focuses on review of Mechanical ventilators, the different modes of ventilation, anatomy tract of the respiratory system, respiratory mechanics, and approaches of ventilation.
Experimental study on the surface microstructural evolution and fatigue wear resistance of pearlite wheel steels during rolling-sliding condition
Authors: Zhao Hai , He Yizhu , Jiang Bo , Zou Qiang , An Tao , Chen Gang
Published: June 2021

In present paper, the relationship between fatigue and wear of three kinds of pearlite wheel steel samples is investigated by using rolling wear tester under 0.2% slip ratio condition. The results show that the weight loss, the surface hardness and the thickness of plastic deformation layer of three kinds of wheel samples are increased as the increase of cycles during rolling wear process. The weight loss of the G1 wheel sample is the highest owing to the existence of a large amount of proeutectoid ferrite (PF)grains. The correlation between weight loss and fatigue is competitive. High weight loss of the G1 wheel sample can hinder the formation of fatigue wear cracks. As a result, the G1 wheel sample surface changes to smooth after wear. The low weight loss of the G2 wheel sample and the G3 wheel sample cannot hinder the production of fatigue wear cracks during wear process. At the late wear stage, the wheel sample surface produces many fatigue wear cracks, and the wear mechanism becomes fatigue wear. Fatigue wear cracks, which are the rolling contact fatigue (RCF) crack source, can accelerate the RCF failure of wheel samples.
Sex, Age, BMI, and C-Reactive Protein Impact the Odds of Developing Hypertension—Findings Based on Data From the Health and Retirement Study (HRS)
Authors: Speer Hollie , D’Cunha Nathan M , Naumovski Nenad , McKune Andrew J
Published: June 2021

Background

Hypertension is a major contributor to cardiovascular diseases and premature death, therefore determining factors that contribute to such a high burden of disease is critically important. This study examined anthropometric and physical measurements, as well as blood and saliva biomarkers, as predictors for hypertension using datasets from the 2008 Health and Retirement Study.

Methods

A total of 2,924 participants (aged 74.84 ± 6.45 years) were included. Binary logistic regression was performed to ascertain the effects of sex, age, telomere length, C-reactive protein (CRP), body mass index (BMI), and additional markers on the odds of developing hypertension.

Results

Males had 2.3 times the odds (odds ratio (OR) = 2.313, confidence interval (CI) 95% (1.391, 3.845); P = 0.001) of being hypertensive if they were obese, females had 1.7 times the odds (OR = 1.788, CI 95% (1.260, 2.536); P = 0.001) if overweight, and 2.4 times (OR = 2.479, CI 95% (1.693, 3.630); P < 0.001) if obese. Age in females was an independent predictor where every 1-year increase in age was tied to a 5.1% increase in being hypertensive (OR = 1.051, CI 95% (1.027, 1.075); P <0.001), and CRP (>3 mg/l) had 1.4 times the odds (OR = 1.447, CI 95% (1.079, 1.942); P = 0.014).

Conclusions

This study provides verification for BMI as a predictor for hypertension and proposes age and CRP as predictors for females. Specific sex differences and life stage should be considered when evaluating hypertension risk to improve clinical outcomes and promote healthy aging.
Overexpression of MicroRNA-429 Transgene Into the Renal Medulla Attenuated Salt-Sensitive Hypertension in Dahl S Rats
Authors: Zhu Qing , Hu Junping , Wang Lei , Wang Weili , Wang Zhengchao , Li Pin-Lan , Li Ningjun
Published: June 2021

Background

We have previously shown that high salt stimulates the expression of miR-429 in the renal medulla, which induces mRNA decay of HIF prolyl-hydroxylase 2 (PHD2), an enzyme to promote the degradation of hypoxia-inducible factor (HIF)-1α, and increases the HIF-1α-mediated activation of antihypertensive genes in the renal medulla, consequently promoting extra sodium excretion. Our preliminary results showed that high salt-induced increase of miR-429 was not observed in Dahl S rats. This present study determined whether correction of this impairment in miR-429 would reduce PHD2 levels, increase antihypertensive gene expression in the renal medulla and attenuate salt-sensitive hypertension in Dahl S rats.

