bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional homologous recombination assay on FFPE specimens of advanced high-grade serous ovarian cancer predicts clinical outcomes
Authors: Pikkusaari Sanna , Tumiati Manuela , Virtanen Anni , Oikkonen Jaana , Li Yilin , Perez-Villatoro Fernando , Muranen Taru , Salko Matilda , Huhtinen Kaisa , Kanerva Anna , Koskela Heidi , Tapper Johanna , Koivisto-Korander Riitta , Joutsiniemi Titta , Haltia Ulla-Maija , Lassus Heini , Hautaniemi Sampsa , Färkkilä Anniina , Hynninen Johanna , Hietanen Sakari , Carpén Olli , Kauppi Liisa 
Published: October 2022

AbstractDeficiency in homologous recombination (HR), a key DNA repair pathway, is a defining characteristic of many high-grade serous ovarian carcinomas (HGSC) and a major determinant of therapy outcomes. Patients with HR-deficient (HRD) tumors are more sensitive to DNA damaging platinum-based chemotherapy and HR deficiency also confers sensitivity to PARP inhibitors. While PARP inhibitors are highly effective in some patients, they are expensive and not without side effects, thus it is imperative to identify patients most likely to benefit from them. We set out to develop a clinically feasible assay for identifying functionally HRD tumors based on the detection of RAD51, a key HR protein. Our functional HR assay can be performed on FFPE tumor sample sections obtained from both treatment-naïve and neoadjuvant chemotherapy treated HGSC patients. We show that the functional HR test predicts key clinical outcomes, including platinum-free survival and overall survival after PARPi treatment. Our results indicate that RAD51-based HRD testing has great potential to predict platinum and PARPi sensitivity in the clinical setting.
SARS-CoV-2 spike protein induces endothelial dysfunction in 3D engineered vascular networks
Authors: Stern Brett , Monteleone Peter , Zoldan Janet 
Published: October 2022

AbstractWith new daily discoveries about the long-term impacts of COVID-19 there is a clear need to develop in vitro models that can be used to better understand the pathogenicity and impact of COVID-19. Here we demonstrate the utility of developing a model of endothelial dysfunction that utilizes induced pluripotent stem cell-derived endothelial progenitors encapsulated in collagen hydrogels to study the effects of COVID-19 on the endothelium. We found that treating these cell-laden hydrogels with SARS-CoV-2 spike protein resulted in a significant decrease in the number of vessel-forming cells as well as vessel network connectivity. Following treatment with the anti-inflammatory drug dexamethasone, we were able to prevent SARS-CoV-2 spike protein-induced endothelial dysfunction. In addition, we confirmed release of inflammatory cytokines associated with the COVID-19 cytokine storm. In conclusion, we have demonstrated that even in the absence of immune cells, we are able to use this 3D in vitro model for angiogenesis to reproduce COVID-19 induced endothelial dysfunction seen in clinical settings.
Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities
Authors: McDaniel Elizabeth A , Moya Francisco , Mendez Diana , Weathersby Coty , Oyserman Ben O , Flowers Jason , He Shaomei , Petriglieri Francesca , Singleton Caitlin , Nielsen Per H , McMahon Katherine D 
Published: October 2022

