bluuebunny/crossref_metadata_2025 huggingface dataset:
Proposed Use of Land and Building Tax as a Fiscal Policy Instrument to Support Flood Disaster Management Financing in DKI Jakarta
Authors: Yahya I B , Inayati  , Sardjono L F
Published: December 2021

This article discusses a proposal applying an earmarking tax scheme to PBB-P2 in DKI Jakarta Province to support financing and flood disaster management, based on the flood disaster that always occurs every year and has many losses. In addition, the current pattern of financing comes from the APBD or local general fund. This scheme will trigger the potential for discontinuity of budget allocations for flood disaster management. This study aims to identify and compare the practice of financing and handling disasters in other countries. Then it aims to see the advantages and disadvantages of the proposed proposal and explore the policy recommendations that can be given if this proposal is later implemented. By using a qualitative approach, this research is done through in-depth interviews and literature study. The study results found that, there are two financing schemes for flood disaster management, namely (1) national budget and (2) other government funds. Another finding shows that the proposed application of the earmarking tax can legally be carried out in DKI Jakarta. Although, there are advantages and disadvantages, and there are several options for the DKI Jakarta Provincial Government that can be considered if this proposal is later implemented.
The Urgency of Revision of the Law Regarding Conservation of Biological Natural Resources and Its Ecosystems in Indonesia
Authors: Ayuni Q , Arsil F
Published: December 2021

This paper discusses the importance of revising the law on the Conservation of Biological Natural Resources and Its Ecosystems as a priority for national legislation programs. The three important reasons for the revision are accommodating conservation approaches, adapting to the principles of regional autonomy, and strengthening law enforcement. This revision is vital to deal with the widespread destruction of ecosystems and the theft of illegal species in Indonesia. Protection of biological natural resources is essential because it is one of the elements of environmental resilience. With the normative legal approach, this paper argues the importance of revising the law to ensure implementation in protecting Biological Natural Resources in Indonesia.
Blood Lead Levels of Pregnant Women in Agricultural and Coastal Area: A SDG’s Indicator for Health and Pollution in Brebes District
Authors: Sakina N A
Published: December 2021

Maternal mortality is still a severe problem in Indonesia. One of the causes is the blood lead levels. Blood lead levels in pregnant women can increase the risk of preeclampsia which is the cause of high maternal mortality in Indonesia. One of the factors for high blood lead levels is living close to the source of lead pollution. This study determines the differences in blood lead levels in pregnant women in agricultural and coastal areas in Brebes District. The t-test independent is used to analyze the mean differences with SPSS v 21 software with 84 samples. The results show a significant difference in the average blood lead levels in pregnant women in agricultural and coastal areas in Brebes Regency (p-value=0,047). The average blood lead levels are higher in agricultural areas (46.243 µg/dL) than in coastal areas (37.731 µg/dL). It can be implied that the risk of maternal mortality in an agricultural area is higher than in a coastal area.
A SWOT Analysis of Takakura Compost as a Treatment for Household Food Waste (Case Study in Pondok Labu Urban Village)
Authors: Kartini A Z , Hasibuan H S , Tumuyu S S
Published: December 2021

An unstable food system will have an impact on ecosystems and the food chain. One proof of this imbalance is the increasing number of food waste. Currently, food waste in households still dominates. One way to manage food waste is the Takakura composting technique. The purpose of this study to analyze the effectiveness of takakura compost in managing food waste among households. This research method uses a qualitative method with several steps, training about making Takakura compost, counting the food waste in the composter, and observing through a focus group discussion with 25 members of the waste bank. The result of this study that an average of 18.9 kg of food waste produces 11.9 kg of household compost. According to the SWOT analysis, Takakura compost could reduce food waste in the household. Takakura compost could provide business opportunities with its own food waste raw materials, but the processing takes a relatively long time during the compost maturation process, this situation could affect the motivation of participants in the future. The conclusion of this study is Takakura compost could effective in managing food waste among households.
Smart City Implementation and Citizen Engagement in Indonesia
Authors: Kusumastuti R D , Rouli J
Published: December 2021

The smart city concept has been implemented in countries worldwide as the solution for various urban problems. In Indonesia, the smart city movement was initiated in 2017 to create 100 smart cities. Previous studies identify challenges to the implementation and that smart people or smart citizens are essential dimensions of a smart city. This study aims to gain insights into the smart city implementation and citizen engagement in Indonesia through the online social network by conducting a focus group discussion (FGD) with four academicians and in-depth interviews (IDIs) with six representatives of the related government institutions. FGD and IDIs indicate that the implementation of smart cities should be adjusted according to the local situation. The critical success factors of the implementation are namely, local wisdom, transformational leadership, sustainability, and political content. The results also reveal that, in general, the city residents have been involved in implementing of the smart city through the online social network. However, a kind of incentive system is still required to ensure that the city residents are encouraged to solve the city problems.
Restoration and Conservation Based on Community Empowerment and Religious Understanding
Authors: Herdiansyah H , Rizki M N
Published: December 2021