Methods

Lentiviruses encoding rat miR-429 were transfected into the renal medulla in uninephrectomized Dahl S rats. Sodium excretion and blood pressure were then measured.

Results

Transduction of lentiviruses expressing miR-429 into the renal medulla increased miR-429 levels, decreased PHD2 levels, and upregulated HIF-1α target gene NOS-2, which restored the adaptive mechanism to increase the antihypertensive gene after high-salt intake in Dahl S rats. Functionally, overexpression of miR-429 transgene in the renal medulla significantly improved pressure natriuretic response, enhanced urinary sodium excretion, and reduced sodium retention upon extra sodium loading, and consequently, attenuated the salt-sensitive hypertension in Dahl S rats.

Conclusions

Our results suggest that the impaired miR-429-mediated PHD2 inhibition in response to high salt in the renal medulla may represent a novel mechanism for salt-sensitive hypertension in Dahl S rats and that correction of this impairment in miR-429 pathway could be a therapeutic approach for salt-sensitive hypertension.
Self-Measured Blood Pressure Monitoring Among Adults With Self-Reported Hypertension in 20 US States and the District of Columbia, 2019
Authors: Fang Jing , Luncheon Cecily , Wall Hilary K , Wozniak Gregory , Loustalot Fleetwood
Published: June 2021

Background

Hypertension is a major risk factor for cardiovascular disease. Achieving hypertension control requires multiple supportive inventions, including self-measured blood pressure (SMBP) monitoring. The objective of this study is to report the use of SMBP among US adults.

Methods

Behavioral Risk Factor Surveillance System data were used for this study. The 2019 survey included, for the first time, an optional SMBP module. Twenty states and the District of Columbia (N = 159,536) opted to include the module, which assessed whether participants were advised by a healthcare professional to use SMBP, and if they used SMBP monitoring. Among those using SMBP, additional questions assessed the location of SMBP monitoring and whether SMBP readings were shared with a healthcare professional.

Results

Among adults in the study population, 33.9% (95% confidence interval 33.4%–34.5%) reported having hypertension (N = 66,869). Among them, nearly 70% were recommended to use SMBP by their healthcare professional and approximately 61% reported SMBP use regardless of recommendation. The most common location of SMBP was the home (85.6%). Overall, >80% shared their SMBP reading with their healthcare professional, 74% and 7% were shared in person and via the internet or email, respectively. There were differences in healthcare professional recommendations, use of SMBP, and SMBP information sharing across demographic characteristics and state of residency.

Conclusions

SMBP recommendation was common practice among healthcare professionals, as reported by US adults with hypertension. Data from this study can be used to guide interventions to promote hypertension self-management and control.
Stroke Survivors Experience Elevated Levels of Loneliness: A Multi-Year Analysis of the National Survey for Wales
Authors: Byrne Christopher , Saville Christopher W N , Coetzer Rudi , Ramsey Richard
Published: June 2021

Objective

Despite clinical observation that stroke survivors frequently experience loneliness, there is no large-scale empirical evidence to support this observation. Therefore, the primary objective of this research was to provide the first large-scale and comprehensive estimate of loneliness in the stroke survivor population.

Method

To address this issue, we completed two preregistered analyses of a nationally representative annual survey (N > 21,000). A two-phase approach was adopted combining both exploratory (Study 1) and confirmatory (Study 2) phases. The benefit of such an approach is that replication is built into the design, which considerably strengthens the inferences that can be made.

Results

Across two separate cohorts, the results consistently showed that human stroke survivors report higher levels of loneliness compared with healthy individuals, and this relationship could not be accounted for by demographic factors (e.g., age, sex) or objective measures of social isolation (e.g., marital status, number of household members).

