bluuebunny/crossref_metadata_2025 huggingface dataset:
SPECK: An Unsupervised Learning Approach for Cell Surface Receptor Abundance Estimation for Single Cell RNA-Sequencing Data
Authors: Javaid Azka , Frost H. Robert
Published: October 2022

The rapid development of single cell transcriptomics has revolutionized the study of complex tissues. Single cell RNA-sequencing (scRNA-seq) can profile tens-of-thousands of dissociated cells from a tissue sample, enabling researchers to identify cell types, phenotypes and interactions that control tissue structure and function. A key requirement of these applications is the accurate estimation of cell surface protein abundance. Although technologies to directly quantify surface proteins are available, this data is uncommon and limited to proteins with available antibodies. While supervised methods that are trained on Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data can provide the best performance, this training data is also limited by available antibodies and may not exist for the tissue under investigation. In the absence of protein measurements, researchers must estimate receptor abundance from scRNA-seq data. We thereby developed a new unsupervised method for receptor abundance estimation using scRNA-seq data called SPECK (Surface Protein abundance Estimation using CKmeans-based clustered thresholding) and evaluated its performance against other unsupervised approaches on up to 215 human receptors and multiple tissue types. This analysis reveals that techniques based on a thresholded reduced rank reconstruction (RRR) of scRNA-seq data are effective for receptor abundance estimation with SPECK providing the best overall performance.
Live Cell Lineage Tracing of Dormant Cancer Cells
Authors: Kim Hyuna , Wirasaputra Anna , Kundu Aritra Nath , Esteves Jennifer A.E. , Peyton Shelly R.
Published: October 2022

Breast cancer is a leading cause of global cancer-related deaths, and metastasis is the overwhelming culprit of poor patient prognosis. The most nefarious aspect of metastasis is dormancy, a prolonged period between primary tumor resection and relapse. Current therapies are insufficient at killing dormant cells; thus, they can remain quiescent in the body for decades until eventually undergoing a phenotypic switch, resulting in metastases that are more adaptable and more drug resistant. Unfortunately, dormancy has fewin vitromodels, largely because lab-derived cell lines are highly proliferative. Existing models address tumor dormancy, not cellular dormancy, because tracking individual cells is technically challenging. To combat this problem, we adapted a live cell lineage approach to find and track individual dormant cells, distinguishing them from proliferative and dying cells over multiple days. We applied this approach across a range of differentin vitromicroenvironments. Our approach revealed that the proportion of cells that exhibited long-term quiescence was regulated by both cell intrinsic and extrinsic factors, with the most dormant cells found in 3D collagen gels. We hope this approach will prove useful to biologists and bioengineers in the dormancy community to identify, quantify, and study dormant tumor cells.

Abstract Figure
Spatially Multiplexed Single-molecule Translocations through a Nanopore at Controlled Speeds
Authors: Leitao S.M. , Navikas V. , Miljkovic H. , Drake B. , Marion S. , Blanchet G. Pistoletti , Chen K. , Mayer S. F. , Keyser U. F. , Kuhn A. , Fantner G. E. , Radenovic A.
Published: October 2022

Nanopores are one of the most successful label-free single-molecule techniques with several sensing applications such as biological screening, diagnostics, DNA and protein sequencing1–4. In current nanopore technologies, stochastic processes influence both the selection of the translocating molecule, translocation rate and translocation velocity5,6. As a result, single-molecule translocations are difficult to control spatially and temporally. Here we present a novel method where we engineer precise spatial and temporal control into the single-molecule experiment. We use a glass nanopore mounted on a 3D nanopositioner to spatially select molecules, deterministically tethered on a glass surface, for controlled translocations. By controlling the distance between the nanopore and the glass surface, we can actively select the region of interest on the molecule and scan it a controlled number of times and at controlled velocity. Decreasing the velocity and averaging thousands of consecutive readings of the same molecule increases the signal-to-noise ratio (SNR) by two orders of magnitude compared to free translocations. We applied our method to various DNA constructs, achieving down to single nucleotide gap resolution. The spatial multiplexing combined with the sub-nanometer resolution could be used in conjunction with micro-array technologies to enable screening of DNA, improving point of care devices, or enabling high-density, addressable DNA data storage.
Association of Kallikrein Related Peptidase 3 (KLK3) Gene with Dermatophytosis in the UK Biobank cohort
Authors: Lehrer Steven , Rheinstein Peter H.
Published: October 2022

In a previous genome wide association study (GWAS) of UK Biobank (UKB) data, we identified one susceptibility locus, Tubulointerstitial Nephritis Antigen (TINAG), with genome wide significance for dermatophytosis. We used genotype calls from file UKB22418. These data are derived directly from Affymetrix DNA microarrays but are missing many genotype calls. Using computationally efficient approaches, UKB has entered imputed genotypes into a second dataset, UKB22828, increasing the number of testable variants by over 100-fold to 96 million variants. In the current study, we used UKB imputed genotypes in UKB22828 to identify dermatophytosis susceptibility loci.

