bluuebunny/crossref_metadata_2025 huggingface dataset:
Decoding Spatial Configuration: Resiliency in the Periphery (Case Study: Sedati Sidoarjo)
Authors: Mutia Fairuz , Safeyah Muchlisiniyati , Susanti Wiwik Dwi
Published: December 2022

Rural and urban communities merge. Sedati’s districts are vulnerable due to a lack of infrastructure, dispersed populations, disaster management capacities, and subsistence. A city is resilient if its citizens can survive and recover from a disaster. These relationships allow for implementing programs that promote urban and rural resilience. How do urban spatial patterns affect resilience determinants? This research examines the typo-morphological urban layout of Sedati District to discover the periphery’s resilience and current situation. By using typo – morphological analysis and space syntax analysis researcher seeks the configuration of typology and morphology of the area. The results show that global connectivity and integration exist only in the center of Sedati District (HH3). Disconnecting two nodes won’t stop the network if there are multiple pathways. Sedati’s axial lines cease in space. Decreases road strength. Controlling expansion and using land efficiently, fostering urban and peri-urban agriculture, and making urban hubs inaccessible to nature are local solutions. Sedati lacks mixed-use clusters and pedestrian mobility. Urban livelihood, activity, and total life resilience reflect a ‘center-periphery’ spatial structure with expanding and declining gradients. Looping spatial syntactic configurations are needed for a robust urban fabric. Mixed-use land helps urban clusters’ peripheries.
Spatial Study of Oil Palm Plant Health Using Sentinel 2 Imagery at PTPN VIII Cikasungka Plantation, Bogor, West Java
Authors: Akmal Zakiy , Wibowo Adi , Hernina Revi , Pin Tjiong Giok
Published: December 2022

Oil palm (Elaeis guineensis Jacq.) is a plantation commodity that is the highest producer and exporter in Indonesia and has high economic value. Increasing oil palm productivity requires several factors, one of which is plant health. Therefore, detecting the health condition of oil palm plants requires research with spatial analysis and a remote sensing method that can monitor plantation data collection strategies efficiently and effectively. One of them is Sentinel-2 using the NDVI algorithm. The algorithm can estimate the relationship between vegetation and health conditions. This study resulted in very healthy plants having NDVI values ranging from 0.80-0.85, healthy plants having NDVI values ranging from 0.76-0.80, critical plants having NDVI values ranging from 0.72-0.76, and unhealthy plants having NDVI values ranging from 0.68-0.72. The distribution of the NDVI value at the PTPN VIII Cikasungka Plantation in January 2022 has a high NDVI value and is spread over every area of the district.
Diagenesis of Subang Formation in Cibeet River, Bogor, West Java
Authors: Nasution R S , Luthfiyyah A , Aditiyo Rezky , Septyandy M R
Published: December 2022

Subang Formation is one of many turbidite flow-induced sediment that built Bogor Trough, Java. Despite its marine origin, the exposure to the meteoric environment and burial process caused this formation to go under diagenesis, thus altering its primary characteristics. Intensive cementation by equant calcite, feldspar alteration, and grain dissolution indicates diagenesis in a meteoric environment. The cementation process filled primary and secondary pores, decreasing the primary porosity. On the other hand, the dissolution of the grain formed new secondary porosities. The presence of stylolites and fractured fragments indicated the formation had experienced burial. Although compaction often decreases rock’s porosity, the fracturing of the rocks due to compaction leads to fracture porosity formation, increasing rock’s porosity. Analyzing the compaction signs that destroyed the cementation and dissolution features in the rock samples, it is assumed that the diagenesis had occurred in the meteoric environment before it occurred in the burial environment. This study showed that the heterogeneity of the Subang Formation in the Cibeet River resulted from all these diagenesis processes mentioned above. Furthermore, the diagenesis study of the Subang Formation can be implemented as a preliminary stage to determine the quality of the petroleum reservoir. Diagenesis of Subang Formation in Cibeet River, Bogor, West Java.
Environmental Impact Assessment on Plastic Waste Recycling Business in Bengkulu City, Indonesia
Authors: Puspita Sisilia Dwi , Sodri Ahyahudin , Utomo Suyud Warno
Published: December 2022