Community empowerment is one of the effective strategies in conservation efforts. However, empowerment-based conservation still leaves some problems to be solved. The most significant issues in empowerment-based conservation are sustainability and human resource issues. This study sees the problem can be solved by integrating religious aspects in empowerment-based conservation efforts. Through its teaching about the environment, religion can instill values and shape the behavior of people and people who care about the environment. For demonstrating this possibility, this study reviews the literature available in discussions on the role of religion in environmental conservation, community empowerment, and conservation efforts. From the existing literature, religion instills values, shapes behavior, and ensures its sustainability. This is possible through features in religion, such as the message of responsibility in the concept of divinity, karma and reward/sin, or other features such as the ability of institutions to spread values that are intertwined with the emotional, cognitive, and even political aspects of society.
Implementation of Forest Conservation Policies based on Local Wisdom of the Ammatoa Kajang Indigenous Community
Authors: Megawati S , Mahdiannur M A
Published: December 2021

The Ammatoa Kajang indigenous community maintain cultural authenticity from generation to generation, especially in protecting and preserving customary forests from the threat of damage. This research aims to describe the implementation of forest conservation policies based on local wisdom of the Ammatoa Kajang indigenous community. The research method uses a literature/library study approach. Reference documents from 2001-2021. Data analysis methods with data minimization, data visualization, data analysis, and data validation and concluding. The results of the research showed that the Kajang orthodox community in day-to-day forest management is guided by the Pasang ri Kajang, which contains rules, implementation and sanctions for all forms of forest utilization and management, monitoring tools and control over all activities related to forestry, positively correlated with forestry policies governance. The concept of customary forest management is to divide the forest into three areas with certain specifications and rules as well as prohibited from destroying flora and fauna. In the end, the forest is sustainable and indigenous community behave sustainably; it can be concluded that the implementation of forest conservation policies based on local wisdom of the Ammatoa Kajang indigenous community is going well.
Local Communities Participation in Mangrove Management for Tsunami Disaster Mitigation at Palu City Coastal
Authors: Gultom J E I , Hasibuan H S , Patria M P
Published: December 2021

In September 2018 there was an earthquake with a magnitude of 7.5 Mw in Palu Bay, which was followed by a tsunami. The impact of this disaster is the destruction of building infrastructure, the environment, and loss of life. 4,194 people died and damaged 8,107 buildings, 43 health facilities and 386 educational facilities. Mangroves as one of the ecosystems located on the coast can reduce the impact of the tsunami. This research aims to analyze the participation of local communities in mangrove management. The method used in this research is qualitative, and the analysis used in this research is descriptive and comparative method, and the data used in this research is the results of interviews obtained from several communities who live around the coast of Palu city. The importance of this research is to compare the participation of the community in three research locations. The results of the research show that communities at the research locations are starting to realize the importance of mangroves for reducing the impact of the tsunami, so that after 2018 many communities have started planting and managing mangroves.
Determining Factors of Community Participation in Waste Bank
Authors: Meidiana C , Sekito T , Sasongko W
Published: December 2021

The study aims to analyze the factors affecting community involvement in the waste separation and reduction through waste bank for low participation through benefits offered to its member. Logistic regression was used for the analysis, and there were 26 dependents variables applied to the analysis. The result showed that six variables, i.e., age, occupation, participation in social activities, knowledge of sustainable development, distance from HH to WB, and availability of dissemination of 3R, affect people’s motivation to be member and actively involved in waste reduction through the waste bank. All variables except distance are proportional to the motivation of the community to participate in waste bank. The attained model is used to calculate the probability of community participation in waste banks afterward. Using different conditions, where variables are set with values of zero and one representing absence and availability of related variables, respectively various probability values come out ranging from 0% to 94.8% which is the highest probability value if all significant factors are available.
The Community’s Perception and Attitude toward Malapari (Pongamia pinnata) as a Biofuel: A Case Study in Patutrejo Village, Purworejo Regency
Authors: Sanudin  , Sianturi R U D , Fauziyah E
Published: December 2021

Biofuel production as an alternative energy source has been promoted and spread worldwide, but there is actual potential. Malapari (Pongamia pinnata) is a forestry-based biofuel. This paper aims to determine community perception and attitude towards malapari as a biofuel. The research was conducted in August - October 2018 in Patutrejo Village, Grabag District, Purworejo Regency, Central Java. This research was conducted using a survey method. Determination of respondents used a purposive sampling method. Respondents consisted of 38 people. The result showed respondents had poor to feeble perceptions and attitudes towards malapari. It is presumably because public knowledge of the use of malapari as a biofuel is low due to lack of socialization from related parties. There is no evidence of the utilization/processing of malapari seeds as a biofuel.
Community Perspectives on the Implementation of Building Permits (IMB) for Environmental Sustainability in South Jakarta, Indonesia
Authors: Godjali D , Hasibuan H S , Tambunan R P
Published: December 2021