Methods

To identify cases of dermatophytosis, we used ICD10 code B35, which covers Tinea barbae, Tinea capitis, Tinea unguium, Tinea manuum, Tinea pedis, Tinea corporis, Tinea imbricata, Tinea cruris, other dermatophytoses, and dermatophytosis, unspecified. We used PLINK, a whole-genome association analysis toolset, to analyze the UKB22828 chromosome files.

Results

GWAS summary (Manhattan) plot of the meta-analysis association statistics highlighted two susceptibility loci, TINAG and Kallikrein Related Peptidase 3 (KLK3), with genome wide significance for dermatophytosis.

Conclusion

KLK3 may be a dermatophytosis susceptibility gene. KLK3 could affect risk of dermatophytosis, since kallikreins are necessary for normal homeostasis of the skin.
Evidence for a Spoken Word Lexicon in the Auditory Ventral Stream
Authors: Damera Srikanth R. , Chang Lillian , Nikolov Plamen P. , Mattei James A. , Banerjee Suneel , Glezer Laurie S. , Cox Patrick H. , Jiang Xiong , Rauschecker Josef P. , Riesenhuber Maximilian
Published: October 2022

The existence of a neural representation for whole words (i.e., a lexicon) is a common feature of many models of speech processing. Prior studies have provided evidence for a visual lexicon containing representations of whole written words in an area of the ventral visual stream known as the “Visual Word Form Area” (VWFA). Similar experimental support for an auditory lexicon containing representations of spoken words has yet to be shown. Using fMRI rapid adaptation techniques, we provide evidence for an auditory lexicon in the “Auditory Word Form Area” (AWFA) in the human left anterior superior temporal gyrus that contains representations highly selective for individual spoken words. Furthermore, we show that familiarization with novel auditory words sharpens the selectivity of their representations in the AWFA. These findings reveal strong parallels in how the brain represents written and spoken words, showing convergent processing strategies across modalities in the visual and auditory ventral streams.

Highlights

Individual auditory word form areas (AWFA) were defined via an auditory localizer

The AWFA shows tuning for individual real words but not untrained pseudowords

The AWFA develops tuning for individual pseudowords after training
Molecular recognition of two endogenous hormones by the human parathyroid hormone receptor-1
Authors: Zhao Li-Hua , Yuan Qingning , Dai Antao , Chen Chuan-Wei , He Xinheng , Zhang Chao , Xu Youwei , Zhou Yan , Wang Ming-Wei , Yang Dehua , Xu H. Eric
Published: October 2022

Parathyroid hormone (PTH) and PTH-related peptide (PTHrP) are two endogenous hormones recognized by PTH receptor -1 (PTH1R), a member of class B G protein couple receptors (GPCRs). Both PTH and PTHrP analogs including teriparatide and abaloparatide, are approved drugs for osteoporosis, but they exhibit distinct pharmacology. Here we report two cryo-EM structures of human PTH1R bound to PTH and PTHrP in the G protein-bound state at resolutions of 2.6 and 3.2 Å, respectively. Detailed analysis of these structures uncovers both common and unique features for the agonism of PTH and PTHrP. Molecular dynamics (MD) simulation and together with site-directed mutagenesis studies reveal the molecular basis of endogenous hormones recognition specificity and selectivity to PTH1R. These results provide a rational template for the clinical use of PTH and PTHrP analogs as an anabolic therapy for osteoporosis and other disorders.
Domino-like Effect of C112R Mutation on ApoE4 Aggregation and Its Reduction by Alzheimer’s Disease Drug Candidate
Authors: Nemergut Michal , Marques Sergio M. , Uhrik Lukas , Vanova Tereza , Nezvedova Marketa , Gadara Darshak Chandulal , Jha Durga , Tulis Jan , Novakova Veronika , Planas-Iglesias Joan , Kunka Antonin , Legrand Anthony , Hribkova Hana , Pospisilova Veronika , Sedmik Jiri , Raska Jan , Prokop Zbynek , Damborsky Jiri , Bohaciakova Dasa , Spacil Zdenek , Hernychova Lenka , Bednar David , Marek Martin
Published: October 2022

Background

Apolipoprotein E (ApoE) ε4 genotype is the most prevalent risk factor for late-onset Alzheimer’s Disease (AD). Although ApoE4 differs from its non-pathological ApoE3 isoform only by the C112R mutation, the molecular mechanism of its proteinopathy is unknown.

Methods

Here, we reveal the molecular mechanism of ApoE4 aggregation using a combination of experimental and computational techniques, including X-ray crystallography, site-directed mutagenesis, hydrogen-deuterium mass spectrometry (HDX-MS), static light scattering and molecular dynamics simulations. Treatment of ApoE ε3/ε3 and ε4/ε4 cerebral organoids with tramiprosate was used to compare the effect of tramiprosate on ApoE4 aggregation at the cellular level.

Results

We found that C112R substitution in ApoE4 induces long-distance (>15 Å) conformational changes leading to the formation of a V-shaped dimeric unit that is geometrically different and more aggregation-prone than the ApoE3 structure. AD drug candidate tramiprosate and its metabolite 3-sulfopropanoic acid induce ApoE3-like conformational behavior in ApoE4 and reduce its aggregation propensity. Analysis of ApoE ε4/ε4 cerebral organoids treated with tramiprosate revealed its effect on cholesteryl esters, the storage products of excess cholesterol.