In Indonesia, small-scale plastic recycling businesses dominate the plastic waste recycling business. The practice of plastic waste recycling in developing countries also does not pay attention to the Environment and is not energy and material efficient during the process. Andusti Simpari company in Bengkulu City is one of the small-scale plastic waste recycling companies that face common problems such as the use of human labor, inefficient energy, and lack of liquid waste management, which has the potential to cause eutrophication and produce greenhouse gases in the form of CO2 which can contribute to global warming. This study aims to assess the environmental impact of eutrophication and the global warming potential (GWP) of businesses using the Life Cycle Assessment (LCA) method. Cradle to grave LCA is applied to small-scale plastic waste recycling, with 1000kg of shredded plastic/day production capacity. From the LCA analysis, it is known that to produce 1 kg of shredded plastic can produce as much as 0.97363 KgCO2eq of pollutants that contribute to the Global Warming Potential (GWP) and eutrophication of 0.01492 kg PO4.
Processing Efforts and Resource Efficiency in Achieving Green Campus at the State University of Surabaya, Indonesia
Authors: Rahaju Tjitik , Megawati Suci , Meirinawati  , Prabawati Indah , Fanida Eva Hany , Arianto Kurniawan Fery , Salsabila Faza Saila
Published: December 2022

Efforts to reduce global warming based on green campuses are still not widely realized. A green campus is one of the concepts to build a sustainable campus that is environmentally friendly in higher education institutions. A long-term strategy is needed to create a green campus. This study aims to describe efforts to manage and utilize resources to create a green campus area and promote it as an alternative to sustainable campus management at the State University of Surabaya (Unesa). This research is descriptive. The data collection technique was carried out using a literature study approach, collecting, classifying, analyzing, visualizing, validating data, and drawing conclusions. This study found that in realizing a green campus in universities, management actions and resource utilization were needed to initiate the presence of Unesa’s green campus, namely an eco-campus with efficient governance. The management and efficiency of resources at the State University of Surabaya have not only succeeded in bringing about efforts to manage a green campus at the institutional level but also proved that a green campus can have implications for the concept of sustainable development. This study has limitations on the sources of data obtained by the author. However, this limitation opens up opportunities for other researchers to fill it. Realizing a green campus can be an alternative solution amid global efforts to achieve SDGs goals.
The Management Concept of Mountain-Based Destination through Carrying Capacity Analysis
Authors: Rahmafitria Fitri , Nurazizah Ghoitsa Rohmah
Published: December 2022

The increasing number of tourists and the intensive development of infrastructure can lead to the decline of the carrying capacity, especially if ignoring the concept of sustainable management. The preservation aspect embellishes the focal concern in mountainous areas, while the increasing number of tourists has become the main reason to gain financial benefits. The research aims to assess the carrying capacity level in Situ Patengang Nature Park, Bandung. The study was carried out using a descriptive-explanatory approach with three different analytic methods: 1) GIS analysis to map the carrying capacity zones, 2) Important-Performance comparison analysis to assess the management performance, and 3) Triangulation analysis to arrange the tourism development concept. The results show that most Situ Patengang Nature Park areas have low carrying capacity, medium quality of the environment, high tolerance of natural resources, less dispersion of tourist activities, fewer benefits of natural resources, and low environmental management. The development concept of Situ Patengang Nature Park should apply the five principles of ecotourism which lead to ecologically, financially, and socially sustainable activities. For the zonation, the management should bind the core zone in high carrying capacity zones, a service zone in the medium carrying capacity zone, and a buffer zone in the low carrying capacity zone.
Self-Reported Pharmaceutical Storage, Use, and Improper Disposal to The Environment Among Urban Parents in Indonesia
Authors: Nastiti Anindrya , Riyanto Arlieza Raudhah , Supriatin Ade , Roosmini Dwina , Kusumah Siska WD , Milhan Rumaisha , Geerling Gertjan
Published: December 2022

Pharmaceuticals are increasingly used to treat and prevent disease globally. However, this trend has the potential to increase pharmaceutical discharge into the environment, especially from households. Pharmaceuticals released into the environment can harm human health, e.g., antimicrobial resistance. Thus, it is important to understand the drivers of pharmaceutical use, storage, and disposal among the community. The main objectives of this study are twofold: (1) to identify the commonly stored and used pharmaceuticals based on its classification; and (2) to identify the disposal method of unused pharmaceuticals at home. In October 2018, an exploratory online survey was conducted on 262 urban parents in the Jabodetabek area and Bandung with children ≤5 years old. This online survey revealed that the most stored medicine at home was acetaminophen. Irrational use of medicines was more common in the treatment-seeking behavior of parents rather than children. Doctor’s prescription is the most factor affecting buying decisions of pharmaceuticals at home, whether for themselves or their children. In most cases, pharmaceutical waste was treated as domestic waste, which was improper disposal. To reduce improper use and disposal, we suggest a targeted campaign to raise awareness of pharmaceutical waste’s unintended health and environmental impacts.
The Effect of Washing and Air Scouring on The Performance of Immersed Membrane Microfiltration
Authors: Marsono Bowo Djoko , Ujiane Virgina Jane
Published: December 2022