Building construction will increase along with the increase in population in urban areas. For maintaining the carrying capacity of the environment to remain in balance, it is necessary to have a control instrument in the development of urban areas, one of which is through a Building Permit (IMB). To increase the effectiveness of the policy for implementing the IMB, it is essential to know the public’s perception of the IMB and experts regarding their views. Through interviews, questionnaires, spatial analysis, and AHP, this research is expected to be a material consideration for stakeholders in deciding policies for implementing IMB in South Jakarta. Spatial analysis was used to compare land cover, questionnaires were used to see people’s perceptions of building permits as an instrument for controlling and protecting urban areas, and AHP was used to validate the expert team’s opinion regarding IMB. The increase in green land in South Jakarta, the perception of public awareness in South Jakarta regarding the obligation to build a IMB and its impact on the environment is still high, and the accountability factor of the implementing licensing organization is one of the factors that can increase the effectiveness of the application of a building permit (IMB) in South Jakarta.
Diversification of Local Tubers through Optimization of Cocoa Farming in Supporting Sustainable Food Security
Authors: Pribadi H , Jumiyati S , Muis A , Widnyana I K , Mustabi J
Published: December 2021

The rate of world population growth gets faster every year, while on the other hand the land available for food production activities is increasingly limited. Efforts to increase income and food crop production by using cocoa farming to support national food security can be done by optimizing of land through crop diversification patterns by planting local tubers under cocoa farming. This research aims to analyze the optimization of land use, revenue and production costs. In addition, analyzing the nutritional content contained in each type of local tubers, namely sweet potato, cassava and taro. The research was conducted in the the buffer zone of Lore Lindu National Park (TNLL), Palolo District, Sigi Regency, Central Sulawesi Province, Indonesia. The results showed that the optimization of land use and revenue was obtained through the diversification pattern of sweet potato and cocoa. Optimization of the costs use occurs in the use of fertilizer production inputs. In addition, sweet potatoes have a higher calorific value, protein and fat compared to cassava and taro. However, the carbohydrate content of cassava is higher than that of sweet potato and taro.
Screening of Bioactive Metabolites Actinomycetes to Evaluate Potential Sources of Sustainable Marine Natural Products
Authors: Utami T G P , Setiawan A , Juliasih N L G R
Published: December 2021

This study aimed to screen the activity of methanol extract of sponge-derived actinomycetes as an anti-biofilm and antibacterial agent to Staphylococcus aureus. Nine actinomycetes isolates were selected from the UPT LTSIT deposit. S. aureus was obtained from the skin of patients at Abdul Moeloek General Hospital. An antibiotic susceptibility test was performed by the disk diffusion method. Biofilm formation of S. aureus was tested using the crystal violet method. The viability of pathogenic bacteria was measured using the indicator resazurin. The results of the biofilm formation test in vitro revealed that the organic extracts 33A1T2, 33A2T3, 21A1T11, and 38A1T12 inhibited bacterial growth at 0.5 mg/mL. Meanwhile, 50A2T9, 21A1T11, and 38A1T12 significantly inhibited the formation of staphylococcal biofilm on polystyrene at a concentration of 0.25 mg/mL. This information is very important as a basis for further understanding of the mechanism of action of antibiofilm agents.
The Impact of the Toll Road Development on the Environment and Ecosystem in Kukusan Village, Depok, West Java, 2015-2020
Authors: Setiawan A
Published: December 2021

This article analyzes the impact of the construction of the Cinere-Jagorawi (Cijago) Toll Road Section II, which connects the Bogor Highway and the Kukusan area on the environment around the toll road construction site. Most of the Kukusan areas affected by the toll road construction project are open areas and shrubs, which are habitats for wild animals, especially snakes so that the balance of snake habitat in the area is disturbed. The research method used in this study is the historical method which consists of four stages, namely heuristics, verification, interpretation, and historiography. In addition to books obtained from several libraries, the data used in this study were also obtained from interviews with people living near toll road construction projects, especially ornamental plant traders. This research shows that environmental changes due to the construction of toll road infrastructure impact the disruption of the habitat of several wild animals and an increase in temperature and concerns about the availability of clean water in the future, especially in the Kukusan area.
Development of Premium Ecotourism in the Outermost Islands
Authors: Notohamijoyo A , Lestari P , Wiyata A S , Billah M , Sugandhi H
Published: December 2021

The tourism sector is the economic sector hardest hit during the Covid-19 pandemic. A breakthrough is needed in line with health protocols to maintain physical and social distance. Tourism on the outermost islands is an alternative solution. As the largest archipelagic country globally, Indonesia has the potential for the outermost islands that can be used as tourist destinations. A breakthrough policy is needed in the management of ecotourism in the outermost islands related to the limited capability of the Government, such as the high costs for transportation and logistics arrangements in the outermost islands. Tourism in the outermost islands must be directed towards premium tourism. Its market share is middle to upper-class tourists who want a new atmosphere and challenges and are willing to pay quite a lot of money. This study presents a management model that divides each government agency’s duties in managing ecotourism in the outermost islands with a premium scheme and the National Border Management Agency being the operator. The model is expected to encourage the formulation of targeted policies for the management of the outermost islands, including the presence of cruise ships.
Improving Human Resources as Local Food Processors to Accelerate Stunting Prevention to realize the SDGs: Case Study in Asmat, Papua
Authors: Sianipar T M E , Nurhasana R , Hanita M , Ayuningtyas D
Published: December 2021