ABSTRACTMicrobial community dynamics are dictated by both abiotic environmental conditions and biotic interactions. These communities consist of individual microorganisms across the continuum of phylogenetic diversity, ranging from coexisting members of different domains of life and phyla to multiple strains with only a handful of single nucleotide variants. Ecological forces act on a shifting template of population-level diversity that is shaped by evolutionary processes. However, understanding the ecological and evolutionary forces contributing to microbial community interactions and overall ecosystem function is difficult to interrogate for complex, naturally occurring microbial communities. Here, we use two time series of lab-scale engineered enrichment microbial communities simulating phosphorus removal to explore signatures of microbial diversity at multiple phylogenetic scales. We characterized microbial community dynamics and diversity over the course of reactor start-up and long-term dynamics including periods of eubiosis and dysbiosis as informed by the intended ecosystem function of phosphorus removal. We then compared these signatures to lineages from full-scale WWTPs performing phosphorus removal. We found that enriched lineages in lab-scale bioreactors harbor less intra-population diversity than lineages from the full-scale WWTP overall. Our work establishes a foundation for using engineered enrichment microbial communities as a semi-complex model system for addressing the fundamental ecological and evolutionary processes necessary for developing stable microbiome based biotechnologies.
Memory in Repetitive Protein–Protein Interaction Series – in Memory of the Late Professor Robert M. Nerem
Authors: Rosado Aaron M. , Zhang Yan , Choi Hyun-Kyu , Ehrlich Samuel M. , Jin Fengzhi , Grakoui Arash , Evavold Brian D. , Zhu Cheng 
Published: October 2022

AbstractOver the past three decades, the senior author had interacted with and been mentored by the late Professor Robert M. Nerem. In his memory, the authors summarized several observations made, ideas conceptualized, and mathematical models developed during this period for quantitatively analyzing memory effects in repetitive protein–protein interactions (PPI). Interactions between proteins in an organism coordinate its biological processes and may impact its responses to changing environment and diseases through feedback systems. Feedback systems function by using changes in the past to influence behaviors in the future, which we refer here as memory. Specifically, we consider how proteins on cell or in isolation retain information about prior interactions to impact current interactions. The micropipette, biomembrane force probe and atomic force microscopic techniques were used to repeatedly assay several PPIs. The resulting time series were analyzed by a previous and two new models to extract three memory indices of short (seconds), intermediate (minutes), and long (hours) timescales. We found that interactions of cell membrane, but not soluble, T cell receptor (TCR) with peptide-major histocompatibility complex (pMHC) exhibits short-term memory that impacts on-rate, but not off-rate of the binding kinetics. Peptide dissociation from MHC resulted in intermediate- and long-term memories in TCR–pMHC interactions. However, we observed no changes in kinetic parameters by repetitive measurements on living cells over intermediate timescale using stable pMHCs. Parameters quantifying memory effects in PPIs could provide additional information regarding biological mechanisms. The methods developed herein also provide tools for future research.
Deformability Cytometry Clustering with Variational Autoencoders
Authors: Seith Daniel D. , Combs Cody , Siwy Zuzanna S. 
Published: October 2022

AbstractMechanobiology has shown great success in revealing complex cellular dynamics in various pathologies and physiologies. Most methods for assessing a cell’s mechanical properties, however, generally extract only a few physical constants such as Young’s modulus. This can limit the potential for accurate classification given the wide variety of rheological properties of cells, there are many ways for cells to differ. While it was recently shown that deep learning can classify cells more accurately than traditional approaches, it is not clear how this may be extended to unsupervised classification. In this work, we showcase the potential for a deep learning model to classify cells in an unsupervised fashion using a blend of physical properties. We introduce the combination of a variational autoencoder and a previously described clustering loss for classifying cells in an unsupervised fashion.
Contribution of 6mer seed toxicity to HIV-1 induced cytopathicity
Authors: Vaidyanathan Aparajitha , Taylor Harry E. , Hope Thomas J. , D’Aquila Richard T. , Bartom Elizabeth T. , Hultquist Judd F. , Peter Marcus E. 
Published: October 2022