The quality of raw water in Surabaya is decreasing, and conventional treatment units are no longer efficient in treating raw water to become drinking water. Microfiltration membranes applied in sedimentation units can produce better quality results on limited land that uses a small number of chemicals. The material will be deposited on the membrane’s surface throughout the filtration process. The deposition of these materials can cause fouling, leading to a decrease in membrane productivity. This study involved a detailed investigation into the membrane washing method and air scouring implication in the microfiltration process to understand the most efficient technique to increase membrane productivity. Washing was done manually with a gentle scrubbing method and backwashing with time variation for 20 minutes and 10 minutes. Air Scouring was done with air pressure variations of 0,3 bar and 0,6 bar. The study showed that water flux was affected by the washing and air scouring method. Permeate quality was also found to be affected by washing and air scouring variation. Permeate quality analyses in this study are turbidity, TSS, micro-plastics, E-Coli, and organic substances.
Determining the Feasibility of a Circular Economy for Plastic Waste from the Construction Sector in New Zealand
Authors: Berry T-A , Low J K , Wallis S L , Kestle L , Day A , Hernandez G
Published: December 2022

By 2012, the annual quantity of C&D waste produced by 40 countries had reached three billion tonnes, contributing 10-50% to total municipal solid waste around the world. Recent data from Australia and New Zealand estimated a combined contribution of approximately 28 million tonnes C&D waste to landfill for just 0.4% of the world’s population. If C&D waste was produced at an equal rate around the world, global production could be close to seven billion tonnes. In 2015, the global production of plastic waste from building and construction was 13 million tonnes. It is estimated that annually, C&D waste contributes ≥25,000 tonnes to the total amount of plastic landfilled in one major city (Auckland) alone. Waste audits from four sites demonstrated that this was predominantly polyethylene (PE) or polyvinyl chloride (PVC), and was derived from packaging, building componentry and building protection equally. The aims of this study were to implement a ‘foundations to completion’ plastic waste audit on a new secondary school in Auckland, New Zealand. This sheds light on the nature of the plastic waste, e.g., type, use and potential for recyclability or reuse. The aim was to also identify the challenges in the construction industry that hinder effective waste diversion from landfill, and to trial practical on-site solutions.
Development of A Framework for Urban Heat Adaptation in 15-Minute City
Authors: Chen Xueke , He Bao-Jie
Published: December 2022

Urban heat has challenged many cities with serious environmental, economic, social and health consequences. Urban heat also deteriorates the achievement of 15-Minute City (FMC) which is a basic community unit to apply planning and design practices to achieve safety, sustainability, resilience and inclusion required by the goal of Sustainable Cities and Communities (Goal 11) by the United Nations Sustainable Development Goals. Heat adaptation strategies are of importance to secure people from heat-induced immediate impacts. However, there are limited studies on how to integrate heat adaptation strategies into FMC for avoiding heat-induced impacts. Therefore, this paper aims to construct a framework that can support the integration of urban heat adaptation (UHA) into FMC planning and design. The framework is expected to combine FMC and UHA goals, identify urban heat impacts, recognise heat-induced impact influential factors, suggest heat adaptation strategies and optimise adaptation performance. Following this conception, an analysis of FMC and UHA goals, heat-induced impact and assessment indicators, regulatory factors, heat adaptation strategies, and sensitivity assessment models has been conducted. Finally, a comprehensive FMC-UHA framework for addressing urban heat challenges is generated. Overall, this framework provides a reference for creating cool 15-minute cities, as well as guidance on how to avoid heat impacts, health and safety inclusion, low-carbon travel, and outdoor productivity.
Developing a ‘Design with Reuse’ guide. Case study analysis from a design procedural perspective for the integration of reclaimed wood in façade architecture.
Authors: Kawa G. , Galle W. , De Temmerman N.
Published: December 2022

Today’s excessing construction industry leads to exhaustion of raw materials and large-scale waste production, resulting in environmental and societal problems. In response, there is a growing interest among academic researchers, designers, and policymakers to accelerate the shift toward a circular construction sector. To achieve this transition towards an economy with closed material loops, solutions for resources need to be developed and adopted. Material reuse is such a solution. Yet today reuse is still an uncommon practice.

This study aims to increase the viability of reuse possibilities of reclaimed materials in façade architecture and to attain insights into the design processes that enable and support reuse. Reuse projects are emerging, yet limited literature exists on design processes to reuse building materials. Through collaboration with designers of reuse projects, their design approach can be grasped and inspire others. In this paper, the focus is laid on two exemplary building projects, in Belgium and France, where reclaimed wood is used for the façade architecture. Interviews with designers allowed to map and analyse their design processes, revealing similar crucial steps for reuse in each design phase. As a result, a prototype of a ‘design with reuse’ guide is developed. Such a design instrument offers guidance for building designers to consider and include reclaimed materials, and hence, more circular design solutions, in their projects.
Embodied Carbon: A call to the building industry
Authors: Rondinel-Oviedo Daniel R. , Keena Naomi
Published: December 2022