Conclusions

Our results connect the ApoE4 structure with its aggregation propensity, providing a new druggable target for neurodegeneration and ageing.
A first draft genome of Holm oak (Quercus ilexL.), the most representative species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem “dehesa”
Authors: Rey María-Dolores , Labella-Ortega Mónica , Guerrero-Sánchez Víctor M. , Carleial Rômulo , Castillejo María Ángeles , Rodríguez-Franco Antonio , Buggs Richard G. , Ruggieri Valentino , Jorrín-Novo Jesús V.
Published: October 2022

The holm oak (Quercus ilexL.) is the most representative species of the Mediterranean Basin and the agrosilvopastoral Spanish “dehesa” ecosystem. Being part of our life, culture, and subsistence since ancient times, it has great environmental and economic importance. More recently, there has been a renewed interest in using theQ. ilexacorn as a functional food due to its nutritional and nutraceutical properties. However, the holm oak and its related ecosystems are threatened by different factors, with oak decline syndrome and climate change being the most worrying on the short and medium term. Breeding programs informed by selection of elite genotypes seems to be the only plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-qualityQ. ilexreference genome. Here, we introduce the first draft genome assembly ofQ. ilexusing long-read sequencing (PacBio). The assembled nuclear haploid genome has 530 contigs totaling 842.2 Mbp (N50 = 3.3 Mbp), of which 448.7 Mb (53%) are repetitive sequences. We annotated 39,443 protein-coding genes and Benchmarking Universal Single-Copy Orthologs analysis detected 412 out of 425 expected complete and single-copy genes (94.80%) within theQ. ilexgenome. The chloroplast genome size was 142.3 Kbp with 149 protein-coding genes successfully annotated. This first draft should allow for the validation of - omics data as well as the identification and functional annotation of genes related to phenotypes of interest such as those associated to resilience against oak decline syndrome and climate change, higher acorn productivity and nutraceutical value.
Temperature-induced methylome changes during asexual reproduction trigger transcriptomic and phenotypic changes inFragaria vesca
Authors: Zhang YuPeng , Fan Guangxun , Toivainen Tuomas , Tengs Torstein , Yakovlev Igor , Krokene Paal , Hytönen Timo , Fossdal Carl Gunnar , Grini Paul E.
Published: October 2022

Plants must quickly adapt to a changing environment in order to maintain their fitness. One rapid adaptation mechanism that promotes plasticity is epigenetic memory, which may provide long-lived organisms the precious time needed to adapt to climate change. In this study, we used the perennial plantFragaria vescaas a model to determine how the methylome and transcriptome adapt to elevated temperatures (28 vs. 18 °C) over three asexual generations. Changes in flowering time, stolon number, and petiole length were induced in responses to temperature treatment in one or more ecotypes after three asexual generations in a manner indicative of an epigenetic memory. Induced methylome changes differed between four different ecotypes from Norway, Iceland, Italy, and Spain, but there were also some shared responses. Elevated temperature conditions induced significant phenotypic and methylation changes, particularly in the Norwegian ecotype. Most of the differentially methylated regions (DMRs) were in the CHG context, and most CHG and CHH DMRs were hypermethylated. Notably, the four ecotypes shared only eight CHG DMR peaks. Several differentially methylated genes (DMGs) also showed a change in gene expression. Ecotype-specific methylation and expression patterns were observed for genes related to gibberellin metabolism, flowering time, epigenetics. Furthermore, when repetitive elements (REs) were found near (±2 kb) or inside a gene, they showed a negative correlation with gene expression. In conclusion, phenotypic changes induced by elevated temperatures during asexual reproduction were accompanied by changes in DNA methylation patterns. Also, positional influences of REs impacted gene expression, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic plasticity inF. vesca.
Quantifying orthogonal barcodes for sequence census assays
Authors: Booeshaghi A. Sina , Min Kyung Hoi (Joseph) , Gehring Jase , Pachter Lior
Published: October 2022

Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs.
Natural selection and neutral mutations through the lens of viruses
Authors: Chen Ji-Ming , Li Guo-Hui , Gong Huan-Yu , Sun Ming-Hui , Ji Yu-Fei , Chen Rui-Xu , Tan Su-Mei , Chen Ji-Wang
Published: October 2022

The Neutral Theory and the Modern Synthesis, a modified version of Darwin’s theory, have been arguing for decades about the influence of natural selection on molecular evolution1-10. Here we elucidate through the lens of viruses that a frequently used method11-17employing the ratio of nonsynonymous versus synonymous substitution rates has dramatically underestimated the influence of natural selection on molecular evolution. We also find novel evidence from viral sequences to support the co-existence of the crucial role of natural selection in molecular evolution and the ubiquity of neutral mutations. The co-existence has perplexed biologists for decades2,5,7. We then elucidate for the first time the causality between natural selection and the ubiquity of neutral mutations with a novel interpretation of natural selection. This novel interpretation incorporates biochemistry, genetics, epigenetics, physiology, and dynamics. It holds that natural selection acts directly on the overall phenotypic performance of organisms and indirectly on each genomic site or phenotypic trait. It highlights not only restrictions and competitions but also freedom and diversity, besides the overall harmonious development of organisms and human societies. Therefore, this novel interpretation could have far-reaching implications in the natural and social sciences.
Framework for implementing track deterioration analytics into railway asset management
Authors: Sauni Mikko , Luomala Heikki , Kolisoja Pauli , Vaismaa Kalle
Published: October 2022