Asmat is a district with poor nutrition that causes stunting. In 2020 the percentage of stunting in Asmat is 19.54%, in 2021 it will increase to 28.5%. Unir Sirau Subdistrict has the highest percentage reaching 73.37%. The purpose of the study was to analyze human resource factors and local food management to accelerate stunting prevention in Asmat. This research is qualitative with descriptive method. The sampling method is purposive sampling. Data collection was done by interview according to online interview. Results of the interviews state that the high incidence of stunting in Asmat are the influence of people’s habits who still sell their catches and gardening, such as fish, vegetables, corn, etc., to buy less nutritious foodstuffs. Mothers don’t know prepare healthy food for children, often diarrhea due their habit of not washing hands and not having clean water. People are unmotivated to take part in posyandu activities and health education. People come to health services only when the child’s bad condition. Conclusion that stunting can be reduced give education is interesting and direct counseling to monitor people’s lives, provide financial assistance and healthy food is done on a regular basis until the bad habits of the community disappear.
Surface and corrosion properties of Type 430 ferritic stainless steel in parsley (Petroselinum Sativum) essential oil-containing sulphuric acid solution
Authors: Sanni Omotayo , Ren Jianwei , Jen Tien-Chien
Published: December 2021

This study examined the corrosion inhibiting properties of parsley (petroselinum sativum) essential oils, for Type 430 ferritic stainless steel in 0.5 molar sulphuric acid solutions. In this study, weight loss, electrochemical and scanning electron microscope techniques were used in gaining a detailed understanding of inhibition effects of parsley (petroselinum sativum) essential oils (PEO) on Type 430 ferritic stainless steel corrosion. The inhibitor studied exhibits good anti-corrosion performance with 98.65% inhibition efficiency. This result could be ascribed to the adsorbed PEO on the surface of the stainless steel, and this was verified by surface visualization using optical and scanning electron microscope techniques while the crystallographic variation of the inhibited sample is studied by x-ray diffraction (XRD). The adsorption of PEO onto stainless steel surface is controlled by Langmuir adsorption isotherms. Optical images of non-inhibited specimens showed a severely corroded surface with a visible macro pit on the stainless steel from sulphuric solutions. The inhibited sample shows improved surface owing to the surface protection effect of PEO molecules. The corrosion inhibition performance of PEO is due to the presence of active constituents which enhanced the film formation over the surface of the metal, thus, mitigating corrosion.
Synergistic performance of expanded graphite—mica amalgamation based non-asbestos copper-free brake friction composites
Authors: Sathyamoorthy G , Vijay R , Lenin Singaravelu D
Published: December 2021

Recent advancements in brake pad applications emphasise various friction compositions that exclude toxic components such as asbestos, copper etc, in order to provide superior performance without hurting the environment, human life and aquarium species. In this work, brake friction materials were fabricated by the conventional manufacturing process as standard brake pads using expanded graphite with the synergetic effect of thermal resistant material mica flakes. Six standard brake pads were produced based on varying the expanded graphite by 16, 14, 12, 8, 6 & 4 weight percentage, which is compensated using the Mica flakes by 4, 6, 8, 12, 14 & 16 weight percentage, fixing the composition of other ingredients and designated as BM01, BM02, BM03, BM04, BM05 and BM06. Physical, chemical and mechanical, characterisations of the formed friction materials were carried out in accordance with IS 2742 and ISO 6312. A full-scale inertia brake dynamometer was used to determine the fade, recovery characterisations with the pressure and speed sensitivity as of JASO-C-406. From the experimental observations, BM03 friction composites reveal excellent low fade and high recovery characteristics because of the integrated effect of expanded graphite (superior lubricity) & mica (good thermal stability). Worn surface analysis was studied with the help of a scanning electron microscope. The inclusion of expanded graphite-mica as a hybrid ‘lubricant-filler’ combination in composite materials for friction braking application results in performance synergism.
Modulating light absorption and multiferroic properties of BiFeO3-based ferroelectric films by the introduction of ZnO layer
Authors: Li Kexin , Zhang Wanyun , Guo Kaixin , Cui Ruirui , Deng Chaoyong , Wang Xu
Published: December 2021