The demand for building materials will increase drastically in the following decades due to urbanization and population growth. Buildings generate almost 40% of annual global carbon dioxide (CO2) emissions contributing to human-induced climate change. Of this fraction, 11% is associated with material production and building construction, and 28% is contributed to the operational activities of a building (heating, cooling, lighting). One primary measure of the climate impact of buildings is embodied carbon (EC). This paper aims to find the recent developments in relation to embodied carbon within the building industry. To achieve this goal, a literature review was conducted to study the EC concept concerning materials and construction. The article explores and presents the state-of-the-art of diverse research and development related to this concept, focusing primarily on (1) the carbon cycle and the building sector, (2) EC benchmarking, (3) bio-based materials, and (4) other low-carbon material alternatives such as the development of carbon capture technologies. The objective of this paper is to summarize current and emerging trends as well as research priorities and tools to inform designers and engineers and facilitate their decision-making during the design process. It also aims to facilitate in advancing the creation of regulations and policies toward natural-based material solutions and the development of low-carbon high-tech material technologies deemed central for a sustainable built environment.
Variability in modelled reservoir greenhouse gas emissions: comparison of select US hydropower reservoirs against global estimates
Authors: Hansen Carly , Pilla Rachel , Matson Paul , Skinner Bailey , Griffiths Natalie , Jager Henriette
Published: December 2022

Greenhouse gas (GHG) emissions from reservoirs have most often been evaluated on a global extent through areal scaling or linear-regression models. These models typically rely on a limited number of characteristics such as age, size, and average temperature to estimate per reservoir or areal flux. Such approaches may not be sufficient for describing conditions at all types of reservoirs. Emissions from hydropower reservoirs have received increasing attention as industry and policy makers seek to better understand the role of hydropower in sustainable energy solutions. In the United States (US), hydropower reservoirs span a wide range of climate regions and have diverse design and operational characteristics compared to those most heavily represented in model literature (i.e., large, tropical reservoirs). It is not clear whether estimates based on measurements and modeling of other subsets of reservoirs describe the diverse types of hydropower reservoirs in the US. We applied the Greenhouse Gas from Reservoirs (G‐res) emissions model to 28 hydropower reservoirs located in a variety of ecological, hydrological, and climate settings that represent the range of sizes and types of facilities within the US hydropower fleet. The dominant pathways for resulting GHG emissions estimates in the case-study reservoirs were diffusion of carbon dioxide, followed by methane ebullition. Among these case-study reservoirs, total post-impoundment areal flux of carbon ranges from 84 to 767 mgCm−2d−1, which is less variable than what has been reported through measurements at other US and global reservoirs. The net GHG reservoir footprint was less variable and towards the lower end of the range observed from modeling larger global reservoirs, with a range of 138 to 1,052 g CO2 eq m−2 y−1, while the global study reported a range of 115 to 145,472 g CO2 eq m−2 y−1. High variation in emissions normalized with respect to area and generation highlights the need to be cautious when using area or generation in predicting or communicating emissions footprints for reservoirs relative to those of other energy sources, especially given that many of the hydropower reservoirs in the US serve multiple purposes beyond power generation.
Integrated model for BIM and risk data in construction projects
Authors: Yasser Mamdoh , Rashid Ibrahim Abdel , Nagy Alsayed Mohamed , Elbehairy Hatem Shaker
Published: December 2022

The acceleration in the adoption of building information modelling (BIM) techniques in many countries around the world makes BIM technology a global research trend. A few studies have shown how risk information can be properly managed in a BIM environment. This research aims to improve the risk management process using BIM techniques and proposes a new methodology within a BIM system to manage risk information for construction projects. The risk register, which represents the final risk information, and the Revit program, which represents one of the BIM platforms, are integrated using the Dynamo program in this paper’s proposed new method for integrating risk information with the BIM system. Two types of information are automatically transferred from the risk register to the BIM model: first, data and numbers, such as ‘Risk score,’ ‘Risk status,’ etc; this allows integration of risk information with the rest of the project parameters in the BIM system to achieve BIM system integration. Second, colors, where the elements are coloured the same colour as the degree of risk in the risk register. The proposed methodology demonstrates how visualisation can be used to identify risks, as visualisation is one of the most important features of BIM, and how risk information can be linked to BIM, making risk management more effective and accurate than the traditional method.
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
Authors: Beslic Denis , Tscheuschner Georg , Renard Bernhard Y , Weller Michael G , Muth Thilo
Published: December 2022

Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
spaCI: deciphering spatial cellular communications through adaptive graph model
Authors: Tang Ziyang , Zhang Tonglin , Yang Baijian , Su Jing , Song Qianqian
Published: December 2022