AbstractHIV-1 (HIV) infects CD4 positive T cells, the gradual depletion of which can lead to the onset of Acquired Immunodeficiency Syndrome (AIDS) in the absence of antiretroviral therapy (ART). Several forms of cell death have been shown to be involved in HIV-mediated killing of either directly infected or bystander cells. It is still unknown, however, why some cells survive HIV infection and persist as part of the latently infected reservoir that reliably causes recurrent viremia upon ART cessation. Improved understanding of the mechanisms of HIV-mediated cell death could inform innovations designed to clear the latent reservoir. “Death Induced by Survival gene Elimination” (DISE) is an RNA interference (RNAi)-based mechanism that kills cells through short (s)RNAs with toxic 6mer seeds (pos. 2-7 of sRNA). These toxic seeds target reverse complementary seed matches in the 3’UTR of mRNA transcripts to decrease expression of hundreds of genes that are critical for cell survival. In most cells under normal conditions, highly expressed cell-encoded non-toxic microRNAs (miRNAs) block access of toxic sRNAs to the RNA-induced silencing complex (RISC) that mediates RNAi, promoting cell survival. We now report that infection of cells with HIV results in RISC-loading of an HIV-encoded miRNA, v-miRNA HIV-miR-TAR-3p, which kills cells by DISE through a noncanonical (pos. 3-8) 6mer seed. In addition, cellular RISC bound sRNAs shift to lower seed viability. Both these effects also occur with latent HIV provirus reactivation in J-Lat cells, a well-established cell model of HIV latency. Cells lacking expression of miRNA biogenesis genes Drosha, Dicer and Exportin 5 cannot produce protective miRNAs and therefore do not block RISC loading of the v-miRNA HIV-miR-TAR-3p. These mutant cells, as well as cells lacking expression of the RISC component Ago2, are hypersensitive to cell death via DISE induced by HIV infection. More precise targeting of the balance between protective and cytotoxic sRNAs could specifically and transiently increase silencing of cell survival genes to increase DISE. This could be a new addition to a “shock and kill” strategy to enhance depletion of the provirus reservoir during suppressive ART.
Engineering a plant polyketide synthase for the biosynthesis of methylated flavonoids
Authors: Peng Bo , Zhang Lili , He Siqi , Oerlemans Rick , Quax Wim J. , Groves Matthew R. , Haslinger Kristina 
Published: October 2022

AbstractHomoeriodictyol and hesperetin are naturally occurring O-methylated flavonoids with many health-promoting properties. They are produced in plants in low abundance and as complex mixtures of similar compounds that are difficult to separate. Synthetic biology offers the opportunity to produce various flavonoids in a targeted, bottom-up approach in engineered microbes with high product titers. However, the production of O-methylated flavonoids is currently still highly inefficient.In this study, we investigated and engineered a combination of enzymes that had previously been shown to support homoeriodictyol and hesperetin production inEscherichia colifrom fed O-methylated cinnamic acids. We determined the crystal structures of the enzyme catalyzing the first committed step of the pathway, chalcone synthase fromHordeum vulgare, in three ligand-bound states. Based on these structures and a multiple sequence alignment with other chalcone synthases, we constructed mutant variants and assessed their performance inE. colitowards producing methylated flavonoids. With our best mutant variant, HvCHS (Q232P, D234V), we were able to produce homoeriodictyol and hesperetin at 2 times and 10 times higher titers than previously reported. Our findings will facilitate the further engineering of this enzyme towards higher production of methylated flavonoids.
DNA Modifications Enabling Proximity Biotinylation
Authors: Wilbanks Brandon , Pearson Keenan , Byrne Shane R. , Bickart Laura B. , Dedon Peter C. , Maher L. James 
Published: October 2022

ABSTRACTAdvances in peroxidase- and biotin ligase-mediated signal amplification have enabled high-resolution subcellular mapping of endogenous RNA localization and protein-protein interactions. Application of these technologies has been limited to RNA and proteins because of the reactive groups required for biotinylation in each context. Here we report several novel methods for proximity biotinylation of exogenous oligodeoxyribonucleotides by application of well-established and convenient enzymatic tools. We describe approaches using simple and efficient conjugation chemistries to modify deoxyribonucleotides with “antennae” sensitive to phenoxy radical or biotinoyl-5’-adenylate. In addition, we report chemical details of a previously undescribed adduct between tryptophan and a phenoxy radical group. These developments have potential application in the selection of exogenous nucleic acids capable of unaided entry into living cells.
Navigational space for the absence of sustainability assurance in China
Authors: Li Teng , Hidayah Nunung Nurul , Lyu Ou , Lowe Alan 
Published: October 2022

