bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway
Authors: Gagne Matthew , Corbett Kizzmekia S. , Flynn Barbara J. , Foulds Kathryn E. , Wagner Danielle A. , Andrew Shayne F. , Todd John-Paul M. , Honeycutt Christopher Cole , McCormick Lauren , Nurmukhambetova Saule T. , Davis-Gardner Meredith E. , Pessaint Laurent , Bock Kevin W. , Nagata Bianca M. , Minai Mahnaz , Werner Anne P. , Moliva Juan I. , Tucker Courtney , Lorang Cynthia G. , Zhao Bingchun , McCarthy Elizabeth , Cook Anthony , Dodson Alan , Mudvari Prakriti , Roberts-Torres Jesmine , Laboune Farida , Wang Lingshu , Goode Adrienne , Kar Swagata , Boyoglu-Barnum Seyhan , Yang Eun Sung , Shi Wei , Ploquin Aurélie , Doria-Rose Nicole , Carfi Andrea , Mascola John R. , Boritz Eli A. , Edwards Darin K. , Andersen Hanne , Lewis Mark G. , Suthar Mehul S. , Graham Barney S. , Roederer Mario , Moore Ian N. , Nason Martha C. , Sullivan Nancy J. , Douek Daniel C. , Seder Robert A. 
Published: October 2021

ABSTRACTmRNA-1273 vaccine efficacy against SARS-CoV-2 Delta wanes over time; however, there are limited data on the impact of durability of immune responses on protection. We immunized rhesus macaques at weeks 0 and 4 and assessed immune responses over one year in blood, upper and lower airways. Serum neutralizing titers to Delta were 280 and 34 reciprocal ID50 at weeks 6 (peak) and 48 (challenge), respectively. Antibody binding titers also decreased in bronchoalveolar lavage (BAL). Four days after challenge, virus was unculturable in BAL and subgenomic RNA declined ∼3-log10 compared to control animals. In nasal swabs, sgRNA declined 1-log10 and virus remained culturable. Anamnestic antibody responses (590-fold increase) but not T cell responses were detected in BAL by day 4 post-challenge. mRNA-1273-mediated protection in the lungs is durable but delayed and potentially dependent on anamnestic antibody responses. Rapid and sustained protection in upper and lower airways may eventually require a boost.
The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC
Authors: Javitt Aaron , Shmueli Merav D. , Kramer Matthias P , Kolodziejczyk Aleksandra A. , Cohen Ivan J. , Kamer Iris , Litchfield Kevin , Bab-Dinitz Elizabeta , Zadok Oranit , Neiens Vanessa , Ulman Adi , Radomir Lihi , Wolf-Levy Hila , Eisenberg-Lerner Avital , Kacen Assaf , Alon Michal , Rêgo Ana Toste , Stacher-Priehse Elvira , Lindner Michael , Koch Ina , Bar Jair , Swanton Charles , Samuels Yardena , Levin Yishai , da Fonseca Paula C. A. , Elinav Eran , Friedman Nir , Meiners Silke , Merbl Yifat 
Published: October 2021

SummaryProtein degradation by proteasomes is important for the immune response against tumors. Antigens generated by the proteasome promote immune cell infiltration into tumors and improve tumors’ responses to immunotherapy. For example, immunoproteasomes – a subset of proteasomes induced by inflammatory signals – may improve the response of melanomas to immune checkpoint inhibitors (ICI) by eliciting tumor inflammation. Yet, it is unclear whether and how protein degradation by proteasomes impacts cancer progression and contributes to immune evasion and resistance. Here, we profile the proteasome-cleaved peptides in lung cancers and find that PSME4 serves as a novel inhibitory regulator of the immunoproteasome, playing an anti-inflammatory role in cancer. Biochemical assays combined with scRNA-seq, immunopeptidomics and in vivo analyses demonstrate that PSME4 promotes an immunosuppressive environment around the tumor and abrogates anti-tumor immunity by inhibiting antigen presentation and attenuating tumor inflammation. Furthermore, we find that PSME4 expression is correlated with responsiveness to ICI across several cancer types. Our findings suggest that PSME4-mediated regulation of proteasome activity is a novel mechanism of immune evasion in non-small-cell lung carcinoma and may be targeted therapeutically for restoring anti-tumor immunity.Graphical AbstractHighlightsMapping the degradation landscape in Non-Small Cell Lung Cancer (NSCLC) uncovers altered proteasome activity and compositionProteasome regulator PSME4 plays an anti-inflammatory role in NSCLC by attenuating immunoproteasome activityPSME4 restricts tumor antigen presentation and cytokine secretion, defining a ‘cold’ tumor environmentPSME4 drives tumor immune evasion and is associated with resistance to immunotherapy
NLR immune receptor-nanobody fusions confer plant disease resistance
Authors: Kourelis Jiorgos , Marchal Clemence , Kamoun Sophien 
Published: October 2021