Cell–cell communications are vital for biological signalling and play important roles in complex diseases. Recent advances in single-cell spatial transcriptomics (SCST) technologies allow examining the spatial cell communication landscapes and hold the promise for disentangling the complex ligand–receptor (L–R) interactions across cells. However, due to frequent dropout events and noisy signals in SCST data, it is challenging and lack of effective and tailored methods to accurately infer cellular communications. Herein, to decipher the cell-to-cell communications from SCST profiles, we propose a novel adaptive graph model with attention mechanisms named spaCI. spaCI incorporates both spatial locations and gene expression profiles of cells to identify the active L–R signalling axis across neighbouring cells. Through benchmarking with currently available methods, spaCI shows superior performance on both simulation data and real SCST datasets. Furthermore, spaCI is able to identify the upstream transcriptional factors mediating the active L–R interactions. For biological insights, we have applied spaCI to the seqFISH+ data of mouse cortex and the NanoString CosMx Spatial Molecular Imager (SMI) data of non-small cell lung cancer samples. spaCI reveals the hidden L–R interactions from the sparse seqFISH+ data, meanwhile identifies the inconspicuous L–R interactions including THBS1−ITGB1 between fibroblast and tumours in NanoString CosMx SMI data. spaCI further reveals that SMAD3 plays an important role in regulating the crosstalk between fibroblasts and tumours, which contributes to the prognosis of lung cancer patients. Collectively, spaCI addresses the challenges in interrogating SCST data for gaining insights into the underlying cellular communications, thus facilitates the discoveries of disease mechanisms, effective biomarkers and therapeutic targets.
NetSHy: network summarization via a hybrid approach leveraging topological properties
Authors: Vu Thao , Litkowski Elizabeth M , Liu Weixuan , Pratte Katherine A , Lange Leslie , Bowler Russell P , Banaei-Kashani Farnoush , Kechris Katerina J
Published: December 2022

Motivation

Biological networks can provide a system-level understanding of underlying processes. In many contexts, networks have a high degree of modularity, i.e. they consist of subsets of nodes, often known as subnetworks or modules, which are highly interconnected and may perform separate functions. In order to perform subsequent analyses to investigate the association between the identified module and a variable of interest, a module summarization, that best explains the module’s information and reduces dimensionality is often needed. Conventional approaches for obtaining network representation typically rely only on the profiles of the nodes within the network while disregarding the inherent network topological information.

Results

In this article, we propose NetSHy, a hybrid approach which is capable of reducing the dimension of a network while incorporating topological properties to aid the interpretation of the downstream analyses. In particular, NetSHy applies principal component analysis (PCA) on a combination of the node profiles and the well-known Laplacian matrix derived directly from the network similarity matrix to extract a summarization at a subject level. Simulation scenarios based on random and empirical networks at varying network sizes and sparsity levels show that NetSHy outperforms the conventional PCA approach applied directly on node profiles, in terms of recovering the true correlation with a phenotype of interest and maintaining a higher amount of explained variation in the data when networks are relatively sparse. The robustness of NetSHy is also demonstrated by a more consistent correlation with the observed phenotype as the sample size decreases. Lastly, a genome-wide association study is performed as an application of a downstream analysis, where NetSHy summarization scores on the biological networks identify more significant single nucleotide polymorphisms than the conventional network representation.

Availability and implementation

R code implementation of NetSHy is available at https://github.com/thaovu1/NetSHy

Supplementary information

Supplementary data are available at Bioinformatics online.
NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data
Authors: Huang Neng , Xu Minghua , Nie Fan , Ni Peng , Xiao Chuan-Le , Luo Feng , Wang Jianxin
Published: December 2022

Motivation

Oxford Nanopore sequencing has great potential and advantages in population-scale studies. Due to the cost of sequencing, the depth of whole-genome sequencing for per individual sample must be small. However, the existing single nucleotide polymorphism (SNP) callers are aimed at high-coverage Nanopore sequencing reads. Detecting the SNP variants on low-coverage Nanopore sequencing data is still a challenging problem.

Results

We developed a novel deep learning-based SNP calling method, NanoSNP, to identify the SNP sites (excluding short indels) based on low-coverage Nanopore sequencing reads. In this method, we design a multi-step, multi-scale and haplotype-aware SNP detection pipeline. First, the pileup model in NanoSNP utilizes the naive pileup feature to predict a subset of SNP sites with a Bi-long short-term memory (LSTM) network. These SNP sites are phased and used to divide the low-coverage Nanopore reads into different haplotypes. Finally, the long-range haplotype feature and short-range pileup feature are extracted from each haplotype. The haplotype model combines two features and predicts the genotype for the candidate site using a Bi-LSTM network. To evaluate the performance of NanoSNP, we compared NanoSNP with Clair, Clair3, Pepper-DeepVariant and NanoCaller on the low-coverage (∼16×) Nanopore sequencing reads. We also performed cross-genome testing on six human genomes HG002–HG007, respectively. Comprehensive experiments demonstrate that NanoSNP outperforms Clair, Pepper-DeepVariant and NanoCaller in identifying SNPs on low-coverage Nanopore sequencing data, including the difficult-to-map regions and major histocompatibility complex regions in the human genome. NanoSNP is comparable to Clair3 when the coverage exceeds 16×.

