bluuebunny/crossref_metadata_2025 huggingface dataset:
Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data
Authors: Liu Long , Meng Qingyu , Weng Cherry , Lu Qing , Wang Tong , Wene Yalu
Published: January 2022

Building an accurate disease risk prediction model is an essential step in the modern quest for precision medicine. While high-dimensional genomic data provides valuable data resources for the investigations of disease risk, their huge amount of noise and complex relationships between predictors and outcomes have brought tremendous analytical challenges. Deep learning model is the state-of-the-art methods for many prediction tasks, and it is a promising framework for the analysis of genomic data. However, deep learning models generally suffer from the curse of dimensionality and the lack of biological interpretability, both of which have greatly limited their applications. In this work, we have developed a deep neural network (DNN) based prediction modeling framework. We first proposed a group-wise feature importance score for feature selection, where genes harboring genetic variants with both linear and non-linear effects are efficiently detected. We then designed an explainable transfer-learning based DNN method, which can directly incorporate information from feature selection and accurately capture complex predictive effects. The proposed DNN-framework is biologically interpretable, as it is built based on the selected predictive genes. It is also computationally efficient and can be applied to genome-wide data. Through extensive simulations and real data analyses, we have demonstrated that our proposed method can not only efficiently detect predictive features, but also accurately predict disease risk, as compared to many existing methods.

Author summary

Accurate disease risk prediction is an essential step towards precision medicine. Deep learning models have achieved the state-of-the-art performance for many prediction tasks. However, they generally suffer from the curse of dimensionality and lack of biological interpretability, both of which have greatly limited their applications to the prediction analysis of whole-genome sequencing data. We present here an explainable deep transfer learning model for the analysis of high-dimensional genomic data. Our proposed method can detect predictive genes that harbor genetic variants with both linear and non-linear effects via the proposed group-wise feature importance score. It can also efficiently and accurately model disease risk based on the detected predictive genes using the proposed transfer-learning based network architecture. Our proposed method is built at the gene level, and thus is much more biologically interpretable. It is also computationally efficiently and can be applied to whole-genome sequencing data that have millions of potential predictors. Through both simulation studies and the analysis of whole-genome sequencing data obtained from the Alzheimer’s Disease Neuroimaging Initiative, we have demonstrated that our method can efficiently detect predictive genes and it has better prediction performance than many existing methods.
Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions
Authors: Parker Edyth , Anderson Catelyn , Zeller Mark , Tibi Ahmad , Havens Jennifer L. , Laroche Geneviève , Benlarbi Mehdi , Ariana Ardeshir , Robles-Sikisaka Refugio , Latif Alaa Abdel , Watts Alexander , Awidi Abdalla , Jaradat Saied A. , Gangavarapu Karthik , Ramesh Karthik , Kurzban Ezra , Matteson Nathaniel L. , Han Alvin X. , Hughes Laura D. , McGraw Michelle , Spencer Emily , Nicholson Laura , Khan Kamran , Suchard Marc A. , Wertheim Joel O. , Wohl Shirlee , Côté Marceline , Abdelnour Amid , Andersen Kristian G. , Abu-Dayyeh Issa
Published: January 2022

Regional connectivity and land-based travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions such as Europe. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the wider Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding from Europe in the early pandemic to more regional seeding for the period travel restrictions were in place. We show that land-based travel, particularly freight transport, drove introduction risk during the period of travel restrictions. Consistently, high regional connectivity and land-based travel also disproportionately drove Jordan’s export risk to other Middle Eastern countries. Our findings emphasize regional connectedness and land-based travel as drivers of viral transmission in the Middle East. This demonstrates that strategies aiming to stop or slow the spread of viral introductions (including new variants) with travel restrictions need to prioritize risk from land-based travel alongside intercontinental air travel to be effective.

Highlights

Regional connectivity drove SARS-CoV-2 introduction risk in Jordan during the period travel restrictions were in place in genomic and travel data.

Land-based travel rather than air travel disproportionately drove introduction risk during travel restrictions.

High regional connectivity disproportionately drove Jordan’s export risk, with significant contribution from land-based travel.