Conclusions

These findings demonstrate that elevated levels of loneliness poststroke are robust in that they replicate in large nationally representative samples and cannot be reduced to objective measures of social isolation. The work has clinical and societal relevance by suggesting that loneliness poststroke is unlikely to be adequately “treated” if only the quantity and not the quality of social experiences are considered.
MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting
Authors: Zou Meng , Duren Zhana , Yuan Qiuyue , Li Henry , Hutchins Andrew Paul , Wong Wing Hung , Wang Yong
Published: June 2021

Multi-omics data allow us to select a small set of informative markers for the discrimination of specific cell types and study of cellular heterogeneity. However, it is often challenging to choose an optimal marker panel from the high-dimensional molecular profiles for a large amount of cell types. Here, we propose a method called Mixed Integer programming Model to Identify Cell type-specific marker panel (MIMIC). MIMIC maintains the hierarchical topology among different cell types and simultaneously maximizes the specificity of a fixed number of selected markers. MIMIC was benchmarked on the mouse ENCODE RNA-seq dataset, with 29 diverse tissues, for 43 surface markers (SMs) and 1345 transcription factors (TFs). MIMIC could select biologically meaningful markers and is robust for different accuracy criteria. It shows advantages over the standard single gene-based approaches and widely used dimensional reduction methods, such as multidimensional scaling and t-SNE, both in accuracy and in biological interpretation. Furthermore, the combination of SMs and TFs achieves better specificity than SMs or TFs alone. Applying MIMIC to a large collection of 641 RNA-seq samples covering 231 cell types identifies a panel of TFs and SMs that reveal the modularity of cell type association networks. Finally, the scalability of MIMIC is demonstrated by selecting enhancer markers from mouse ENCODE data. MIMIC is freely available at https://github.com/MengZou1/MIMIC.
Consensus clustering of single-cell RNA-seq data by enhancing network affinity
Authors: Cui Yaxuan , Zhang Shaoqiang , Liang Ying , Wang Xiangyun , Ferraro Thomas N , Chen Yong
Published: June 2021

Elucidation of cell subpopulations at high resolution is a key and challenging goal of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data analysis. Although unsupervised clustering methods have been proposed for de novo identification of cell populations, their performance and robustness suffer from the high variability, low capture efficiency and high dropout rates which are characteristic of scRNA-seq experiments. Here, we present a novel unsupervised method for Single-cell Clustering by Enhancing Network Affinity (SCENA), which mainly employed three strategies: selecting multiple gene sets, enhancing local affinity among cells and clustering of consensus matrices. Large-scale validations on 13 real scRNA-seq datasets show that SCENA has high accuracy in detecting cell populations and is robust against dropout noise. When we applied SCENA to large-scale scRNA-seq data of mouse brain cells, known cell types were successfully detected, and novel cell types of interneurons were identified with differential expression of gamma-aminobutyric acid receptor subunits and transporters. SCENA is equipped with CPU + GPU (Central Processing Units + Graphics Processing Units) heterogeneous parallel computing to achieve high running speed. The high performance and running speed of SCENA combine into a new and efficient platform for biological discoveries in clustering analysis of large and diverse scRNA-seq datasets.
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases
Authors: Staton Margaret , Cannon Ethalinda , Sanderson Lacey-Anne , Wegrzyn Jill , Anderson Tavis , Buehler Sean , Cobo-Simón Irene , Faaberg Kay , Grau Emily , Guignon Valentin , Gunoskey Jessica , Inderski Blake , Jung Sook , Lager Kelly , Main Dorrie , Poelchau Monica , Ramnath Risharde , Richter Peter , West Joe , Ficklin Stephen
Published: June 2021

Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.
wQFM: highly accurate genome-scale species tree estimation from weighted quartets
Authors: Mahbub Mahim , Wahab Zahin , Reaz Rezwana , Rahman M Saifur , Bayzid Md Shamsuzzoha
Published: June 2021

Motivation

Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree–species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging.

Results

We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset, which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL.

Availability and implementation

Datasets studied in this article and wQFM (in open-source form) are available at https://github.com/Mahim1997/wQFM-2020.

Supplementary information

Supplementary data are available at Bioinformatics online.
HPTLC Method for the Ultrasensitive Detection of Triamterene in Plasma
Authors: Khorshed Ahmed A , Elsutohy Mohamed M , Mohamed Abobakr A , Oraby Mohamed
Published: June 2021