PurposeThis case study presents a critical analysis of why and how corporate managers in China are reluctant to adopt sustainability reporting assurance (SRA) provided by externally independent third-party assurers, despite the fact that it is acknowledged as a value-adding activity globally.Design/methodology/approachA longitudinal fieldwork case study was conducted from 2014 to 2019 in a Chinese central state-owned enterprise (CSOE), a pioneer in sustainability reporting practice since the mid-2000s, to collect first-hand empirical data on managerial perceptions of the adoption of external SRA. Semi-structured interviews with 25 managers involved in sustainability (reporting) practice were conducted. The interview data were triangulated with an analysis of archival documents and board meeting minutes pertaining to the undertakings of sustainability practices in the case study organization.FindingsOur empirical analysis suggests that while managers recognize the benefits of adopting external SRA in enhancing the legitimacy of sustainability accountability, they oppose SRA because of their deep-rooted allegiance to the dominant logic of sociopolitical stability in China. SRA is envisaged to risk the stability of the socialist ideology with which CSOEs are imbued. Therefore, any transformational approach to accepting a novel (foreign) practice must be molded to gain control and autonomy, thereby maintain the hegemony of stability logic. Instead of disregarding external verification, managers of our case SOE appear to harness sustainability reporting as a navigational space to engage in internally crafted alternative manners in order to resist the rationality of SRA.Originality/valueThe empirical analysis presents a nuanced explanation as to why internal managers have hitherto been reluctant to embrace the embedding of independent assurance into the sustainability reporting process. Our prolonged fieldwork provides ample context-specific, intra-organizational evidence regarding the absence of SRA in Chinese CSOEs, which warrants more attention given their considerable presence in the global economy. In addition, the empirical analysis contributes to our understanding of the managerial capture of sustainability issues in a specific context of state capitalism and how organizations and individuals in an authoritarian regime interpret and respond to novel discourses derived from distinct institutional settings.
The lived experience of medical students during COVID-19 pandemic: the impact on lifestyle and mental wellbeing
Authors: Alzayani Salman , Al-Roomi Khaldoon , Ahmed Jamil 
Published: October 2022

PurposeThe paper intends to explore the lived experiences of medical students during the COVID-19 pandemic and its impact on their lifestyles and mental wellbeing.Design/methodology/approachFourteen medical students from the College of Medicine and Medical Sciences, Arabian Gulf University, Bahrain, were enrolled, and their narratives were obtained. Data were analyzed and conducted using Colaizzi’s phenomenological descriptive method of enquiry.FindingsThe analysis identified two themes, along with nine subthemes, that were generated. The first theme focused on mental and social experiences, while the second focused on lifestyle changes. During the pandemic, students had time to reflect on themselves and started to think positively about their lives, although they felt fearful, uncertain, stressed and anxious due to preventive control measures that were mandated, including social distancing and lockdowns. Participants’ lifestyles changed generally negatively, as they adapted to the preventive measures, rendering them physically inactive and exposing them to unhealthy food and disturbed sleep.Originality/valueThe findings provide an insight into the negative impact of the COVID-19 pandemic on the lifestyle and mental wellbeing of medical students. Educational institutes need to offer their students both short as well as long-term health, social and mental support to overcome the impact of the pandemic on their lives.
Assessing the performance and productivity of labour in building construction projects through the application of work-based training practices
Authors: Manoharan Kesavan , Dissanayake Pujitha , Pathirana Chintha , Deegahawature Dharsana , Silva Renuka 
Published: October 2022

Purpose
Sources highlight that lack of systematic labour training components results in low performance and productivity of labour, which leads the construction industry of many countries to face various challenges. This study aims to quantify the variations in the performance and productivity levels of labour in building construction projects through the applications of effective work-based training components.