Purpose

Recent research outputs can be difficult to implement into ongoing safety critical processes. Hence, research is well beyond current practices in railway asset management. This paper demonstrates the process of creating tangible change within a railway asset management organization by introducing a framework for advancing track geometry deterioration analyses (TGDA) in practice.

Design/methodology/approach

The research was conducted in three parts: (1) maturity models were reviewed and adapted as the basis for the framework, (2) the initial maturity level was investigated by conducting semi-structured expert interviews, and (3) a framework for development was created in cooperation with stakeholders during three workshops. The methodology and findings were tested and applied in the Finnish state rail network asset management.

Findings

The main output of this study is the framework for advancing TGDA in railway asset management. The novel framework provides structure for controlled incremental development, which is essential when altering a safety critical process.

Practical implications

The research process was successfully applied in Finland. Following the steps presented in this article, any organization can apply the framework to plan their development schemes for railway asset management.

Originality/value

Full-scale implementation of novel models and methods is often overlooked, which prevents practical asset management from obtaining tangible benefits from research. This research provides an innovative approach in narrowing the overlooked research gap and brings research results within the reach of practitioners.
The impact of organizational support for the project management process on project and firm performance
Authors: Azevedo Ana , Jugdev Kam , Mathur Gita
Published: October 2022

Purpose

This research draws on the resource-based view of the firm from strategic management and applies it to a study of competitive advantage in the project management context. The relationship between the characteristics of project management resources, focusing on organizational support for the project management process, and outcomes of the project management process are examined.

Design/methodology/approach

This study uses data gathered from 437 North American project management professionals with an existing survey tool that was used in a prior smaller sample study. The study uses Barney’s VRIO framework that assesses resources as valuable (V), rare (R), inimitable (I) and organizationally supported to leverage their value (O). The conceptual model hypothesizes relationships between the project management asset characteristics (valuable, rare, and inimitable), organizational support for the project management process, and project management performance outcomes (both project and firm level). Hypotheses are tested using factors extracted from a confirmatory factor analysis (CFA). The factors extracted include two factors representing valuable project management asset characteristics, one factor representing rare project management asset characteristics, one factor representing inimitable project management asset characteristics, two factors representing organizational support for the project management process, one factor representing project-level performance and one factor representing firm-level performance.

Findings

Project management assets that are considered valuable and organizational support for the project management process are found to contribute positively to project management process outcomes. No advantage was perceived from rare and inimitable project management assets. Project-level performance was found to significantly mediate the relationship between organizational support and firm-level performance.

Practical implications

This study draws managerial attention to organizational support for the project management process as a source of competitive advantage through its positive affect on both project-as well as firm-level performance.

Originality/value

The study uses a survey tool from previous research with a new, larger dataset to contribute to the understanding of the importance of organizational support for the project management process in a quest for both project success as well as a firm's competitive advantage.
Educational approaches to enable marketplace metacognition and social intelligence in subsistence consumers
Authors: Sharma Yukti , Jaikumar Saravana
Published: October 2022

Purpose

Subsistence marketplace can be characterized as a marketplace with widespread cognitive and social vulnerabilities, due to low income and low literacy levels. This may result in retailers exploiting the consumers. The purpose of this research paper is to develop a holistic learning program to impart marketplace intelligence to overcome these vulnerabilities of subsistence consumers.

Design/methodology/approach

Using vicious cycle approach, the authors illustrate the self-perpetuating nature of consumer vulnerabilities. The authors argue that retailers behave in an opportunistic manner and exploit the consumers. This further reinforces the vulnerabilities of subsistence consumers resulting in a vicious cycle. The authors draw insights from Sen’s capability approach and propose marketplace intelligence as a potential solution to eradicate consumers’ vulnerabilities. The authors apply Biggs’s 3Ps model to design a learning program to impart two types of marketplace intelligence – marketplace metacognition and marketplace social intelligence.

Findings

Based on a review of literature on subsistence marketplace initiatives, persuasive knowledge management and education research, the authors have devised a holistic learning program comprising an integrated learning environment (presage), problem-based approach (process) and assessment strategies for learning outcomes (product).

Originality/value

This study marks a pioneering effort toward liberating subsistence consumers from the vicious cycle of retailers’ exploitation by empowering them with marketplace intelligence. This study’s novelty lies in conceptualizing consumer vulnerabilities in the subsistence marketplace as a self-perpetuating phenomenon and subsequently designing a holistic learning program to impart intelligence toward alleviating these vulnerabilities.
Victimisation of investors from fraudulent investment schemes and their protection through financial education
Authors: Singh Kamakhya Narain , Misra Gaurav
Published: October 2022

Purpose

The purpose of this study is to identify the significant demographic and socio-economic characteristics of individuals who are likely to invest in a fraudulent investment scheme. It also quantifies the extent to which financial literacy helps in reducing the odds of investments in such schemes. Based on these findings, it provides policy recommendations to regulators and governments.