ABSTRACTPlant pathogens cause recurrent epidemics that threaten crop yield and global food security. Efforts to retool the plant immune system have been limited to modifying natural components and can be nullified by the emergence of new pathogen races. Therefore, there is a need to develop made-to-order synthetic plant immune receptors with resistance tailored to the pathogen genotypes present in the field. Here we show that plant immune receptors can be used as scaffolds for VHH nanobody fusions that bind fluorescent proteins (FPs). The receptor-nanobody fusions signal in the presence of the corresponding FP and confer resistance against plant viruses expressing FPs. Given that nanobodies can be raised against virtually any molecule, immune receptor-nanobody fusions have the potential to generate resistance against all major plant pathogens and pests.One-Sentence SummaryPlant immune receptor-nanobody fusions enable made-to-order disease resistance genes.
Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family
Authors: Li Chunhua , Yang Xianwei , Shao Libin , Zhang Rui , Liu Qun , Zhang Mengqi , Liu Shanshan , Pan Shanshan , Xue Weizhen , Wang Congyan , Mao Chunyan , Zhang He , Fan Guangyi 
Published: October 2021

AbstractThe Bicolor Angelfish, Centropyge bicolor, is a tropical coral reef fish. It is named for its striking two-color body. However, a lack of high-quality genomic data means little is known about the genome of this species. Here, we present a chromosome-level C. bicolor genome constructed using Hi-C data. The assembled genome is 650 Mbp in size, with a scaffold N50 value of 4.4 Mbp, and a contig N50 value of 114 Kbp. Protein-coding genes numbering 21,774 were annotated. Our analysis will help others to choose the most appropriate de novo genome sequencing strategy based on resources and target applications. To the best of our knowledge, this is the first chromosome-level genome for the Pomacanthidae family, which might contribute to further studies exploring coral reef fish evolution, diversity and conservation.
Three-echelon apparel supply chain coordination with triple bottom line approach
Authors: Kumar Patanjal , Sharma Dheeraj , Pandey Peeyush 
Published: October 2021

PurposeAn apparel supply chain primarily consists of geographically distant suppliers, manufacturers and retailers. The coordination among the members of the supply chain becomes difficult when we consider the triple bottom line of sustainability in it. Moreover, the complexity increases with the change in dominance power of the respective members. However, the task of managing the channel further becomes complicated after incorporating sustainability and dominance power simultaneously into the supply chain. To fill this gap, this paper focuses on designing of mechanism and demonstration of three-echelon model to coordinate sustainable supply chain.Design/methodology/approachIn this paper, the noncooperative game theoretic method has been applied for the exploration of models. The various structures of the centralized and decentralized supply chain are considered on the basis of a player's dominance power. The model uses simultaneous and sequential move games to analyze optimal profit of supply chain agents, total channel profit, green innovation level and corporate social innovation level.FindingsAnalytical results show that simultaneous game performs better than the sequential game. The consumer sensitivity toward green and social innovations increases total channel profit. We also proposed a linear two-part tariff contract model. The proposed model enhances the sustainability level and leads to perfect channel coordination. Using a numerical example, we present the effectiveness of multiple game structures under centralized and decentralized settings. The results reveal that channel efficiency is the highest in the two-part tariff contract followed by a simultaneous move game structure and lower in the cases of sequential move game.Research limitations/implicationsIn this research, model setting are deterministic and there is no any information asymmetry. Therefore researchers are encouraged to study multiechelon sustainable supply chain coordination models under stochastic and information asymmetry settings.Practical implicationsThe paper includes implications for the development of sustainable supply chain coordination model to tackle the problems of dominance power, sustainability issues and lower channel efficiency of supply chain.Originality/valueThis study proposes game-theory-based three-echelon sustainable supply chain for the channel coordination.
Coworking space practices: assessing space users’ preferences and challenges in Ibadan, Nigeria
Authors: Ayodele Timothy Oluwafemi , Ogunbayo Oyeronke Toyin , Kajimo-Shakantu Kahilu , Babatunde Theophilus 
Published: October 2021

Purpose
Coworking spaces are recent developments in commercial property investment portfolio in Nigeria. Given the user-centered nature of coworking space practices, the purpose of this paper is to examine the factors influencing users’ preference for coworking, and the challenges associated with the use of coworking spaces in the emerging Nigeria property market.