Regional transmission dynamics were underestimated in genomic data due to unrepresentative sampling.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Authors: Gangavarapu Karthik , Latif Alaa Abdel , Mullen Julia L. , Alkuzweny Manar , Hufbauer Emory , Tsueng Ginger , Haag Emily , Zeller Mark , Aceves Christine M. , Zaiets Karina , Cano Marco , Zhou Jerry , Qian Zhongchao , Sattler Rachel , Matteson Nathaniel L , Levy Joshua I. , Lee Raphael TC , Freitas Lucas , Maurer-Stroh Sebastian ,   GISAID core and curation team, Suchard Marc A. , Wu Chunlei , Su Andrew I. , Andersen Kristian G. , Hughes Laura D.
Published: January 2022

The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 10 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info, a platform that currently tracks over 40 million combinations of PANGO lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials, and the general public. We describe the interpretable and opinionated visualizations in the variant and location focussed reports available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data, and the server infrastructure that enables widespread data dissemination via a high performance API that can be accessed using an R package. We present a case study that illustrates how outbreak.info can be used for genomic surveillance and as a hypothesis generation tool to understand the ongoing pandemic at varying geographic and temporal scales. With an emphasis on scalability, interactivity, interpretability, and reusability, outbreak.info provides a template to enable genomic surveillance at a global and localized scale.
A Machine Learning Approach to Differentiate Between COVID-19 and Influenza Infection Using Synthetic Infection and Immune Response Data
Authors: Farhang-Sardroodi Suzan , Ghaemi Mohammad Sajjad , Craig Morgan , Ooi Hsu Kiang , Heffernan Jane M
Published: January 2022

Data analysis is widely used to generate new insights into human disease mechanisms and provide better treatment methods. In this work, we used the mechanistic models of viral infection to generate synthetic data of influenza and COVID-19 patients. We then developed and validated a supervised machine learning model that can distinguish between the two infections. Influenza and COVID-19 are contagious respiratory illnesses that are caused by different pathogenic viruses but appeared with similar initial presentations. While having the same primary signs COVID-19 can produce more severe symptoms, illnesses, and higher mortality. The predictive model performance was externally evaluated by the ROC AUC metric (area under the receiver operating characteristic curve) on 100 virtual patients from each cohort and was able to achieve at least AUC=91% using our multiclass classifier. The current investigation highlighted the ability of machine learning models to accurately identify two different diseases based on major components of viral infection and immune response. The model predicted a dominant role for viral load and productively infected cells through the feature selection process.
Widespread alterations in microRNA biogenesis in human Huntington’s disease putamen
Authors: Petry Serena , Keraudren Rémi , Nateghi Behnaz , Loiselle Andréanne , Pircs Karolina , Jakobsson Johan , Sephton Chantelle , Langlois Mélanie , St-Amour Isabelle , Hébert Sébastien S.
Published: January 2022

Altered microRNA (miRNA) expression is a common feature of Huntington’s disease (HD) and could participate in disease onset and progression. However, little is known about the underlying causes of miRNA disruption in HD. We and others have previously shown that mutant Huntingtin (mHTT) binds to Ago2, a central component of miRNA biogenesis, and disrupts mature miRNA levels. In this study, we sought to determine if miRNA maturation per se was compromised in HD. Towards this end, we characterized t major miRNA biogenesis pathway components and miRNA maturation products (pri-miRNA, pre-miRNA, and mature) in human HD (N=41, Vonsattel grades HD2-4) and healthy control (N=25) subjects. Notably, the striatum (putamen) and cortex (BA39) from the same individuals were analyzed in parallel. We show that Ago2, Drosha, and Dicer were strongly downregulated in human HD at early stages of disease. Using a panel of HD-related miRNAs (miR-10b, miR-196b, miR-132, miR-212, miR-127, miR-128), we uncovered various types of maturation defects in HD brain, the most prominent occurring at the pre-miRNA to mature miRNA maturation step. Consistent with earlier findings, we provide evidence that alterations in autophagy could participate in miRNA maturation defects. Notably, most changes occurred in the striatum, which is more prone to HTT aggregation and neurodegeneration. Likewise, we observed no significant alterations in miRNA biogenesis in human HD cortex and blood, strengthening tissue-specific effects. Overall, these data provide important clues into the underlying mechanisms behind miRNA alterations in HD-susceptible tissues. Further investigations are now required to understand the biological, diagnostic, and therapeutic implications of miRNA/RNAi biogenesis defects in HD and related neurodegenerative disorders.
Decoding the temporal dynamics of affective scene processing
Authors: Bo Ke , Cui Lihan , Yin Siyang , Hu Zhenhong , Hong Xiangfei , Kim Sungkean , Keil Andreas , Ding Mingzhou
Published: January 2022

Natural images containing affective scenes are used extensively to investigate the neural mechanisms of visual emotion processing. Functional fMRI studies have shown that these images activate a large-scale distributed brain network that encompasses areas in visual, temporal, and frontal cortices. The underlying spatial and temporal dynamics among these network structures, however, remain to be characterized. We recorded simultaneous EEG-fMRI data while participants passively viewed affective images from the International Affective Picture System (IAPS). Applying multivariate pattern analysis to decode EEG data, and representational similarity analysis to fuse EEG data with simultaneously recorded fMRI data, we found that: (1) ~100 ms after picture onset, perceptual processing of complex visual scenes began in early visual cortex, proceeding to ventral visual cortex at ~160 ms, (2) between ~200 and ~300 ms (pleasant pictures: ~200 ms; unpleasant pictures: ~260 ms), affect-specific neural representations began to form, supported mainly by areas in occipital and temporal cortices, and (3) affect-specific neural representations, lasting up to ~2 s, were stable and exhibited temporally generalizable activity patterns. These results suggest that affective scene representations in the brain are formed in a valence-dependent manner and are sustained by recurrent neural interactions among distributed brain areas.
Factors associated with secondhand smoke exposure among non-smoking employees in the workplace: A cross-sectional study in Qingdao, China
Authors: Jia Xiaocen , Wang Rui , Qiu Xiaofei , Huang Yiqing , Wang Yani , Jia Xiaorong , Li Shanpeng , Wu Yibo , Qi Fei
Published: January 2022