Availability and implementation

https://github.com/huangnengCSU/NanoSNP.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
SIMBSIG: similarity search and clustering for biobank-scale data
Authors: Adamer Michael F , Roellin Eljas , Bourguignon Lucie , Borgwardt Karsten
Published: December 2022

In many modern bioinformatics applications, such as statistical genetics, or single-cell analysis, one frequently encounters datasets which are orders of magnitude too large for conventional in-memory analysis. To tackle this challenge, we introduce SIMBSIG (SIMmilarity Batched Search Integrated GPU), a highly scalable Python package which provides a scikit-learn-like interface for out-of-core, GPU-enabled similarity searches, principal component analysis and clustering. Due to the PyTorch backend, it is highly modular and particularly tailored to many data types with a particular focus on biobank data analysis.

Availability and implementation

SIMBSIG is freely available from PyPI and its source code and documentation can be found on GitHub (https://github.com/BorgwardtLab/simbsig) under a BSD-3 license.
Surviving rectal cancer at the cost of a colostomy: global survey of long-term health-related quality of life in 10 countries
Authors: Kristensen Helle Ø , Thyø Anne , Emmertsen Katrine J , Smart Neil J , Pinkney Thomas , Warwick Andrea M , Pang Dong , Elfeki Hossam , Shalaby Mostafa , Emile Sameh H , Abdelkhalek Mohamed , Zuhdy Mohammad , Poskus Tomas , Dulskas Audrius , Horesh Nir , Furnée Edgar J B , Verkuijl Sanne J , Rama Nuno José , Domingos Hugo , Maciel João , Solis-Peña Alejandro , Espín-Basany Eloy , Hidalgo-Pujol Marta , Biondo Sebastiano , Sjövall Annika , Christensen Peter
Published: December 2022

Background

Colorectal cancer management may require an ostomy formation; however, a stoma may negatively impact health-related quality of life (HRQoL). This study aimed to compare generic and stoma-specific HRQoL in patients with a permanent colostomy after rectal cancer across different countries.

Method

A cross-sectional cohorts of patients with a colostomy after rectal cancer in Denmark, Sweden, Spain, the Netherlands, China, Portugal, Australia, Lithuania, Egypt, and Israel were invited to complete questionnaires regarding demographic and socioeconomic factors along with the Colostomy Impact (CI) score, European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire (QLQ-C30) and five anchor questions assessing colostomy impact on HRQoL. The background characteristics of the cohorts from each country were compared and generic HRQoL was measured with the EORTC QLQ-C30 presented for the total cohort. Results were compared with normative data of reference European populations. The predictors of reduced HRQoL were investigated by multivariable logistic regression, including demographic and socioeconomic factors and stoma-related problems.

Results

A total of 2557 patients were included. Response rates varied between 51–93 per cent. Mean time from stoma creation was 2.5–6.2 (range 1.1–39.2) years. A total of 25.8 per cent of patients reported that their colostomy impairs their HRQoL ‘some’/‘a lot’. This group had significantly unfavourable scores across all EORTC subscales compared with patients reporting ‘no’/‘a little’ impaired HRQoL. Generic HRQoL differed significantly between countries, but resembled the HRQoL of reference populations. Multivariable logistic regression showed that stoma dysfunction, including high CI score (OR 3.32), financial burden from the stoma (OR 1.98), unemployment (OR 2.74), being single/widowed (OR 1.35) and young age (OR 1.01 per year) predicted reduced stoma-related HRQoL.

Conclusion

Overall HRQoL is preserved in patients with a colostomy after rectal cancer, but a quarter of the patients interviewed reported impaired HRQoL. Differences among several countries were reported and socioeconomic factors correlated with reduced quality of life.
Digital distributive leadership in the time of the Covid-19 pandemic—New light on the transition from physical workplaces to digital spaces in Swedish eldercare
Authors: Elmersjö Magdalena , Seldén Daniel
Published: December 2022

The Covid-19 pandemic has had a huge effect on working life in many welfare sectors. An ongoing qualitative study on distributed leadership work in Swedish eldercare has highlighted the premises of needs assessment during the pandemic. This article applies the concepts of distributed leadership, space and temporality to shed new light on the transition from physical workplaces to digital spaces. The article stresses the importance of co-working, co-responsibility and close interaction between leaders and employees, and argues that the ongoing pandemic can help us understand how the digital transition is changing the premises for leadership work in eldercare needs assessments. The empirical material was derived from several organisational levels of needs assessment and both individual interviews and participant observations were conducted. The results confirm how managerial work is in a state of transition that changes the interaction between managers and the needs assessors. Both the challenges and the importance of interaction are enhanced in the digital space.
The biomechanical signature of loss of consciousness: computational modelling of elite athlete head injuries
Authors: Zimmerman Karl A , Cournoyer Janie , Lai Helen , Snider Samuel B , Fischer David , Kemp Simon , Karton Clara , Hoshizaki Thomas B , Ghajari Mazdak , Sharp David J
Published: December 2022

Sports related head injuries can cause transient neurological events including loss of consciousness and dystonic posturing. However, it is unknown why head impacts that appear similar produce distinct neurological effects. The biomechanical effect of impacts can be estimated using computational models of strain within the brain.