Design/methodology/approach

This study uses nationally representative data from the “India Assessment of Financial Capability 2018” survey. It further uses logistic regression with a binary outcome variable to assess the individual-level odds of investments in fraudulent investment schemes.

Findings

This study concludes that males between 40 and 59 years of age, who are well-educated (are at least graduates), score low in financial literacy, belong to the middle-income group, and SEC A3 households are most vulnerable to victimization by financial fraudulent investment schemes. It finds that financial literacy significantly reduces the odds of investment into fraudulent schemes to the extent of 39.118%.

Originality/value

This study quantifies the extent to which financial literacy helps in reducing the odds of individual investments in a fraudulent investment scheme. As financial literacy has a significant and negative relationship with the likelihood of investment in such schemes, this study provides policy interventions and recommendations to regulators and governments to safeguard the interest of individual investors.
Unexplored themes in expatriate management: inspirations from the new mobilities paradigm
Authors: Guttormsen David S. A. , Lauring Jakob
Published: October 2022

Purpose

The purpose of this paper is to present a different perspective on the concept of global mobility and apply the multifaceted concept in proposing new themes to explore in expatriate management research.

Design/methodology/approach

This study draws upon the theoretical underpinnings relating to the New Mobilities paradigm from sociology to outline a new perspective on global mobility and thereby describe novel themes to include in future expatriate management studies.

Findings

This study identifies four themes in need of further development within the expatriate management research field: materiality, infrastructure and access, inequality and immobility and emotional dynamics. Within each of these themes, this study presents several examples of research questions that can provide new thrust to the theory development of expatriate management research.

Originality/value

To the best of the authors’ knowledge, this paper is the first attempt to draw on central ideas in the New Mobilities paradigm to propose a future research agenda for expatriate management studies. This study aims to enhance the study of “mobility” in new and unorthodox ways.
Professional relationships both within and outside the school: barriers and opportunities from an intergenerational perspective
Authors: Azorín Cecilia , Portela Antonio , Nieto José Miguel , Alfageme María Begoña
Published: October 2022

Purpose

This paper draws on data from a research project that examined the professional relationships that existed between teachers of different generations within an educational setting, including both those inside and outside school.

Design/methodology/approach

A qualitative approach was adopted to better understand participants' intergenerational relationships. Data were collected via semi-structured interviews conducted online. Data analysis was carried out using Atlas.ti 22 software. This focused on participants' professional relationships, generationally-inflected professional relationships, links to the school and connections with their environment.

Findings

The paper shows that commitment to the profession and work climate were among the key aspects referred to by the interviewees. The different age groups agreed that they had experienced intergenerational feedback and that there was closer contact between peers of the same generation, which led to greater levels of affinity. The shared responsibility that comes with teaching and the sense of belonging were essential links to the school. The generational groups underlined the importance of building bridges and participating in collaborative networks to form connections with their environment.

Originality/value

Although several studies have considered various factors influencing professional relationships from an intergenerational perspective, this paper adds value to the existing literature by providing new data and analyzing the barriers and opportunities experienced by teachers of different generations (novice, veteran and retired) in their professional work within and beyond the educational setting.
A multisensor fusion algorithm of indoor localization using derivative Euclidean distance and the weighted extended Kalman filter
Authors: Chen Jian , Song Shaojing , Gu Yang , Zhang Shanxin
Published: October 2022

Purpose

At present, smartphones are embedded with accelerometers, gyroscopes, magnetometers and WiFi sensors. Most researchers have delved into the use of these sensors for localization. However, there are still many problems in reducing fingerprint mismatching and fusing these positioning data. The purpose of this paper is to improve positioning accuracy by reducing fingerprint mismatching and designing a weighted fusion algorithm.

Design/methodology/approach

For the problem of magnetic mismatching caused by singularity fingerprint, derivative Euclidean distance uses adjacent fingerprints to eliminate the influence of singularity fingerprint. To improve the positioning accuracy and robustness of the indoor navigation system, a weighted extended Kalman filter uses a weighted factor to fuse multisensor data.

Findings

The scenes of the teaching building, study room and office building are selected to collect data to test the algorithm’s performance. Experiments show that the average positioning accuracies of the teaching building, study room and office building are 1.41 m, 1.17 m, and 1.77 m, respectively.

Originality/value

The algorithm proposed in this paper effectively reduces fingerprint mismatching and improve positioning accuracy by adding a weighted factor. It provides a feasible solution for indoor positioning.
Optimizing ecological surveys for conservation
Authors: Hanson Jeffrey O. , McCune Jenny L. , Chadès Iadine , Proctor Caitlyn A. , Hudgins Emma J. , Bennett Joseph R.
Published: October 2022

Conservation decisions must be made with limited funding and incomplete information. Ecological surveys can help reduce uncertainty and, in turn, potentially lead to better management decisions. However, conducting surveys can reduce funds available for implementing management actions and, in turn, can potentially lead to worse conservation outcomes.