Objective

The study was designed to describe secondhand smoke (SHS) exposure among non-smoking employees in the workplace and identify factors that related exposure in Qingdao.

Methods

The study subjects covered the key non-smoking places stipulated in the “Qingdao City Smoking Control Regulations”. Airborne nicotine concentration in the workplace and saliva cotinine concentration of employees were measured. Questionnaire included employees’ demographics factors, smoke-free measures in the workplace, the employer’s tobacco hazard knowledge and attitudes towards smoke-free policy.

Results

A total of 222 non-smoking employees and 46 employees were included in the study. The median concentrations of airborne nicotine and salivary cotinine were 0.389 μg/m3 and 0.575 ng/ml. Educational status, average number of smokers per day and exposure time of SHS in the workplace, whether to divide smoking and non-smoking areas were related to the airborne nicotine concentration significantly. Age, educational status, exposure time of SHS in the workplace, tobacco control training and publicity and whether the employers support the “Qingdao Tobacco Control Regulation” were related to the salivary cotinine concentration significantly.

Conclusions

Exposure to SHS is highly prevalent among non-smoking employees in the workplace. Interventions to reduce SHS exposure in the workplace are urgently needed.
Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data
Authors: Ehsan Nava , Kotis Bence M. , Castel Stephane E. , Song Eric J. , Mancuso Nicholas , Mohammadi Pejman
Published: January 2022

Expression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human genome have been associated with one or more eQTLs. Here we introduce a multi-variant generalization of allelic Fold Change (aFC), aFC-n, to enable accurate quantification of the cis-regulatory effects in genes with multiple conditionally independent eQTLs. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvement in accuracy over the current tools for estimating the eQTL effect size and predicting genetically regulated gene expression. We characterize some of the empirical properties of the eQTL data and use this framework to assess the current state of eQTL data in terms of characterizing cis-regulatory landscape in individual genomes. Notably, we show that 77.4% of the genes with an allelic imbalance in a sample show 0.5 log2 fold or more of residual imbalance after accounting for the eQTL data underlining the remaining gap in characterizing regulatory landscape in individual genomes. We further contrast this gap across tissue types, and ancestry backgrounds to identify its correlates and guide future studies.
A single nucleotide polymorphism determines constitutive versus inducible type VI secretion in Vibrio cholerae
Authors: Drebes Dörr Natália C. , Proutière Alexis , Jaskólska Milena , Stutzmann Sandrine , Bader Loriane , Blokesch Melanie
Published: January 2022

Vibrio cholerae is a well-studied human pathogen that is also a common inhabitant of marine habitats. In both environments, the bacterium is subject to interbacterial competition. A molecular nanomachine that is often involved in such competitive behavior is the type VI secretion system (T6SS). Interestingly and in contrast to non-pandemic or environmental isolates, the T6SS of the O1 El Tor clade of V. cholerae, which is responsible for the ongoing 7th pandemic, is largely silent under standard conditions. Instead, these strains induce their full T6SS capacity only under specific conditions such as growth on chitinous surfaces (signaled through TfoX and QstR) or when the cells encounter low intracellular c-di-GMP levels (TfoY-driven). In this study, we identified a single nucleotide polymorphism (SNP) within an intergenic region of the major T6SS gene cluster of V. cholerae that determines the T6SS status of the cell. We show that SNP conversion is sufficient to induce T6SS production in numerous pandemic strains, while the converse approach renders non-pandemic/environmental V. cholerae strains T6SS-silent. We further demonstrate that SNP-dependent T6SS production occurs independently of the known T6SS regulators TfoX, QstR, and TfoY. Finally, we identify a putative promoter region adjacent to the identified SNP that is required for all forms of T6SS regulation.
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence
Authors: Kuipers Jack , Singer Jochen , Beerenwinkel Niko
Published: January 2022

Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patient’s tumour composition and evolutionary history is key for personalised therapies. Single-cell sequencing now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the uncertainty of the underlying evolutionary process. By modelling the noise processes and allowing mutations to be lost or to reoccur during tumour evolution, we present a method to jointly call mutations in each cell, reconstruct the phylogenetic relationship between cells, and determine the locations of mutational losses and recurrences. Our Bayesian approach allows us to accurately call mutations as well as to quantify our certainty in such predictions. We show the advantages of allowing mutational loss or recurrence with simulated data and present its application to tumour single-cell sequencing data.
Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites
Authors: Leipart Vilde , Ludvigsen Jane , Kent Matthew , Sandve Simen , To Thu-Hien , Árnyasi Mariann , Kreibich Claus D , Dahle Bjørn , Amdam Gro V.
Published: January 2022

Proteins are under selection to maintain central functions and to accommodate needs that arise in ever-changing environments. The positive selection and neutral drift that preserve functions result in a diversity of protein variants. The amount of diversity differs between proteins: multifunctional or disease-related proteins tend to have fewer variants than proteins involved in some aspects of immunity. Our work focuses on the extensively studied protein Vitellogenin (Vg), which in honey bees(Apis mellifera)is multifunctional and highly expressed and plays roles in immunity. Yet, almost nothing is known about the natural variation in the coding sequences of this protein or how amino acid-altering variants might impact structure–function relationships. Here, we map out allelic variation in honey bee Vg using biological samples from 15 countries. The successful barcoded amplicon Nanopore sequencing of 543 bees revealed 121 protein variants, indicating a high level of diversity in Vg. We find that the distribution of non-synonymous single nucleotide polymorphisms (nsSNPs) differs between protein regions with different functions; domains involved in DNA and protein–protein interactions contain fewer nsSNPs than the protein’s lipid binding cavities. We outline how the central functions of the protein can be maintained in different variants and how the variation pattern may inform about selection from pathogens and nutrition.
Molecular hydrogen is an overlooked energy source for marine bacteria
Authors: Lappan Rachael , Shelley Guy , Islam Zahra F. , Leung Pok Man , Lockwood Scott , Nauer Philipp A. , Jirapanjawat Thanavit , Chen Ya-Jou , Kessler Adam J. , Williams Timothy J. , Cavicchioli Ricardo , Baltar Federico , Cook Perran L.M. , Morales Sergio E. , Greening Chris
Published: January 2022

Molecular hydrogen (H2) and carbon monoxide (CO) are supersaturated in seawater relative to the atmosphere and hence are readily accessible energy sources for marine microbial communities. Yet while marine CO oxidation is well-described, it is unknown whether seawater communities consume H2. Here we integrated genome-resolved metagenomics, biogeochemistry, thermodynamic modelling, and culture-based analysis to profile H2and CO oxidation by marine bacteria. Based on analysis of 14 surface water samples, collected from three locations spanning tropical to subantarctic fronts, three uptake hydrogenase classes are prevalent in seawater and encoded by major marine families such as Rhodobacteraceae, Flavobacteriaceae, and Sphingomonadaceae. However, they are less abundant and widespread than carbon monoxide dehydrogenases. Consistently, microbial communities in surface waters slowly consumed H2and rapidly consumed CO at environmentally relevant concentrations, with H2oxidation most active in subantarctic waters. The cell-specific power from these processes exceed bacterial maintenance requirements and, for H2, can likely sustain growth of bacteria with low energy requirements. Concordantly, we show that the polar ultramicrobacteriumSphingopyxis alaskensisgrows mixotrophically on H2by expressing a group 2a [NiFe]-hydrogenase, providing the first demonstration of atmospheric H2oxidation by a marine bacterium. Based on TARA Oceans metagenomes, genes for trace gas oxidation are globally distributed and are fourfold more abundant in deep compared to surface waters, highlighting that trace gases are important energy sources especially in energy-limited waters. Altogether, these findings show H2is a significant energy source for marine communities and suggest that trace gases influence the ecology and biogeochemistry of oceans globally.
Structural equation modeling of the critical driving forces of offsite construction in Ghana
Authors: Guribie Francis Lanme , Kheni Nongiba Alkanam , Sule Mohammed
Published: January 2022

Purpose

The construction sector suffers significant challenges which are intertwined with processes and products of the traditional onsite construction approach. The quest for a lasting solution to these problems is heralding the change toward offsite construction. Amid the scaling drive, to date there are no official reports and contribution to knowledge on the drivers of offsite construction in Ghana. This study models the structural paths of the critical drivers of offsite construction in Ghana.

Design/methodology/approach

Data were collected through a questionnaire from 95 respondents in the Ghanaian construction industry. Exploratory factor analysis and Partial least squares structural equation modeling were employed to analyze the data.

Findings

The results revealed that industry dynamics are the governing drivers of offsite construction in Ghana. As such, factors such as the rocketing housing deficits, high cost of acquiring land permanently, high cost of cast-in-situ construction, the utilization of prefabricated shipping containers for construction and construction market demand constitute the governing drivers of offsite construction in Ghana. Similarly, concern for higher productivity is a critical driver of offsite construction in the Ghanaian construction industry. On the contrary, findings show that performance-related drivers, government policy and regulation, and technological innovation exert little influence in driving offsite construction in Ghana.