Here, we investigate the strain and strain rates produced by professional American football impacts that led to loss of consciousness, posturing or no neurological signs. We reviewed 1280 National Football League American football games and selected cases where the team’s medical personnel made a diagnosis of concussion. Videos were then analysed for signs of neurological events. We identified 20 head impacts that showed clear video signs of loss of consciousness and 21 showing clear abnormal posturing. Forty-one control impacts were selected where there was no observable evidence of neurological signs, resulting in 82 videos of impacts for analysis. Video analysis was used to guide physical reconstructions of these impacts, allowing us to estimate the impact kinematics. These were then used as input to a detailed 3D high-fidelity finite element model of brain injury biomechanics to estimate strain and strain rate within the brain.

We tested the hypotheses that impacts producing loss of consciousness would be associated with the highest biomechanical forces, that loss of consciousness would be associated with high forces in brainstem nuclei involved in arousal and that dystonic posturing would be associated with high forces in motor regions.

Impacts leading to loss of consciousness compared to controls produced higher head acceleration (linear acceleration; 81.5 g ± 39.8 versus 47.9 ± 21.4; P = 0.004, rotational acceleration; 5.9 krad/s2 ± 2.4 versus 3.5 ± 1.6; P < 0.001) and in voxel-wise analysis produced larger brain deformation in many brain regions, including parts of the brainstem and cerebellum. Dystonic posturing was also associated with higher deformation compared to controls, with brain deformation observed in cortical regions that included the motor cortex. Loss of consciousness was specifically associated with higher strain rates in brainstem regions implicated in maintenance of consciousness, including following correction for the overall severity of impact. These included brainstem nuclei including the locus coeruleus, dorsal raphé and parabrachial complex.

The results show that in head impacts producing loss of consciousness, brain deformation is disproportionately seen in brainstem regions containing nuclei involved in arousal, suggesting that head impacts produce loss of consciousness through a biomechanical effect on key brainstem nuclei involved in the maintenance of consciousness.
Altered localization of nucleoporin 98 in primary tauopathies
Authors: Dickson John R , Frosch Matthew P , Hyman Bradley T
Published: December 2022

Nucleoporin 98 is a nuclear pore complex component that is mislocalized in Alzheimer’s disease and the alteration in nucleoporin 98 has been attributed to tau. In order to determine if nucleoporin 98 mislocalization is a general feature of tauopathies, we assessed the localization of nucleoporin 98 in neurons in primary tauopathies, including frontotemporal lobar degeneration-tau, corticobasal degeneration and progressive supranuclear palsy. Immunofluorescence staining was performed on frontal cortex and occipital cortex tissue from cases of primary tauopathies and controls without neurodegenerative disease using antibodies to identify nucleoporin 98, phospho-tau (Ser202, Thr205) monoclonal antibody and neuronal marker microtubule-associated protein 2. The stained tissue was imaged by fluorescence microscopy and the number of neurons with mislocalized nucleoporin 98 and phospho-tau (Ser202, Thr205) monoclonal antibody staining was quantified. In frontal cortex tissue, all primary tauopathies examined demonstrated significantly increased numbers of neurons with abnormal localization of nucleoporin 98 along the nuclear envelope compared with control tissue. Additionally, frontotemporal lobar degeneration-tau and corticobasal degeneration in the frontal cortex demonstrated significantly increased numbers of neurons with a cytoplasmic mislocalization of nucleoporin 98 compared with control tissue. The number of neurons with mislocalized nucleoporin 98 was significantly correlated with the number of neurons with phospho-tau (Ser202, Thr205) monoclonal antibody-positive tau staining. In the occipital cortex, which is relatively spared from pathological tau accumulations in these primary tauopathies, the localization of nucleoporin 98 was not significantly altered. This study demonstrates that nucleoporin 98 mislocalization is a feature of primary tauopathies and is associated with pathological tau accumulation. In the context of prior research demonstrating nucleoporin 98 mislocalization in Alzheimer’s disease and an interaction between tau and nucleoporin 98, these results further support the hypothesis that pathological tau may contribute to nucleoporin 98 mislocalization. Given the critical role of the nuclear pore complex in nucleocytoplasmic transport, the identification of nucleoporin 98 mislocalization in primary tauopathies highlights a potential pathophysiological disruption in these disorders.
Timing and frequency of high temperature events bend the onset of behavioural thermoregulation in Atlantic salmon (Salmo salar)
Authors: O’Sullivan Antóin M , Corey Emily M , Collet Elise N , Helminen Jani , Curry R Allen , MacIntyre Chris , Linnansaari Tommi
Published: December 2022