Here we develop a value of information framework to evaluate and optimize survey plans. Our framework evaluates survey plans based on their ability to improve how likely resulting protected area systems are to secure species of interest, and accounts for survey and land acquisition costs. Using an example of eight imperilled plant species in Middlesex County (Ontario, Canada), we assessed our framework against conventional approaches for designing survey plans that involve selecting places with (i) maximal geographic coverage, (ii) diverse environmental conditions, (iii) highly uncertain information, (iv) high imperilled species richness and (v) low protected area establishment costs.

We found that optimized survey plans could improve the protected area system by, on average, 57.52% (0.21 SD) (up to 105.25%) over conventional survey approaches. These optimized plans could also improve the protected area system by, on average, 19.91% (up to 32.37%) over simply prioritizing based on existing information. Survey plans designed using conventional approaches, in many cases, led to a worse protected area system than simply using existing information. Such conventional approaches performed the worst when they allocated a large percentage of the available budget to data collection.

Synthesis and applications.Our findings demonstrate that conventional approaches for designing ecological surveys can impede conservation efforts by squandering funds on data that have little chance of improving decision making. Indeed, conventional approaches for designing surveys had the poorest performance under limited budgets, which are typical in real world planning exercises. We recommend that conservation practitioners carefully consider how data collection efforts can potentially improve conservation decisions, and also the costs associated with data collection. By applying the principles of value of information, our framework enables conservation practitioners to cost‐effectively collect data in places that will maximize conservation outcomes.
Spatio‐temporal variation in deep soil water use patterns of overstorey and understorey layers in subtropical plantations predicts community assembly
Authors: Jiang Peipei , Meinzer Frederick C. , Wang Huimin , Dai Xiaoqin , Meng Shengwang , Kou Liang , Chen Yifan , Fu Xiaoli
Published: October 2022

Deep soil water utilization allows plants to cope with drought stress. However, little is known about the roles of the understorey layers in driving spatio‐temporal variations of deep soil water in forests and how the patterns of deep soil water use among life‐forms contribute to community assembly processes.

We assessed the spatio‐temporal patterns and determinants of deep water utilization of tree, shrub and herb layers in subtropical coniferous plantations and investigated associations between deep water use parameters and dominance and richness of understorey vegetation.

We found that the understorey layer had a higher reliance on deep soil water in the dry season, a larger seasonal plasticity of deep soil water uptake, but lower spatial variability in deep soil water utilization than the tree layer. We showed that greater reliance of the tree layer on deep soil water was associated with decreased shrub layer diversity, whereas greater reliance of the shrub layer on deep water was associated with increased herb layer diversity.

Synthesis. Our results highlight the roles of understorey layers in driving the temporal dynamics of deep soil water in forests and improve our understanding of how deep soil water use patterns among life‐forms shape community assembly in forests.
Local Government and the Everyday Economy
Authors: Lanning Tess , Laurence Rachel
Published: October 2022

While national government approaches to economic policy have focussed on economic output as measured through gross domestic product (GDP), many local government approaches see it as their primary economic responsibility to make the local economy work well for their residents—both in terms of quantity and quality of jobs, and of the provision of adequate local services, amenities and culture. In recent years a growing interventionist inclination has emerged in local government, seeking to shape the local economy in response to many waves of national economic crises. This article explores a range of such approaches and models, with deep‐dive analysis of Barking and Dagenham, where both authors have worked. It draws out the lessons for national economic policy and strategy in shaping a more resilient, functional and prosperous everyday economy for people.
Theorising health equity research for people with intersex variance through new materialism
Authors: Zeeman Laetitia , Aranda Kay
Published: October 2022

Health inequalities impact sex‐variant people in highly differentiated ways. This is evidenced in much academic and activist intersex research documenting the highly specific forms of inequalities arising from misrecognition, discrimination and human rights abuses inherent to pathologised accounts of non‐normative bodies. Important theoretical work further interrogates the implications of sex variant subjectivities, identities and bodies for static or binary notions of both sex and gender. In this paper, we aim to contribute further to this scholarship. We draw upon feminist materialist and Deleuzean‐informed understandings of materials or matter to rethink debates over sex‐variant subjectivities, identities and bodies in relation to inequalities in health. We argue ‘the turn to matter’ and associated new materialist theories draw attention to the complex, dynamic relational assemblages and entanglements mutually constituting the affective, embodied and socio‐material worlds of intersex people. Informed by these theories, we propose that inequalities can be more fully addressed through a new health equity research agenda that is co‐produced with sex‐variant people. This agenda will enable a fuller exploration of the unsettling but transformative capacities of intersex matters and meanings with the contextually specific understandings of equity in relation to health and health care.
Risk factors for pre‐eclampsia: Received wisdom versus reality
Authors: Kane Stefan C. , Da Silva Costa Fabricio
Published: October 2022

Linked article: This is a mini commentary on Terteel Elawad et al, pp. 46–62 in this issue. To view this article visit https://doi.org/10.1111/1471‐0528.17320
Resolution of comorbidities and outcomes after revision of sleeve gastrectomy to duodenal switch for patients with body mass index more than 60 kg/m2
Authors: Ghosh Anirban , Hussein Adam , Askari Alan , Jain Vigyan , Adil Md Tanveer
Published: October 2022

Aim

Patients with body mass index (BMI) more than 60 kg/m2 pose unique challenges in management and their ability to lose significant weight after a single‐stage bariatric procedure is debatable. The aim of this study is to explore resolution of comorbidities and report quality of life (QoL) in patients who have a laparoscopic sleeve gastrectomy (LSG) revised to duodenal switch (DS).