A high-performance thin-layer chromatographic (HPTLC) method has developed for the selective detection of a diuretic drug, triamterene (TRIAM), in pure form, tablets and human plasma. The method was based on chromatographic separation of TRIAM using HPTLC plates, precoated with silica gel, and a mobile phase consisted of ethyl acetate: dimethylformamide: ammonia (7.0: 2.7: 0.3, by volume). The native fluorescence signal of TRIAM was detected at 440 nm and used to quantify TRIAM using the proposed method, improving the method sensitivity to ~250-folds in comparison to that reported in previous HPTLC studies. The developed method enabled the detection of TRIAM in pure drug and biological samples (human plasma) within linear concentrations ranged from 0.8 to 60 ng/band or 1.0 to 60 ng/band for pure drug and plasma samples, respectively. Furthermore, the method was validated according to the official guidelines to permit its applicability in quality control and clinical laboratories.
Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in All of Us Research Program Participants, 2 January to 18 March 2020
Authors: Althoff Keri N , Schlueter David J , Anton-Culver Hoda , Cherry James , Denny Joshua C , Thomsen Isaac , Karlson Elizabeth W , Havers Fiona P , Cicek Mine S , Thibodeau Stephen N , Pinto Ligia A , Lowy Douglas , Malin Bradley A , Ohno-Machado Lucila , Williams Carolyn , Goldstein David , Kouame Aymone , Ramirez Andrea , Roman Adrienne , Sharpless Norman E , Gebo Kelly A , Schully Sheri D
Published: June 2021

Background

With limited severe acute respiratory syndrome coronavirus (SARS-CoV-2) testing capacity in the United States at the start of the epidemic (January–March 2020), testing was focused on symptomatic patients with a travel history throughout February, obscuring the picture of SARS-CoV-2 seeding and community transmission. We sought to identify individuals with SARS-CoV-2 antibodies in the early weeks of the US epidemic.

Methods

All of Us study participants in all 50 US states provided blood specimens during study visits from 2 January to 18 March 2020. Participants were considered seropositive if they tested positive for SARS-CoV-2 immunoglobulin G (IgG) antibodies with the Abbott Architect SARS-CoV-2 IgG enzyme-linked immunosorbent assay (ELISA) and the EUROIMMUN SARS-CoV-2 ELISA in a sequential testing algorithm. The sensitivity and specificity of these ELISAs and the net sensitivity and specificity of the sequential testing algorithm were estimated, along with 95% confidence intervals (CIs).

Results

The estimated sensitivities of the Abbott and EUROIMMUN assays were 100% (107 of 107 [95% CI: 96.6%–100%]) and 90.7% (97 of 107 [83.5%–95.4%]), respectively, and the estimated specificities were 99.5% (995 of 1000 [98.8%–99.8%]) and 99.7% (997 of 1000 [99.1%–99.9%]), respectively. The net sensitivity and specificity of our sequential testing algorithm were 90.7% (97 of 107 [95% CI: 83.5%–95.4%]) and 100.0% (1000 of 1000 [99.6%–100%]), respectively. Of the 24 079 study participants with blood specimens from 2 January to 18 March 2020, 9 were seropositive, 7 before the first confirmed case in the states of Illinois, Massachusetts, Wisconsin, Pennsylvania, and Mississippi.

Conclusions

Our findings identified SARS-CoV-2 infections weeks before the first recognized cases in 5 US states.
Design-based research approach for teacher learning: a case study from Singapore
Authors: Lim Fei Victor , Nguyen Thi Thu Ha
Published: June 2021

In this article, we describe how a design-based research approach brought about teacher learning in terms of both confidence and competence to design and enact a multiliteracies lesson package. This study is situated within the efforts to grow a community of practice comprising teacher champions across schools as they work closely with researchers. Based on a single case study of a teacher, the article discusses her discernible trajectory of growth as evident from her reflections collected after each of the lesson co-design sessions, the lesson plans that she designed, and her actual classroom practices. The findings from the study suggest that the design-based research approach, given its features, can be productive in bringing about a deeper and more reflective teacher learning and as a platform to strengthen the nexus between research and practice.
Management of acute coronary syndromes in older adults
Authors: Morici Nuccia , De Servi Stefano , De Luca Leonardo , Crimi Gabriele , Montalto Claudio , De Rosa Roberta , De Luca Giuseppe , Rubboli Andrea , Valgimigli Marco , Savonitto Stefano
Published: June 2021