The role of temperature on biological activities and the correspondent exponential relationship with temperature has been known for over a century. However, lacking to date is knowledge relating to (a) the recovery of ectotherms subjected to extreme temperatures in the wild, and (b) the effects repeated extreme temperatures have on the temperatures that induce behavioural thermoregulation (aggregations). We examined these questions by testing the hypothesis that thermal thresholds which initiate aggregations in juvenile Atlantic salmon (AS) (Salmo salar) are not static, but are temporally dynamic across a summer and follow a hysteresis loop. To test our hypothesis, we deployed custom-made underwater camera (UWC) systems in known AS thermal refuges to observe the timing of aggregation events in a natural system and used these data to develop and test models that predict the temperatures that induce thermal aggregations. Consistent with our hypothesis our UWC observations revealed a range of aggregation onset temperatures (AOT) ranging from 24.2°C to 27.1°C, thus confirming our hypothesis that AOTs are dynamic across summer. Our models suggest it take ~ 11 days of non-thermally taxing temperatures for the AOT to rebound in the study river. Conversely, we found that as the frequency of events increased, the AOT declined, from 27.1°C to 24.2°C. Integrating both model components led to more robust model performance. Further, when these models were tested against an independent data set from the same river, the results remained robust. Our findings illustrate the complexity underlying behavioural thermoregulation in AS—a complexity that most likely extends to other salmonids. The frequency of extreme heat events is predicted to increase, and this has the capacity to decrease AOT thresholds in AS, ultimately reducing their resilience to extreme temperature events.
Comparative outcomes of Toupet fundoplication and magnetic sphincter augmentation
Authors: Asti Emanuele , Milito Pamela , Froiio Caterina , Milani Valentina , Bonavina Luigi
Published: December 2022

Laparoscopic fundoplication is the current surgical gold standard for the treatment of refractory gastroesophageal reflux disease (GERD). Magnetic sphincter augmentation (MSA) is a less invasive, standardized, and reversible option to restore competency of the lower esophageal sphincter. A comparative cohort study was conducted at a tertiary-care referral center on patients with typical GERD symptoms treated with systematic crural repair combined with Toupet fundoplication or MSA. Primary study outcome was decrease of Gastroesophageal Reflux Disease-Health Related Quality of Life (GERD-HRQL) score. Between January 2014 and December 2021, a total of 199 patients (60.3% female, median [Q1–Q3] age: 51.0 [40.0–61.0]) underwent MSA (n = 130) or Toupet fundoplication (n = 69). Operative time and hospital stay were significantly shorter in MSA patients (P < 0.0001). At a median follow-up of 12.0 [12.0–24.0] months, there was a statistically significant decrease of GERD-HRQL score in both patient groups (P = 0.001). The mean delta values did not significantly differ between groups (P = 0.7373). The incidence of severe gas bloating symptoms was similar in the two groups (P = 0.7604), but the rate of persistent postoperative dysphagia was greater in MSA patients (P = 0.0009). Six (8.7%) patients in the Toupet group had recurrent hiatal hernia requiring revisional surgery in one (1.4%). In the MSA group, eight (7.9%) patients necessitated through-the-scope balloon dilation for relief of dysphagia, and six patients had the device removed (4.6%) because of persistent dysphagia (n = 3), device disconnection (n = 1), persistent reflux (n = 1) or need of magnetic resonance (n = 1). Toupet and MSA procedures provide similar clinical outcomes, but MSA is associated with a greater risk of reoperation. Randomized clinical trials comparing fundoplication and MSA are eagerly awaited.
Inference in regression discontinuity designs with high-dimensional covariates
Authors: Kreiss Alexander , Rothe Christoph
Published: December 2022

We study regression discontinuity designs in which many predetermined covariates, possibly much more than the number of observations, can be used to increase the precision of treatment effect estimates. We consider a two-step estimator which first selects a small number of ‘important’ covariates through a localised lasso-type procedure, and then, in a second step, estimates the treatment effect by including the selected covariates linearly into the usual local linear estimator. We provide an in-depth analysis of the algorithm’s theoretical properties, showing that, under an approximate sparsity condition, the resulting estimator is asymptotically normal, with asymptotic bias and variance that are conceptually similar to those obtained in low-dimensional settings. Bandwidth selection and inference can be carried out using standard methods. We also provide simulations and an empirical application.