Methods

Patients who completed two‐stage DS from 1 January 2011 to 31 December 2017 were analysed for excess weight loss (EWL), total weight loss (TWL), resolution of comorbidities and QoL. Validated questionnaires were used to assess QoL.

Results

A total of 9/1975 bariatric patients underwent two‐stage DS during the study period, all of whom had had a previous LSG. The median preoperative weight before the first stage was 207.0 kg [interquartile range (IQR) 175.3‐278.9 kg] and the median BMI was 75.0 kg/m2 (IQR 65.1‐92.0 kg/m2). Length of hospital stay following the first stage (ie, LSG) was a median of 1 day (IQR 1‐2 days) and 2 days (IQR 1‐3 days) after revision to DS. The median EWL following LSG was 58.0% (IQR 33.3%‐100.8%) and the median TWL was 16.1% (IQR 13.7%‐25.2%). Following DS, the median EWL was 57.1% (IQR 47.1%‐60.8%) and the median TWL was 21.2% (IQR 19.5%‐26.7%). Significant improvement in obesity‐related comorbidities were observed. QoL improved in overall feeling, physical activity, social life, work and approach to food. No immediate postoperative complications were observed. Long‐term outcome of all patients was rated to be ‘very good’, ‘good’ or ‘fair’.

Conclusions

Two‐stage DS leads to sustained weight loss, resolution of comorbidities and improvement in QoL in carefully selected patients with BMI more than 60 kg/m2.
Sarcoidosis with axial spondyloarthritis: A case‐based review of simultaneous occurrence
Authors: Ince Bugra , Kultur Esra , Sayilir Safiye , Kucukakkas Okan
Published: October 2022

This article presents a 47‐year‐old female patient who was concurrently diagnosed with sarcoidosis and axial spondyloarthritis. The coexistence of spondyloarthritis and sarcoidosis, the involvement of bone and sacroiliac synovium in sarcoidosis, and treatment options were discussed.
Do foreign institutional investors monitor opportunistic managerial behaviour? Evidence from real earnings management
Authors: Gu Xiaolong , An Zhe , Chen Chen , Li Donghui
Published: October 2022

Employing a large sample of 13,860 firms in 41 economies from 2000 to 2017, we document that the ownership by foreign institutional investors (FIIs) is negatively associated with firms' real earnings management (REM) but unrelated to their accrual earnings management (AEM). We adopt a few identification strategies to tackle the endogeneity issues, including firm‐ and year‐fixed effects regression, two‐stage least squares (2SLS) regression, and difference‐in‐differences (DiD) estimation based on the passage of the Jobs and Growth Tax Relief Reconciliation Act (JGTRRA). In addition, we show that the role of FIIs in curbing REM is achieved through the expertise channel and the monitoring channel. These results suggest that when facing disadvantages in curbing AEM, FIIs make the most of their monitoring strengths by curbing firms' REM, where they have both incentives and capabilities to monitor. Overall, this study highlights the important role of FIIs in monitoring opportunistic managerial behaviour.
Interdisciplinary management of an adult patient with significant tooth wear
Authors: Wong J , Ong DCV , Khan A
Published: October 2022

Adult patients may present with compromised dentitions which require extensive oral rehabilitation. This case report shows the fulfilment of both functional and aesthetic treatment objectives for a patient with significant tooth wear through carefully planned interdisciplinary management. © 2022 Australian Dental Association.
Euganean trachytic grinding stones in the Caput Adriae from the Iron Age to the Roman period: Reassessment of the Protohistoric quarries
Authors: Bernardini Federico , Velicogna Matteo , De Min Angelo , Antonelli Fabrizio , Gambacurta Giovanna , Bressan Daniele , Fabec Tomaz
Published: October 2022

A group of Euganean trachytic grinding stones from Slovenia and the available data about the same type of artefacts in the whole Caput Adriae are presented. The occurrence of Iron Age saddle querns in Karst and Istria is confirmed, but our study suggests a likely provenance from Mts Cero/Murale instead of Mts Altore/Rocca Pendice, as previously suggested. Este, an important Venetic centre, is just south of Mts Cero/Murale, suggesting its central role in the production and distribution of saddle querns. During the Roman period Euganean trachytes are still used for rotary millstones, but new quarries (Mt Rosso), relatively close to ancient Padua, are exploited. Such shift in the position of millstone quarries most probably reflects the changed geopolitical framework.
Reconstruction of smelting conditions during 16th‐ to 18th‐century copper ore processing in the Kielce region (Old Polish Industrial District) based on slags from Miedziana Góra, Poland
Authors: Kupczak Krzysztof , Warchulski Rafał , Gawęda Aleksandra
Published: October 2022