Older patients are underrepresented in prospective studies and randomized clinical trials of acute coronary syndromes (ACS). Over the last decade, a few specific trials have been conducted in this population, allowing more evidence-based management. Older adults are a heterogeneous, complex, and high-risk group whose management requires a multidimensional clinical approach beyond coronary anatomic variables. This review focuses on available data informing evidence-based interventional and pharmacological approaches for older adults with ACS, including guideline-directed management. Overall, an invasive approach appears to demonstrate a better benefit–risk ratio compared to a conservative one across the ACS spectrum, even considering patients’ clinical complexity and multiple comorbidities. Conversely, more powerful strategies of antithrombotic therapy for secondary prevention have been associated with increased bleeding events and no benefit in terms of mortality reduction. An interdisciplinary evaluation with geriatric assessment should always be considered to achieve a holistic approach and optimize any treatment on the basis of the underlying biological vulnerability.
Can mental health competence reduce the higher risk of smoking initiation among teenagers with parents who smoke?
Authors: Pearce Anna , Rougeaux Emeline , Deighton Jessica , Viner Russell M , Law Catherine , Hope Steven
Published: June 2021

Background

Parental smoking strongly influences adolescent smoking, yet few studies have examined factors that may protect against this. We investigated whether skills-based components of positive mental health (‘mental health competence’, MHC) modified the association between parental and teenager smoking, in the UK-representative Millennium Cohort Study (approximately 18 000 children, born 2000–02; analytic sample: n = 10 133).

Methods

Cohort members (CMs) reported at 14 years (y) whether they had ever smoked cigarettes. A dichotomized variable indicated whether one/both parents smoked when CMs were 11 y. A four-class latent MHC measure captured learning skills and prosocial behaviours at 11 y: High, High–Moderate, Moderate, Low. We examined effect measure modification (on the additive scale) by comparing risk differences (RDs) for CM smoking according to parental smoking, within each MHC class. We then estimated RDs for CM smoking according to combinations of parental smoking and MHC. Analyses accounted for confounding, sample design, attrition and item missingness.

Results

CMs were more likely to smoke cigarettes if their parent(s) smoked (27%) than CMs with no parent(s) who smoked (11%; RD: 16%). When stratified by MHC, RDs were stronger for low MHC (21%; 95% CI 11–31%) than other MHC classes (ranging: 7–11%). Compared to CMs with high MHC and non-smoker parents, those with low MHC and parent(s) who smoked had an RD of 28% (95% CI 20–36%). This was greater than the sum of RDs for those with low MHC and non-smoker parent(s) [7% (2–14%)] plus those with high MHC and whose parent(s) smoked [11% (7–15%)]. There was limited effect measure modification by moderate or High–Moderate MHC.

Conclusion

Improving MHC to moderate levels may help reduce intergenerational transference of smoking.
Social distancing measures: barriers to their implementation and how they can be overcome – a systematic review
Authors: Sadjadi Mahan , Mörschel Katharina S , Petticrew Mark
Published: June 2021

Background

Despite their central role in the global response to the COVID-19 pandemic and previous infectious disease outbreaks, factors influencing the acceptability and implementation of social distancing measures are poorly understood. This systematic review aims to identify such factors drawing on qualitative literature.

Methods

A systematic search was carried out in eleven databases. Papers were included in the review if they reported on qualitative studies of factors influencing the implementation of social distancing measures in potentially epidemic infectious diseases. An adapted meta-ethnographical approach was used for synthesis. Review findings were assessed for strength and reliability using GRADE-CERQual.

Results

Twenty-nine papers were included from the systematic search that yielded 5620 results, and supplementary methods. The review identifies two broad categories of barriers to social distancing measures: individual- or community-level psychosocial phenomena, and shortcomings in governmental action or communication. Based on this, 25 themes are identified that can be addressed to improve the implementation of social distancing.

Conclusion

Among other findings, the review identifies the need for good communication as well as the need for authorities to provide comprehensive support as two key opportunities to increase acceptability and adherence. Further important enablers of adherence are adequate preparedness and appropriate legislation, the presence of community involvement, solidarity within communities and trust in governments and authorities.
OCT1 – a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway
Authors: Vrzoňová Romana , Tóth Renáta , Siváková Barbara , Moťovská Anna , Gaplovská-Kyselá Katarína , Baráth Peter , Tomáška Ľubomír , Gácser Attila , Gabaldón Toni , Nosek Jozef , Neboháčová Martina
Published: June 2021

The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.