Design/methodology/approach
This study used a quantitative research approach. This study sampled nine (9) traditional coworking spaces in Ibadan property market, from which 15 coworking space users were randomly selected in each of the coworking hubs. From a total of 135 respondents, only 45 (33.33%) questionnaires were retrieved and found suitable for analysis. The data collected were analyzed using descriptive and inferential statistics.

Findings
The results showed that economic and social motivators were significant drivers influencing coworkers’ decision to cowork. Personal factors were the least rated. Also, top-rated features/facilities that users prefer in the workstations include a neat environment and conveniences, uninterrupted power supply, serenity of the neighborhood and ease of signing up. The findings also showed that the challenges being faced by the users were predominantly about disturbance/noise from guests and/or other users, lack of privacy, poor internet connectivity, power failure and inability to personalize workspace (in decreasing order).

Practical implications
This study has implications for investors and users of coworking spaces in comparable developing markets. Also, the study will influence strategies and decisions of private firms/companies, as it relates to the work pattern of their employees.

Originality/value
This paper is relevant given the emergent behavioral changes, necessitated by the changing work practices. This compels the need for a reevaluation of the preferences and challenges associated with coworking spaces, especially as it relates to the users of flexible office spaces in emerging economies.
A cross-country analysis of the relationship between human capital and foreign direct investment
Authors: Sethi Madhvi , Baby Saina , Sharma Aarti Mehta 
Published: October 2021

PurposeThe Zhang–Markusen (Z-M) inverse U-shape theory uses education as a human capital variable to investigate the impact of educational attainment on foreign direct investment (FDI) inflows to a country. The objective of this research is to empirically test this theory in a cross-country framework.Design/methodology/approachFixed effect panel regression has been used to test the Z-M hypothesis for 172 countries for the period 1990–2015. For the purpose of this study, countries were divided into four groups as per the World Bank classification: Low-income economies, lower middle-income countries, upper middle-income economies and high-income economies.FindingsThe findings of this study reinforce the proposition that macroeconomic factors are the major determinants of FDI inflows into various countries. The authors find that the size of the market measured by gross domestic product (GDP), the growth potential of the market measured by real GDP growth rate and the availability of infrastructure are the major factors that enhance the attractiveness of a country as an FDI destination.Originality/valueThough the Z-M theory has been empirically tested in cross-country frameworks, no consensus has been reached. Thus, it is interesting to look again at the validity of the Z-M hypothesis using data covering longer and more recent periods. The study includes both macroeconomic and human capital determinants of FDI, so as to arrive at a comprehensive model explaining the FDI flows into various countries.
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples
Authors: Reynolds Nicole K. , Jusino Michelle A. , Stajich Jason E. , Smith Matthew E. 
Published: October 2021

AbstractMetabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with “standard” metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.
Drivers of fish biodiversity in a rapidly changing permafrost landscape
Authors: Murdoch Alyssa , Gray Derek K. , Korosi Jennifer , Vucic Jasmina M. , Cohen Rachel S. , Sharma Sapna 
Published: October 2021

Abstract

Rapid environmental change occurring in northern permafrost regions may have profound implications for fish biodiversity but remains poorly understood. Climate change, increasing human development, and resultant permafrost thaw may combine to alter the quality and quantity of fish habitat including reductions in preferred thermal habitat, changes in water quality, and modified drainage patterns.

Our study objective was to understand how lake fish communities residing on permafrost landscapes may be responding to climate change and land use disturbance. We investigated the drivers of freshwater fish community health in lakes of the lower Mackenzie River basin, an ice‐rich permafrost region that is experiencing substantial warming, permafrost thaw, and new major highway development. We collected lake morphometry, water quality, and fish community data from 50 lakes and derived several indicators of aquatic health including fish species richness, relative abundance, and the occurrence of three culturally important fish species.

We found that water quality and lake size were significant co‐drivers of fish community health whereas relationships with summer thermal habitat, as represented by July air temperature, were relatively negligible. Dissolved organic carbon (an indicator for lake browning) emerged as a particularly important driver of fish community structure, and fish community health steeply declined when dissolved organic carbon concentrations exceeded 17–18 mg/L. We suggest potential mechanisms for these declines including light inhibition during summer and a reduced capacity for overwintering in smaller and murkier lakes that may experience faster oxygen depletion rates.