This study presents the first reconstruction of the smelting conditions in 16th‐ to 18th‐century smelters from Miedziana Góra (Holy Cross Mountains, Poland). Based on geochemical (inductively coupled plasma mass spectrometry/emission spectrometry, X‐ray fluorescence) and mineralogical analysis (X‐ray diffractometry, scanning electron microscopy, electron probe micro‐analysis) of historical slags, their chemical/phase composition and the basic smelting parameters (temperature, melt viscosity, and oxygen fugacity) were determined. Due to the differences in chemical and phase composition, slags from different smelting stages have been distinguished: hypocrystalline slags (MG6) from speiss/matte production and glassy (MG1–MG5) from matte conversion. In glassy slags, pyroxenes, quartz/cristobalite grains, and aggregates composed of metallic Cu and PbO are dispersed in the glass. Hypocrystalline slags are composed of wollastonites, anorthites, and metallic Cu. The temperature range at which the slags were formed was from ~1100°C (solidus temperature) to 1150–1200°C (liquidus temperature). The silicate melt's viscosity was from log η = 1.19 to 4.42 Pa s (at 1100–1200°C). The higher viscosity of MG1–MG5 slags indicates that, unlike MG6 slags, they were not formed during gravity separation. Information about the phase composition made it possible to determine the oxygen fugacity in the range of log fO2 = −4 to −12 atm. High oxygen fugacity indicates the oxidizing nature of the smelting process.
Differences in antimicrobial components between bacterial culture‐positive and culture‐negative bovine clinical mastitis milk
Authors: Tsugami Yusaku , Chiba Tomoyuki , Obayashi Tetsu , Higuchi Hidetoshi , Watanabe Atsushi , Isobe Naoki , Kawai Kazuhiro
Published: October 2022

A bacterial culture of milk is the most common test to determine the presence of mastitis‐causing pathogens, which informs appropriate treatment. However, a certain proportion of clinical mastitis milk shows no growth of any mastitis‐causing pathogens. We hypothesized that bacterial culture‐negative clinical mastitis milk is associated with the activity of antimicrobial components contained in the milk. In this study, the differences in antimicrobial components (lactoferrin, transferrin, lysozyme, lactoperoxidase, and lingual antimicrobial peptide [LAP]) between bacterial culture‐positive and culture‐negative bovine clinical mastitis milk were investigated using Holstein cows. Our results showed that 37 out of 71 samples of clinical mastitis milk had negative bacterial cultures. The LAP concentration in bacterial culture‐negative milk was lower than that in positive milk (31.95 ± 1.64 nM vs. 42.85 ± 4.01 nM). In contrast, the lysozyme concentration in bacterial culture‐negative milk was higher than that in positive milk (0.76 ± 0.15 μg/ml vs. 0.42 ± 0.06 μg/ml). In conclusion, the concentration of antimicrobial components was different between bacterial culture‐positive and culture‐negative bovine clinical mastitis milk, which suggests that antimicrobial components are related to bacterial culture results.
Cryptogams and dwarf evergreen shrubs are vulnerable to nitrogen addition in a boreal permafrost peatland of Northeast China
Authors: Shi Fu‐Xi , Wang Xian‐Wei , Lin Gui‐Gang , Zhang Xin‐Hou , Chen Hui‐Min , Mao Rong
Published: October 2022

Aim

Boreal peatlands are very sensitive to nitrogen (N) enrichment due to the low soil N availability. Our aim was to reveal how increased N availability altered plant composition in boreal permafrost peatlands with dense vascular plants (>50%).

Location

Greater Khingan Mountains, Northeast China.

Methods

A nitrogen addition experiment with four N addition levels (0, 3, 6, and 12 g N m−2 year−1) was conducted in a poor fen in the continuous permafrost zone with vascular plant coverage above 60%. Plant diversity, community composition, and above‐ground biomass were investigated after four, six, and eight years of N addition.

Results

Nitrogen addition decreased species richness and diversity but enhanced total above‐ground biomass. Plant height determined the plants’ responses to N addition, and the magnitudes increased with N addition level and experimental duration. The relative coverage of high‐stature (>50 cm) species increased, but the relative coverage of low‐stature (<50 cm) species decreased with elevating N addition levels. When N addition proceeded, the relative coverage and above‐ground biomass of tall deciduous shrubs and nitrophilous grasses increased, whereas the relative coverage and above‐ground biomass of dwarf evergreen shrubs, mosses, and lichens declined. Regardless of N addition levels, cryptogams (i.e., mosses and lichens) and a dwarf evergreen shrub (Chamaedaphne calyculata) disappeared after eight‐year N addition.

Conclusions

Cryptogams and dwarf evergreen shrubs are highly vulnerable to increased N availability, and N enrichment‐induced biodiversity loss, especially the disappearance of cryptogams, will deteriorate ecosystem structure and function in boreal permafrost peatlands.