Practical implications

The appreciation of the drivers may help stakeholders to understand the important mechanisms underlying offsite construction in Ghana, and thereafter help them to make more informed decisions regarding its implementation.

Originality/value

The findings contribute some interesting dimensions to the global debate on offsite construction by discovering and adding two drivers of offsite construction peculiar to developing countries (high cost of acquiring land permanently, and the utilization of shipping containers for construction) to the literature.
Organizing for permanent beta: performance measurement before vs performance monitoring after release of digital services
Authors: van Oorschot Kim E. , Akkermans Henk A. , Van Wassenhove Luk N. , Wang Yan
Published: January 2022

Purpose

Due to the complexity of digital services, companies are increasingly forced to offer their services “in permanent beta”, requiring continuous fine-tuning and updating. Complexity makes it extremely difficult to predict when and where the next service disruption will occur. The authors examine what this means for performance measurement in digital service supply chains.

Design/methodology/approach

The authors use a mixed-method research design that combines a longitudinal case study of a European digital TV service provider and a system dynamics simulation analysis of that service provider's digital service supply chain.

Findings

With increased levels of complexity, traditional performance measurement methods, focused on detection of software bugs before release, become fragile or futile. The authors find that monitoring the performance of the service after release, with fast mitigation when service incidents are discovered, appears to be superior. This involves organizational change when traditional methods, like quality assurance, become less important.

Research limitations/implications

The performance of digital services needs to be monitored by combining automated data collection about the status of the service with data interpretation using human expertise. Investing in human expertise is equally important as investing in automated processes.

Originality/value

The authors draw on unique empirical data collected from a digital service provider's struggle with performance measurement of its service over a period of nine years. The authors use simulations to show the impact of complexity on staff allocation.
Direct and indirect influences of supply chain management practices on competitive advantage in fast fashion manufacturing industry
Authors: Jahed Mohammed Abu , Quaddus Mohammed , Suresh Nallan C. , Salam Mohammad Asif , Khan Eijaz Ahmed
Published: January 2022

Purpose

This study investigates supply chain management (SCM) practices in a specific fast fashion apparel (FFA) industry. The impacts of SCM practices on competitive advantage (CA) are investigated via mediating roles of supply chain agility (SCA) and partnership quality (PQ). Resource advantage (R-A) theory, in addition to resource-based view (RBV) and dynamic capability theories, is used as theoretical underpinning.

Design/methodology/approach

A mixed-method approach is adopted: a qualitative field study and survey research. Data from 296 apparel manufacturers in Bangladesh are analyzed using the partial least squares structural equation modeling (PLS-SEM) approach, involving reflective and formative, first- and second-order constructs and mediation tests using the Hayes PROCESS macro.

Findings

Both SCM practices and PQ significantly affect SCA. SCM practices are found to directly enhance CA, but, counterintuitively, only marginally. Only through mediations of SCA and PQ do SCM practices enhance CA significantly. This is a departure from past research that has postulated direct effects between SCM practices and CA.

Research limitations/implications

This research is confined to the FFA industry and one national setting, Bangladesh. The data analyzed is also cross-sectional, with customary limitations on the temporal dimension.

Practical implications

SCM practices contribute to CA, but only through the mediation of PQ and SCA. This is an important directive to practitioners. Also, the second-order reflective measures for each construct indicate the specific SCM practices needed to maximize CA.

Originality/value

This study contributes to the literature on SCM practices in FFA industry, specifically the mediating roles of PQ and SCA, resulting in new, more nuanced findings that are important in dynamic business settings, driven by new theoretical perspectives incorporating R-A theory, which has hardly been utilized before in SCM research.
Social innovation in extreme institutional contexts: the case of Palestine
Authors: Morrar Rabeh , Baba Sofiane
Published: January 2022

Purpose

This paper focuses on social innovation dynamics in extreme contexts where institutional volatility is deeply rooted and enduring. In other words, the authors focus their discussion on the challenges that social innovators are facing in their endeavor of solving wicked social problems within an extreme institutional environment. This research is guided by the following question: How does an extreme institutional environment influence social innovation processes?

Design/methodology/approach

This qualitative research builds on the unique case of the Palestinian non-governmental organization (NGO) sector, a rarely studied context in organizational studies. The authors combine archival sources with 24 semi-structured interviews with Palestinian NGOs.

Findings

The authors theorize three barriers that hinder social innovation in such contexts: institutional trap, effectiveness trap and sustainability trap. The authors also theorize five mechanisms through which these barriers influence each other dynamically: mingling, surviving, undermining, binding and reinforcing. Taken together, these barriers and mechanisms shed light on social innovation processes taking place within extreme institutional environments.