Pure bismuth ferrite (BiFeO3, BFO) and ZnO thin films, as well as BFO/ZnO and ZnO/BFO composite thin films were successfully deposited by a sol-gel process on Pt/Ti/SiO2/Si and FTO/glass substrates, respectively. The chemical composition, surface morphology, optical properties, and multiferroicity were systematically investigated. X-ray diffraction and electron microscopy measurements were used to determine the crystalline phase and to analyze the surface morphology. Evidently, the absorption edges of both BFO/ZnO and ZnO/BFO films show a redshift, broadening the absorption range. The leakage current density decreases with the introduction of ZnO, and the ferroelectricity was significantly improved of the bilayers. Thereinto, BFO/ZnO and ZnO/BFO show the highest saturate polarization (2P
s) of 46.7 μc cm−2 and the maximum remanent polarization (2P
r) of 18.5 μc cm−2, respectively. Meanwhile, the magnetization measurement revealed that both BFO/ZnO and ZnO/BFO exhibiting an enhanced magnetization, especially, BFO/ZnO displays the highest saturation magnetization (2M
s, 68.87 emu cm−3) and remanent magnetization (2M
r, 4.87 emu cm−3).
Prediction of weldment mechanical properties in GMAW with robot-assisted using fuzzy logic systems
Authors: Devendran P , Ashoka Varthanan P
Published: December 2021

Welding operation decides the quality of product standards in all metal work products like automobiles, aerospace vehicles, and many more. The quality of the welding process is more reliable by automating the process with robots. In this research work, the GMAW operation is automated with the ‘Fanuc Robot Arc mate 100iC/12’ robot. The material characteristics such as ultimate tensile strength, hardness, and impact strength of weldments are predicted using a fuzzy system using triangular membership function (TrMF) and trapezoidal membership function (TMF). The simulated results are validated by comparing with experimental work, the experiments are designed using orthogonal array L18, and material characteristics are studied using fractography test. The fuzzy system is trained with experimental results using the IF-Then rule base with the help of the L18 orthogonal array. The inference system has predicted the accuracy rate of weldment mechanical properties, showing a lower error rate.
Programmable quantum simulator boasts up to 256 qubits
Authors: Jarman Sam
Published: December 2021

Physicists have demonstrated a largescale, programmable quantum simulator that features a 2D array of 256 quantum bits (qubits).
Fizzy water droplets levitate at room temperature
Authors: Dumé Isabelle
Published: December 2021

Researchers have come up with a room-temperature way to recreate the Leidenfrost effect and levitate liquid droplets by pumping gaseous carbon dioxide into deionized water.
Japanese particle physicist Toshihide Maskawa dies aged 81
Authors: Banks Michael
Published: December 2021

The Japanese Nobel-prize-winning physicist Toshihide Maskawa has died aged 81. He shared the 2008 Nobel prize for work that led to the prediction of a new family of quarks.
New non-COVID research projects plunge by a third
Authors: Randall Ian
Published: December 2021

A new US analysis suggests that the number of new non-COVID research projects may have fallen by almost a third since the start of the pandemic.
Caroline Herschel medal to honour women in astronomy
Authors: Banks Michael
Published: December 2021

The Caroline Herschel medal is a new award to celebrate outstanding research by women astrophysicists in the UK and Germany with an accompanying prize fund of £10,000.
John Enderby: a passion for physics and publishing
Authors: Banks Michael
Published: December 2021

Michael Banks joins the tributes to Sir John Enderby, the physicist and former chief scientific adviser to IOP Publishing, who died last month aged 90
The wonder of Weinberg
Authors: Durrani Matin
Published: December 2021

Steven Weinberg, who has died at 88, was probably the greatest theorist of his age
Where did all the calculus go?
Authors: Bell Niki
Published: December 2021

Niki Bell argues that mathematics A-level could be reformed so that it does more to support physics students.
Crossing the valley
Authors: McKenzie James
Published: December 2021

In his third article on funding hi-tech firms, James McKenzie looks at recent initiatives to help them jump over the “valley of death”.
The enduring mystery of the solar corona
Authors: Judge Philip G
Published: December 2021

Physicists have long known that the Sun’s magnetic fields make its corona much hotter than the surface of the star itself. But how – and why – those fields transport and deposit their energy is still a mystery, as Philip G Judge explains.
Keeping nuclear secrets
Authors: Harris Margaret
Published: December 2021

Margaret Harris reviews Restricted Data: the History of Nuclear Secrecy in the United States.
Flights of fancy, feet on the ground
Authors: Moriarty Philip
Published: December 2021

Philip Moriarty reviews Fear of a Black Universe: an Outsider’s Guide to the Future of Physics by Stephon Alexander.
A demon of a puzzle
Authors: Randall Ian
Published: December 2021

In 1871 James Clerk Maxwell proposed a puzzle now known as “Maxwell’s Demon” in his book Theory of Heat. We celebrate its 150th anniversary in this thermodynamics-themed cryptic crossword compiled by Ian Randall.
Global perspectives of the bulk electronic structure of URu2Si2 from angle-resolved photoemission
Authors: Denlinger J D , Kang J-S , Dudy L , Allen J W , Kim Kyoo , Shim J-H , Haule K , Sarrao J L , Butch N P , Maple M B
Published: December 2021