Design/methodology/approach
A comprehensive literature review and a series of experts’ discussions with action-oriented communication approaches were conducted to develop a set of practices related to labour training, performance assessment and productivity measurements within a framework. The developed practices were applied to around 100 labourers working on nine building construction projects through a construction supervisory training programme.

Findings
The study presents the detailed patterns of the significant changes in labour performance and productivity levels. The majority of trained labourers have grown to perform the work process with some relevant theoretical and operational knowledge and skills. The overall results spotlight the significant behavioural changes that can be observed in workforce operations by improving labour performance, which resulted in implementing effective labour-rewarding practices within a framework.

Research limitations/implications
Although the study findings were limited to the Sri Lankan context, the proposed practices can be applied to the industry practices of the construction sector of other developing countries and the other developing industries in similar ways/scenarios.

Practical implications
The study outcomes contribute to uplifting the work qualities of labourers with life-long learning opportunities and unlocking the potential barriers for expanding the local labour supply while controlling the excessive inclination of the local firms towards foreign labour. This paper describes further implications and future scopes of the study elaborately.

Originality/value
The study provides generalised mechanisms and practices that transform the labour characteristics and add new attributes for strengthening the values of construction supervision practices to obtain well-improved work outputs. The study outcomes reinforce the chain relationships among the training elements, labour performance and productivity levels, leading to upgrading current planning and operational management practices, especially adding constructive mechanisms in resource levelling and productivity benchmarking practices.
Towards a successful learning process of companies from developing countries involved in offshore outsourcing: proposal for an integrative analytical framework
Authors: N’Dri Amoin Bernadine , Su Zhan 
Published: October 2022

Purpose
This paper aims to contribute to international business research by providing an integrative framework of the factors determining the learning process of outsourcing companies in developing countries.

Design/methodology/approach
A systematic review of the literature was performed with an analysis of 84 articles published in peer-reviewed academic journals, published between 2000 and 2020.

Findings
The results show that the different factors should be seen as complementary and not mutually exclusive. It is the interaction between macro and micro factors that jointly shape the learning of developing country subcontractors. Moreover, the results of the analysis show that many existing studies have not been based on specific theoretical frameworks.

Research limitations/implications
This study develops a roadmap of the current state of research on the determinants of learning among developing country subcontractors and offers suggestions to guide future research. The authors conclude with a call for methodological advancement and theory development on the topic.

Originality/value
To the best of the authors’ knowledge, this study proposes the first comprehensive review of the literature on the factors determining the learning of subcontractors in developing countries. The authors have tried to provide an integrative analytical framework to discuss what has been known and what needs to be known in this regard.
Factors affecting entrepreneurial intention among the rural population in India
Authors: Ali Jabir , Burhan Muqbil , Jabeen Zakia 
Published: October 2022

PurposeThis paper aims at examining the factors affecting entrepreneurial intention (EI) among the rural adult population in India using the social cognitive theory (SCT).Design/methodology/approachThis study is based on the Adult Population Survey of the Global Entrepreneurship Monitor of 2017, covering 1,397 rural respondents from India. The data has been analysed using simple techniques such as Chi-square statistics, correlation and logistics regression.FindingsAbout 16% of the rural adults have reported EI in India. A significant relationship emerged between the demographics of rural adults with and without intention towards entrepreneurship. Finally, the regression model representing two components of the SCT, that is, confidence towards entrepreneurship and outcome expectations from entrepreneurship, showed a significant impact on EI among the rural population when controlled by family size and working status.Practical implicationsThis paper provides insights on factors affecting EI among rural adults, which can help in developing a policy framework for promoting new ventures among rural entrepreneurs. The result of the analysis indicates that the rural population need to be imparted the necessary skills to gain confidence in entrepreneurship, which should be aligned with the outcome expectations of the entrepreneurs.Originality/valueThis piece of research can be valuable for different stakeholders in adopting inclusive entrepreneurial initiatives. Moreover, entrepreneurship in rural areas has not gained much attention among scholars, and this study is intended to provide future research motivation.