Using a more expansive regional water quality database of 203 lakes, we observed potential supporting evidence that warming and new road development increased dissolved organic carbon and total phosphorus concentrations, possibly reducing fish habitat quality in this region.

Together, these results highlight how fishes relying on the numerous small and shallow lakes that dominate permafrost landscapes may be vulnerable to the combined effects of rapid warming and new infrastructure.
Biodiversity scale‐dependence and opposing multi‐level correlations underlie differences among taxonomic, phylogenetic and functional diversity
Authors: Mirochnitchenko Nadejda A. , Stuber Erica F. , Fontaine Joseph J. 
Published: October 2021

AbstractAimBiodiversity is a multi‐dimensional property of biological communities that represents different information depending on how it is measured, but how dimensions relate to one another and under what conditions is not well understood. We explore how taxonomic, phylogenetic, and functional diversity can differ in scale‐of‐effect dependence and habitat‐biodiversity relationships, and subsequently how spatial differences among biodiversity dimensions may arise.LocationNebraska, United States.TaxonBirds.MethodsAcross 2016 and 2017, we conducted 2,641 point counts at 781 sites. We modeled the occupancy of 141 species using Bayesian Bernoulli‐Bernoulli hierarchical logistic regressions. We calculated species richness (SR), phylogenetic diversity (PD) and functional diversity (FD) for each site and year based on predicted occupancy, accounting for imperfect detection. Using Bayesian latent indicator scale selection and multivariate modeling, we quantified the spatial scales‐of‐effect that best explained the relationships between environmental characteristics and SR, PD and FD. Additionally, we decomposed the residual between‐site and within‐site biodiversity correlations using our repeated measures design.ResultsAlthough relationships between specific land cover types and SR, PD and FD were qualitatively similar, the spatial scales at which these variables were important in explaining biodiversity differed among dimensions. Between‐site residual biodiversity correlations were negative, yet within‐site biodiversity residual correlations were positive.Main conclusionsOur results demonstrate how spatial differences among biodiversity dimensions may arise from biodiversity‐specific scale‐dependent habitat relationships, low shared environmental correlations and opposing residual correlations between dimensions, suggesting that single‐scale and single‐dimension analyses are not entirely appropriate for quantifying habitat‐biodiversity relationships. After accounting for shared habitat relationships, we found positive within‐site residual correlations between SR, PD and FD, suggesting that habitat change over time influenced all biodiversity dimensions similarly. However, negative between‐site residual correlation among biodiversity dimensions may indicate trade‐offs in achieving maximum biodiversity across multiple biodiversity dimensions at any given location.
Lessons for deprescribing from a nonessential medication hold policy in US nursing homes
Authors: McConeghy Kevin W. , Cinque Michael , White Elizabeth M. , Feifer Richard A. , Blackman Carolyn , Mor Vincent , Gravenstein Stefan , Zullo Andrew R. 
Published: October 2021

AbstractBackgroundAt the height of the COVID‐19 pandemic, a large nursing home chain implemented a policy to temporarily hold potentially unnecessary medications. We describe rates of held and discontinued medications after a temporary hold policy of potentially unnecessary or nonessential medications.MethodsThis retrospective cohort study uses electronic health record (EHR) data on 3247 residents of 64 nursing homes operated by a multistate long‐term care provider. Medications were documented in the electronic medication administration record. Overall medication held and discontinued incidences are reported. Hierarchical Bayesian modeling is used to determine individual probabilities for medication discontinuation within each facility.ResultsIn total, 3247 residents had 5297 nonessential medications held. Multivitamins were most likely to be held, followed by histamine‐2 receptor antagonists, antihistamines, and statins. At the end of the hold policy, 2897 of 5297 (54%) were permanently discontinued, including probiotics (73%), histamine‐2 receptor antagonists (66%), antihistamines (64%), and statins (45%). Demographics, cognitive and functional impairment were similar between residents with medications who were discontinued versus continued. For most medications, more than 50% of the variance in whether medications were discontinued was explained by facility rather than resident‐level factors.ConclusionA temporary medication hold policy implemented during the CoVID‐19 pandemic led to the deprescribing of a plurality of ‘nonessential’ medications. This type of organization‐wide initiative may be an effective mechanism for altering future prescribing behaviors to reduce the use of unnecessary medications.