Previous high-resolution angle-resolved photoemission (ARPES) studies of URu2Si2 have characterized the temperature-dependent behavior of narrow-band states close to the Fermi level (E
F) at low photon energies near the zone center, with an emphasis on electronic reconstruction due to Brillouin zone folding. A substantial challenge to a proper description is that these states interact with other hole-band states that are generally absent from bulk-sensitive soft x-ray ARPES measurements. Here we provide a more global k-space context for the presence of such states and their relation to the bulk Fermi surface (FS) topology using synchrotron-based wide-angle and photon energy-dependent ARPES mapping of the electronic structure using photon energies intermediate between the low-energy regime and the high-energy soft x-ray regime. Small-spot spatial dependence, f-resonant photoemission, Si 2p core-levels, x-ray polarization, surface-dosing modification, and theoretical surface slab calculations are employed to assist identification of bulk versus surface state character of the E
F-crossing bands and their relation to specific U- or Si-terminations of the cleaved surface. The bulk FS topology is critically compared to density functional theory (DFT) and to dynamical mean field theory calculations. In addition to clarifying some aspects of the previously measured high symmetry Γ, Z and X points, incommensurate 0.6a* nested Fermi-edge states located along Z–N–Z are found to be distinctly different from the DFT FS prediction. The temperature evolution of these states above T
HO, combined with a more detailed theoretical investigation of this region, suggests a key role of the N-point in the hidden order transition.
Effects of uniform-allocation constraints in networked common-pool resource extraction games
Authors: Schauf Andrew , Oh Poong
Published: December 2021

Communities that share common-pool resources (CPRs) often coordinate their actions to sustain resource quality more effectively than if they were regulated by some centralized authority. Networked models of CPR extraction suggest that the flexibility of individual agents to selectively allocate extraction effort among multiple resources plays an important role in maximizing their payoffs. However, empirical evidence suggests that real-world CPR appropriators may often de-emphasize issues of allocation, for example by responding to the degradation of a single resource by reducing extraction from multiple resources, rather than by reallocating extraction effort away from the degraded resource. Here, we study the population-level consequences that emerge when individuals are constrained to apply an equal amount of extraction effort to all CPRs that are available to them within an affiliation network linking agents to resources. In systems where all resources have the same capacity, this uniform-allocation constraint leads to reduced collective wealth compared to unconstrained best-response extraction, but it can produce more egalitarian wealth distributions. The differences are more pronounced in networks that have higher degree heterogeneity among resources. In the case that the capacity of each CPR is proportional to its number of appropriators, the uniform-allocation constraint can lead to more efficient collective extraction since it serves to distribute the burden of over-extraction more evenly among the network’s CPRs. Our results reinforce the importance of adaptive allocation in self-regulation for populations who share linearly degrading CPRs; although uniform-allocation extraction habits can help to sustain higher resource quality than does unconstrained extraction, in general this does not improve collective benefits for a population in the long term.
A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings
Authors: Shen Hongru , Shen Xilin , Feng Mengyao , Wu Dan , Zhang Chao , Yang Yichen , Yang Meng , Hu Jiani , Liu Jilei , Wang Wei , Li Yang , Zhang Qiang , Yang Jilong , Chen Kexin , Li Xiangchun
Published: December 2021

Advancement in single-cell RNA sequencing leads to exponential accumulation of single-cell expression data. However, there is still lack of tools that could integrate these unlimited accumulations of single-cell expression data. Here, we presented a universal approach iSEEEK for integrating super large-scale single-cell expression via exploring expression rankings of top-expressing genes. We developed iSEEEK with 11.9 million single cells. We demonstrated the efficiency of iSEEEK with canonical single-cell downstream tasks on five heterogenous datasets encompassing human and mouse samples. iSEEEK achieved good clustering performance benchmarked against well-annotated cell labels. In addition, iSEEEK could transfer its knowledge learned from large-scale expression data on new dataset that was not involved in its development. iSEEEK enables identification of gene–gene interaction networks that are characteristic of specific cell types. Our study presents a simple and yet effective method to integrate super large-scale single-cell transcriptomes and would facilitate translational single-cell research from bench to bedside.
TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power
Authors: Fancello Laura , Guida Alessandro , Frige Gianmaria , Ceol Arnaud Gerard Michel , Babini Gabriele , Scaglione Giovanni Luca , Zanfardino Mario , Mazza Tommaso , Ferrando Lorenzo , Pelicci Pier Giuseppe , Mazzarella Luca
Published: December 2021

Motivation

Tumor mutational burden (TMB) has been proposed as a predictive biomarker for immunotherapy response in cancer patients, as it is thought to enrich for tumors with high neoantigen load. TMB assessed by whole-exome sequencing is considered the gold standard but remains confined to research settings. In the clinical setting, targeted gene panels sampling various genomic sizes along with diverse strategies to estimate TMB were proposed and no real standard has emerged yet.

Results

We provide the community with TMBleR, a tool to measure the clinical impact of various strategies of panel-based TMB measurement.

Availability and implementation

R package and docker container (GPL-3 Open Source license): https://acc-bioinfo.github.io/TMBleR/. Graphical-user interface website: https://bioserver.ieo.it/shiny/app/tmbler.