Research limitations/implications

The main limitation of this study is the methodological design, based on an extreme single case-study which, on a bunch of features, is quite unique in the world. The authors argue that the results are all the same transferable to other relatively similar contexts.

Practical implications

By theorizing the institutional barriers to social innovation in an extreme institutional context, the research thus sheds light on how social innovation could be sustained and stimulated in Palestine and other contexts that face similar institutional challenges.

Social implications

From an engaged scholarship perspective, studying Palestine cannot be more relevant than today considering the turmoil in which Palestinians are. The research thus provides a deeper understanding of organizational and institutional dynamics with crucial social repercussions.

Originality/value

The social innovation literature has overemphasized success stories to the detriment of the struggles that hinder social innovations in extreme institutional environments. By focusing on the barriers that social innovators experience in these contexts, the authors provide novel empirical insight. Furthermore, this study enriches the understanding of the institutional dynamics of social innovations by proposing a process model that elucidates how an extreme institutional context can influence social innovations.
The mediating role of absorptive capacity on innovation among technology business incubators in the Philippines
Authors: Novino Marlo
Published: January 2022

Purpose

The paper aims to explore the knowledge management and innovative outputs (IO) of university-based technology business incubators funded by the Department of Science and Technology in the Philippines.

Design/methodology/approach

The respondents, which include heads, managers, coordinators, and staff,were reached out via email using a database. The instrument was generally adopted from various related studies in the literature. Data were analyzed quantitively using partial least squares – structural equations modeling.

Findings

The main findings reveal that the mediated relationship between potential absorptive capacity (PACAP), realized absorptive capacity (RACAP) and IO explained 38.7% of the variance both predicted by PACAP and mainly explained by RACAP. Among new organizational antecedents measured, slack resources and willingness to cannibalize did not predict PACAP, while tolerance for failure and external openness predicted PACAP. Consequently, PACAP and RACAP positively mediated the relationship between significant organizational antecedents and IO.

Originality/value

The validation of the positive and significant link of absorptive capacity (ACAP) and innovation with an emphasis on the Philippine context. The study pointed out the unidimensionality of PACAP and RACAP as a single ACAP variable and not two separate constructs.
Warped mapping–based blind deconvolution for resolution improvement
Authors: Li Chao , Liu Guochang
Published: January 2022

Owing to the influence of absorption and scattering, the components of seismic waves, especially those with higher frequencies, always suffer amplitude attenuation and phase distortion during their propagation through the earth. Nonstationary blind deconvolution takes such attenuations into account for prestack seismic data. This not only compensates for attenuation‐induced energy loss but also simultaneously addresses the energy loss associated with the reflectivity series and wavelet. Additionally, nonstationary blind deconvolution can greatly improve the resolution of seismic data. However, prestack nonstationary blind deconvolution is difficult to implement because it is not easy to estimate the attenuation function of prestack seismic data unless the quality factor of the Earth is assumed to be constant. In this regard, we introduced a nonstationary blind deconvolution method for prestack gathering. First, we used warped mapping to calculate the attenuation function of the prestack data. Then, we incorporated the attenuation function into the nonstationary sparse spike deconvolution based on Toeplitz‐sparse matrix factorization for reflectivity series and wavelet estimation. The proposed method is velocity‐independent and can be adapted to the time‐varying Q model. To validate its stability and effectiveness, numerical and real data examples were adopted. The results show that the proposed method provides a straightforward routine for the estimation of prestack reflectivity coefficients for further processing and inversion.
A qualitative exploration of how oral trials are used in dysphagia management in one inpatient hospital
Authors: Julier Rebecca , Benfield Jacqueline K.
Published: January 2022

Background

The lack of high‐quality evidence to support specific treatment approaches has been widely documented in the existing literature, with evidence suggesting speech and language therapists (SLTs) frequently rely on experience and expert opinion to inform treatment. One approach that is commonly used within dysphagia management, in spite of a lack of existing evidence to support its efficacy, is the use of oral trials, otherwise known as swallow trials or tasters. This approach involves offering specified, limited amounts of oral diet or fluids for those at risk of aspiration or choking if full amounts are taken orally and may be recommended for rehabilitation or quality of life.

Methods & Procedures

A total of nine SLTs working in one acute hospital volunteered to participate in focus groups in order to discuss their experience and clinical reasoning for using oral trials within one inpatient hospital setting in the UK. The objectives of this study were (1) to explore how oral trials are used within one inpatient hospital; (2) to consider the barriers and facilitators to the approach; and (3) to consider why this approach may be favoured over other evidenced dysphagia therapies. A grounded theory approach was used to guide data analysis, using two independent coders to identify themes within the focus groups.