Supplementary information

Supplementary data are available at Bioinformatics online.
Identifying cancer pathway dysregulations using differential causal effects
Authors: Jablonski Kim Philipp , Pirkl Martin , Ćevid Domagoj , Bühlmann Peter , Beerenwinkel Niko
Published: December 2021

Motivation

Signaling pathways control cellular behavior. Dysregulated pathways, for example, due to mutations that cause genes and proteins to be expressed abnormally, can lead to diseases, such as cancer.

Results

We introduce a novel computational approach, called Differential Causal Effects (dce), which compares normal to cancerous cells using the statistical framework of causality. The method allows to detect individual edges in a signaling pathway that are dysregulated in cancer cells, while accounting for confounding. Hence, technical artifacts have less influence on the results and dce is more likely to detect the true biological signals. We extend the approach to handle unobserved dense confounding, where each latent variable, such as, for example, batch effects or cell cycle states, affects many covariates. We show that dce outperforms competing methods on synthetic datasets and on CRISPR knockout screens. We validate its latent confounding adjustment properties on a GTEx (Genotype–Tissue Expression) dataset. Finally, in an exploratory analysis on breast cancer data from TCGA (The Cancer Genome Atlas), we recover known and discover new genes involved in breast cancer progression.

Availability and implementation

The method dce is freely available as an R package on Bioconductor (https://bioconductor.org/packages/release/bioc/html/dce.html) as well as on https://github.com/cbg-ethz/dce. The GitHub repository also contains the Snakemake workflows needed to reproduce all results presented here.

Supplementary information

Supplementary data are available at Bioinformatics online.
Safety of transoesophageal echocardiography during structural heart disease interventions under procedural sedation: a single-centre study
Authors: Afzal Shazia , Zeus Tobias , Hofsähs Timo , Kuballa Matti , Veulemans Verena , Piayda Kerstin , Heidari Houtan , Polzin Amin , Horn Patrick , Westenfeld Ralf , Kelm Malte , Hellhammer Katharina
Published: December 2021

Aims

The aim of this study was to determine the incidence of transoesophageal echocardiography (TOE)-related adverse events (AEs) during structural heart disease (SHD) interventions and to identify potential risk factors.

Methods and results

We retrospectively analysed 898 consecutive patients undergoing TOE-guided SHD interventions under procedural sedation. TOE-related AEs were classified as bleeding complications, mechanical lesions, conversion to general anaesthesia with intubation, and the occurrence of pneumonia. A follow-up was conducted up to 3 months after the intervention. TOE-related AEs were observed in 5.3% of the patients (n = 48). The highest rate of AEs was observed in the percutaneous mitral valve repair (PMVR) group with 8.2% (n = 32), whereas 4.8% (n = 11) of the patients in the left atrial appendage group and 1.8% (n = 5) in the patent foramen ovale/atrial septal defect group developed a TOE-related AE (P = 0.001). The most frequent AE was pneumonia with an incidence of 2.6% (n = 26) in the total cohort. Bleeding events occurred in 1.8% (n = 16) of the patients, mostly in the PMVR group with 2.1% (n = 8). In the multivariate regression analysis, we found a lower haemoglobin {odds ratio (OR) [95% confidence interval (CI)]: 8.82 (0.68–0.98) P = 0.025} and an obstructive sleep apnoea syndrome (OSAS) [OR (95% CI): 2.51 (1.08–5.84) P = 0.033] to be associated with AE. Furthermore, AEs were related to procedural time [OR (95% CI): 1.01 (1.0–1.01) P = 0.056] and oral anticoagulation [OR (95% CI): 1.97 (0.9–4.3) P = 0.076] with borderline significance in the multivariate regression analysis. No persistent damages were observed.

Conclusion

TOE-related AEs during SHD interventions are clinically relevant. It was highest in patients undergoing PMVR. A lower baseline haemoglobin level and an OSAS were found to be associated with the occurrence of a TOE-related AE.
Multi-territory stroke preceded by pulmonary embolism with asymptomatic coronavirus disease 2019: a case report
Authors: Van Herck Jakob , Thoen Hendrik , Delens Christophe , Voet Joeri
Published: December 2021

Background

Non-bacterial thrombotic endocarditis is characterized by the presence of sterile vegetations on a cardiac valve. We present a case of multi-territory stroke caused by embolism of a non-bacterial thrombotic aortic valve endocarditis, leading to the diagnosis of a prostate adenocarcinoma with bone metastases.

Case summary

A 66-year-old patient was diagnosed with pulmonary embolism, first attributed to an asymptomatic coronavirus disease 2019 infection. Edoxaban was started, which was discontinued by the patient. Four weeks later, he presented with subacute vertigo and balance disorders. Magnetic resonance imaging showed a multi-territory stroke. A transoesophageal echocardiogram demonstrated a small vegetation on the aortic valve with moderate aortic insufficiency. Blood cultures remained negative. Malignancy screening showed a markedly elevated prostate-specific antigen. Prostate adenocarcinoma was confirmed on biopsy. A positron emission tomography revealed metastatic disease. A diagnosis of non-bacterial thrombotic endocarditis and paraneoplastic pulmonary embolism secondary to prostate cancer was made. Edoxaban was restarted and the patient was referred for treatment of the prostate adenocarcinoma. Follow-up after 5 months showed no evidence of aortic valve vegetations.

Discussion

Coronavirus disease 2019 in ambulatory patients may be insufficient as a predisposing factor for venous thrombo-embolism and these patients, especially the elderly, should undergo a screening for malignancy. Non-bacterial thrombotic endocarditis is a rare cause of multi-territory stroke. When related to cancer, the prostate can be the primary tumour.
Do individuals’ attitudes toward immigrants affect their own health? Analysis of 15 European countries
Authors: Pinillos-Franco Sara , Kawachi Ichiro
Published: December 2021

Background

Hostility toward others is related to negative emotions, which is hypothesized to have negative health consequences. In this article, we sought to test the relationship between individuals’ attitudes toward immigrants and their self-rated health (SRH) across time in large dataset of 15 European countries.

Methods

We used the 2010, 2012, 2014 and 2016 waves of the European Social Survey, which include information about attitudes toward immigrants and individuals’ SRH.

Results

Combining all countries and survey years, we found an association between negative attitudes toward immigrants and fair/poor SRH. However, when analyzing the relationship within each country, we found variations (depending on the year of the survey) in some countries, such as Hungary, Poland, Portugal, Sweden and Slovenia. Additionally, we found that there are more middle class individuals who hold unfavorable attitudes toward immigrants over time.

Conclusions

In general, poor attitudes toward immigrants are associated with higher odds of reporting fair/poor health, although the ‘health advantage’ of those with favorable attitudes is diminishing over time. However, in some countries, this relationship is contingent on when the survey was conducted, possibly reflecting the changing composition of individuals who hold unfavorable attitudes toward immigrants.
The role of health literacy in the association between academic performance and substance use
Authors: Kinnunen Jaana M , Paakkari Leena , Rimpelä Arja H , Kulmala Markus , Richter Matthias , Kuipers Mirte A G , Kunst Anton E , Lindfors Pirjo L
Published: December 2021

Background

To address social inequalities in adolescent substance use and consequent disparities in health, it is important to identify the mechanisms of the association between substance use and academic performance. We study the role of health literacy (HL) in the association between academic performance and weekly smoking, monthly alcohol use and cannabis ever-use among adolescents in Europe.

Methods

SILNE-R school survey data, which was collected in 2016–17 with paper-and-pencil-method from Hanover (GE), Amersfoort (NL) and Tampere (FI), were used (N = 5088, age 13–19). Health Literacy for School-aged Children instrument was used to assess students’ HL. Logistic regression analyzed the association of substance use with academic performance and HL, separately and in the same model. Linear and multinomial logistic regression analyzed the association between academic performance and HL.

Results

Poor academic performance compared with high was associated with smoking [odds ratio (OR) 3.94, 95% confidence interval (CI) 2.83–5.49], alcohol use (OR: 2.94, 95% CI: 2.34–3.68) and cannabis use (OR: 2.56, 95% CI: 1.89–3.48). Poor HL was also associated with each substance use (with ORs of 2.32, 1.85 and 1.29). HL was positively associated with academic performance (β = 1.04, 95% CI: 0.89–1.20). The associations between academic performance and substance use were only slightly attenuated after controlling for HL.

Conclusions

Academic performance and HL were both determinants of substance use, confirming their role in tackling the disparities in substance use. However, HL did not demonstrably mediate the association between academic performance and substance use. A wider set of factors needs to be tackled to address emerging social inequalities in adolescent substance use.
Strip Clearcutting Drives Vegetation Diversity and Composition in the Moso Bamboo Forests
Authors: Zheng Yaxiong , Fan Shaohui , Guan Fengying , Xia Wen , Wang Shumei , Xiao Xiao
Published: December 2021

Strip clearcutting of Moso bamboo forests in southern China has seen increasing interest as a way of reducing harvesting costs. Previous research has shown that cutting influences the overstory structure and drives changes in the microclimate and soil properties. However, the effects of strip cutting on understory vegetation diversity and composition remain unclear. To better understand the influence of cutting on the understory vegetation, this study compares sites under natural restoration after cut and uncut sites in the Moso bamboo forest. We selected plots that were cut in 2019 (C19) and 2017 (C17), as well as unharvested plots as controls (CK). The results showed that strip clearcutting increased the understory vegetation richness and diversity, and a significant difference (A = 0.23, P = 0.001) existed in the composition of the vegetation between the three treatments. Furthermore, the decrease of soil total phosphorus and total potassium content resulted in the difference in undergrowth vegetation distribution and composition between the uncut plots and the cut plots. Our results suggest that strip clearcutting may not be harmful to biodiversity on a local scale in the Moso bamboo forest.