Outcomes & Results

Analysis of data revealed the following themes: (1) delivering oral trials requires ‘a whole team approach’; (2) SLTs vary recommendations based on patient and environmental factors; and (3) oral trials as a holistic approach.

Conclusions & Implications

The use of oral trials was considered by SLTs to be a holistic and flexible approach which can be adapted to a range of patient and environmental factors. Although clinical experience guided rationale, an understanding of the principles of neuroplasticity and swallow physiology was also integral to the approach. Further research is warranted to investigate the use and efficacy of oral trials across the SLT community and within specific patient groups and different environments.
Digital forensic investigation methodology for Storage Space: Based on the NIST digital forensic process
Authors: Kim Junho , Lee Sangjin , Jeong Doowon
Published: January 2022

For forensic examiners, investigating the RAID systems of servers has been challenging, as the examiners must reconstruct multiple high‐capacity disks to identify digital evidence. Software‐based RAID systems’ use has been released for personal use, so examiners should consider RAID systems even when they investigate personal computers. Although there is a high probability that the software‐based RAID will become a target of crime, there has been little research into digital forensic methodology for software‐based RAID, as exemplified by Storage Space. In this paper, we introduce details about the structure of Storage Space found through reverse engineering. Storage Space was analyzed by applying the digital forensic process of NIST. We explain how to reconstruct a virtual disk configured using Storage Space and develop an automated tool to do so. To evaluate our study and the tool developed, we created an experimental scenario and describe in detail the forensic procedure and technical methods for the analysis of Storage Space. Our research can be used as the basis of forensic investigations for Storage Space.
Implementation of a revised classification for intrapartum fetal heart rate monitoring and association to birth outcome: A national cohort study
Authors: Jonsson Maria , Söderling Jonas , Ladfors Lars , Nordström Lennart , Nilsson Marianne , Algovik Michael , Norman Mikael , Holzmann Malin
Published: January 2022

Introduction

A revised intrapartum cardiotocography (CTG) classification was introduced in Sweden in 2017. The aims of the revision were to adapt to the international guideline published in 2015 and to adjust the classification of CTG patterns to current evidence regarding intrapartum fetal physiology. This study aimed to investigate adverse neonatal outcomes before and after implementation of the revised CTG classification.

Material and Methods

A before‐and‐after design was used. Cohort I (n = 160 210) included births from June 1, 2014 through May 31, 2016 using the former CTG classification, and cohort II (n = 166 558) included births from June 1, 2018 through May 31, 2020 with the revised classification. Data were collected from the Swedish Pregnancy and Neonatal Registers. The primary outcome was moderate to severe neonatal hypoxic ischemic encephalopathy (HIE 2–3). Secondary outcomes were birth acidemia (umbilical artery pH <7.05 and base excess < −12 mmol/L or pH <7.00), A‐criteria for neonatal hypothermia treatment, 5‐min Apgar scores <4 and <7, neonatal seizures, meconium aspiration, neonatal mortality and delivery mode. Logistic regression was used (period II vs period I), and results are presented as adjusted odds ratios (aORs) with 95% confidence intervals (95% CIs).

Results

There were no statistically significant differences in HIE 2–3 (aOR 1.27; 95% CI 0.97–1.66), proportion of neonates meeting A‐criteria for hypothermia treatment (aOR 0.96; 95% CI 0.89–1.04) or neonatal mortality (aOR 0.68; 95% CI 0.39–1.18) between the cohorts. Birth acidemia (aOR 1.36; 95% CI 1.25–1.48), 5‐min Apgar scores <7 (aOR 1.27; 95% CI 1.18–1.36) and <4 (aOR 1.40; 95% CI 1.17–1.66) occurred more often in cohort II. The absolute risk difference for HIE 2–3 was 0.02% (95% CI 0.00–0.04). Operative delivery (vacuum or cesarean) rates were lower in cohort II (aOR 0.82; 95% CI 0.80–0.85 and aOR 0.94; 95% CI 0.91–0.97, respectively).

Conclusions

Although not statistically significant, a small increase in the incidence of HIE 2–3 after implementation of the revised CTG classification cannot be excluded. Operative deliveries were fewer but incidences of acidemia and low Apgar scores were higher in the latter cohort. This warrants further in‐depth analyses before a full re‐evaluation of the revised classification can be made.
Subjectively felt and objectively measured: Wellbeing in the context of globalization
Authors: Janicki Wojciech , Dłużewska Anna
Published: January 2022

The article contributes to the discussion on the relationship between wellbeing (WB) and subjective wellbeing (SWB). Our aim is to develop a method for measuring SWB by creating a moving matrix scale that will be a reference point in different communities' research on SWB. To do so, we analyzed the relationship between objective WB‐SWB indicators in 146 countries and other political entities where studies on self‐reported life satisfaction (SRLS) were conducted between 2005 and 2017. SRLS values were compared with the values of several of the most frequently accepted objective WB indicators. Additionally, we analyzed variables showing the level of advancement within the process of globalization. The results confirmed that a comparative scale is crucial in determining SWB. Therefore, in many societies, there is a growing awareness of the gap between one's own quality of life and that of others. There is a strong link between HDI and SRLS on a global scale, as well as in the subgroups of high and medium developed countries; this link is missing in poorly developed countries. The disconnection between objective and subjectively perceived change in the situation—that is, the improvement in living standards—does not translate into increased life satisfaction.
Letter: loss of response to anti‐TNFα agents in patients with inflammatory bowel disease depends on treatment duration
Authors: Ben‐Horin Shomron , Ungar Bella
Published: January 2022

LINKED CONTENT

This article is linked to Schultheiss et al papers. To view these articles, visit https://doi.org/10.1111/apt.16605 and https://doi.org/10.1111/apt.16757
Letter: towards gender‐stratified colorectal cancer screening and surveillance?
Authors: Papastergiou Vasilios , Viazis Nikos , Mantzaris Gerassimos J.
Published: January 2022

LINKED CONTENT

This article is linked to Jodal et al papers. To view these articles, visit https://doi.org/10.1111/apt.16686 and https://doi.org/10.1111/apt.16764
Letter: towards gender‐stratified colorectal cancer screening and surveillance? Authors’ reply
Authors: Jodal Henriette C. , Løberg Magnus
Published: January 2022

LINKED CONTENT

This article is linked to Jodal et al papers. To view these articles, visit https://doi.org/10.1111/apt.16686 and https://doi.org/10.1111/apt.16737
Sacred natural sites classification framework based on ecosystem services and implications for conservation
Authors: Ma Jianzhong , Tam Christine , Li Tianjiang , Yu Guangzhi , Hu Guanghui , Yang Feiling , Wang Junjun , Wu Ruidong
Published: January 2022

Sacred natural sites (SNSs) are examples of community‐level governance for sustainable management of natural resources, which can greatly benefit nature conservation. However, the lack of a comprehensive understanding of the role of SNSs in conservation has resulted in overly simplistic classifications of SNSs that challenge current SNS research and conservation practice. Here, we propose an SNS classification framework based on the types and levels of material and spiritual services that SNSs provide, and applied this framework in the Khawa Karpo, an important sacred area in the Tibetan region of China based on detailed field surveys conducted from 2000 to 2004 and 2015 to 2017 that addressed six types of SNSs, including sacred mountains, Ri Vgags, sacred lakes, sacred rocks, sacred caves, and sacred trees. We found that SNSs in this region played a crucial role in sustaining traditional cultures and providing material services. Adoption of our classification framework will assist with the development of management strategies and targeted conservation actions for individual SNSs, thus improving conservation levels particularly in the Tibetan region.
Collecting and Exhibiting Traditional and Popular Alpine Folk Music in Austria—A Case Study
Authors: Biedermann Bernadette
Published: January 2022

This paper presents a case study dedicated to a particular genre of folk music popular in the Alpine countries, and its collection and display in Austria in connection with a project in which the author was involved. The theoretical and practical questions related to this study reflect the needs and challenges posed by this topic in terms of museum documentation and communication. The aim of the paper is to expand the current discourse in the field by discussing the relationships between this genre of music as an intangible social phenomenon and as tangible cultural heritage. The paper presents the case study in an international context of discussion on the display of music culture and the role of sound in exhibitions, and connects theoretical considerations with practical approaches.
Improving the efficiency of last‐mile package deliveries using hybrid driver helpers
Authors: Lu Shih‐Hao , Suzuki Yoshinori , Clottey Toyin
Published: January 2022

An approach widely used by parcel delivery companies to deal with increased shipping volumes, especially during peak seasons, is the use of temporary workers called driver helpers. There are two types of driver helpers: (1) dependent helpers (DH) who work alongside drivers to deliver packages on daily routes, and (2) independent helpers (IDH) who do not travel with the drivers but rather work alone at their assigned locations. The standard practice is for each helper to be used as either a DH or an IDH, but not both. This article introduces the concepts of multitasking to the parcel delivery literature by proposing a new type of helper called the hybrid helper, which allows parcel carriers to utilize each helper as both a DH and an IDH in the same route. The hybrid‐helper concept has several advantages over the existing DH or IDH concepts, including (1) reducing the transfer time of IDHs between locations, (2) allowing multiple delivery points to be serviced concurrently, and (3) increasing the daily work time of each helper. We develop a mathematical model that allows a vehicle to visit the same node more than once to enable IDH operations at selected nodes by a DH. Both numerical and field experiments show that our model outperforms other methods. Our results provide implications to practitioners on effective ways of utilizing helpers and suggest the need for future research to consider helpers in a broader context.