bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duration of mRNA vaccine protection against SARS-CoV-2 Omicron BA.1 and BA.2 subvariants in Qatar
Authors: Chemaitelly Hiam , Ayoub Houssein H. , AlMukdad Sawsan , Coyle Peter , Tang Patrick , Yassine Hadi M. , Al-Khatib Hebah A. , Smatti Maria K. , Hasan Mohammad R. , Al-Kanaani Zaina , Kuwari Einas Al- , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J. 
Published: March 2022

AbstractThe SARS-CoV-2 Omicron (B.1.1.529) variant has two subvariants, BA.1 and BA.2, that are genetically quite divergent. We conducted a matched, test-negative, case-control study to estimate duration of protection of mRNA COVID-19 vaccines, after the second dose and after a third/booster dose, against BA.1 and BA.2 infections in Qatar’s population. BNT162b2 effectiveness against symptomatic BA.1 infection was highest at 46.6% (95% CI: 33.4-57.2%) in the first three months after the second dose, but then declined to ∼10% or below thereafter. Effectiveness rapidly rebounded to 59.9% (95% CI: 51.2-67.0%) in the first month after the booster dose, but then started to decline again. BNT162b2 effectiveness against symptomatic BA.2 infection was highest at 51.7% (95% CI: 43.2-58.9%) in the first three months after the second dose, but then declined to ∼10% or below thereafter. Effectiveness rapidly rebounded to 43.7% (95% CI: 36.5-50.0%) in the first month after the booster dose, but then declined again. Effectiveness against COVID-19 hospitalization and death was in the range of 70-80% any time after the second dose, and was greater than 90% after the booster dose. Similar patterns of protection were observed for the mRNA-1273 vaccine. mRNA vaccines provide only moderate and short-lived protection against symptomatic Omicron infections, with no discernable differences in protection against either the BA.1 or BA.2 subvariants. Vaccine protection against COVID-19 hospitalization and death is strong and durable after the second dose, but is more robust after a booster dose.
Diffusional variance-determined stochastic translation efficiency
Authors: Horvath Attila , Janapala Yoshika , Hannan Ross D. , Eyras Eduardo , Preiss Thomas , Shirokikh Nikolay E. 
Published: March 2022

ABSTRACTFull-transcriptome methods have brought versatile power to protein biosynthesis research, but remain difficult to apply for the quantification of absolute protein synthesis rates. Here we propose and, using modified translation complex profiling, confirm co-localisation of ribosomes on messenger(m)RNA resulting from their diffusional dynamics. We demonstrate that these stochastically co-localised ribosomes are linked with the translation initiation rate and provide a robust variable to model and quantify specific protein output from mRNA.
LANTSA: Landmark-based transferable subspace analysis for single-cell and spatial transcriptomics
Authors: Zhang Chuanchao , Wang Lequn , Li Xinxing , Guo Wei-Feng , Shi Qianqian , Chen Luonan 
Published: March 2022

ABSTRACTSingle-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies provide new insights to understand tissue organization and biological function. Accurately capturing the relationships of samples (e.g., sequenced cells, spatial locations) will result in reliable and consistent outcomes in downstream analyses. However, this undertaking remains a challenge for large-volume or cross-platform datasets due to transcriptional heterogeneity and high computational demands. Here, we introduce landmark-based transferable subspace analysis (LANTSA) to solve such challenges for scRNA-seq and ST datasets. Specifically, LANTSA constructs a representation graph of samples for clustering and visualization based on a novel subspace model, which can learn a more accurate representation and is theoretically proven to be linearly proportional to data size in terms of the time consumption. Furthermore, LANTSA uses a dimensionality reduction technique as an integrative method to extract the discriminants underlying the representation structure, which enables label transfer from one (learning) dataset (i.e., scRNA-seq profiles) to the other (prediction) datasets (e.g., scRNA-seq or ST profiles), thus solving the massive-volume or cross-platform problem. We demonstrated the superiority of LANTSA to identify accurate data structures via clustering evaluation on benchmark datasets of various scRNA-seq protocols, 10x Visium, and Slide-seq ST platforms. Moreover, we confirmed the integration capability of LANTSA to transfer cell annotation on large-scale and cross-platform scRNA-seq datasets. Finally, we validated the effectiveness of LANTSA for the identification of multiple mouse brain areas as well as the spatial mapping of cell types within cortical layers by integrating scRNA-seq and ST data.
Immunization with recombinant accessory protein-deficient SARS-CoV-2 protects against lethal challenge and viral transmission
Authors: Ye Chengjin , Park Jun-Gyu , Chiem Kevin , Dravid Piyush , Allué-Guardia Anna , Garcia-Vilanova Andreu , Kapoor Amit , Walter Mark R. , Kobie James J. , Plemper Richard K. , Torrelles Jordi B. , Martinez-Sobrido Luis 
Published: March 2022

ABSTRACTSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a worldwide Coronavirus Disease 2019 (COVID-19) pandemic. Despite high efficacy of the authorized vaccines, protection against the surging variants of concern (VoC) was less robust. Live-attenuated vaccines (LAV) have been shown to elicit robust and long-term protection by induction of host innate and adaptive immune responses. We sought to develop a COVID-19 LAV by generating 3 double open reading frame (ORF)-deficient recombinant (r)SARS-CoV-2 simultaneously lacking two accessory open reading frame (ORF) proteins (ORF3a/ORF6, ORF3a/ORF7a, and ORF3a/ORF7b). Here, we report that these double ORF-deficient rSARS-CoV-2 have slower replication kinetics and reduced fitness in cultured cells as compared to their parental wild-type (WT) counterpart. Importantly, these double ORF-deficient rSARS-CoV-2 showed attenuation in both K18 hACE2 transgenic mice and golden Syrian hamsters. A single intranasal dose vaccination induced high levels of neutralizing antibodies against different SARS-CoV-2 VoC, and also activated viral component-specific T-cell responses. Notably, the double ORF-deficient rSARS-CoV-2 were able to protect, as determined by inhibition of viral replication, shedding, and transmission, against challenge with SARS-CoV-2. Collectively, our results demonstrate the feasibility to implement these double ORF-deficient rSARS-CoV-2 as safe, stable, immunogenic and protective LAV for the prevention of SARS-CoV-2 infection and associated COVID-19 disease.
Dbx1 controls the development of astrocytes of the intermediate spinal cord by modulating Notch signaling
Authors: Sartoretti M. Micaela , Campetella Carla A. , Lanuza Guillermo M. 
Published: March 2022

AbstractSignificant progress has been made in elucidating the basic principles that govern neuronal specification in the developing central nervous system. In contrast, much less is known about the origin of astrocytic diversity. Here we demonstrate that a restricted pool of progenitors in the mouse spinal cord, expressing the transcription factor Dbx1, produces a subset of astrocytes, in addition to interneurons. Ventral p0-derived astrocytes (vA0) exclusively populate intermediate regions of spinal cord with extraordinary precision. Postnatal vA0 population comprises gray matter protoplasmic and white matter fibrous astrocytes and a group of cells with strict radial morphology contacting the pia. We identified that vA0 cells in the lateral funiculus are distinguished by the expression of Reelin and Kcnmb4. We show that Dbx1 mutants have increased vA0 cells at the expense of p0-derived interneurons. Manipulation of the Notch pathway, together with the alteration in their ligands seen in Dbx1 knock-outs, suggest that Dbx1 controls neuron-glial balance by modulating Notch-dependent cell interactions. In summary, this study highlights that restricted progenitors in dorsal-ventral neural tube produce region-specific astrocytic subgroups and that progenitor transcriptional programs highly influence glial fate and are instrumental in creating astrocyte diversity.
In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer
Authors: Dervovic Dzana , Chen Edward L.Y. , Malik Ahmad , Afiuni-Zadeh Somi , Boucher Jonathan , Berman Jacob M. , Teng Katie , Ayyaz Arshad , Lü YiQing , Narimatsu Masahiro , Mbamalu Geraldine , Loganathan Sampath , Martinez Sebastian , Tsai Ricky , Lee Jong Bock , Zhang Li , Wrana Jeffrey , Roux Philippe P. , Jackson Harland W. , Schramek Daniel 
Published: March 2022

AbstractHow the genetic landscape of a tumor governs the tumor’s response to immunotherapy remains largely elusive. Here, we established a direct in vivo CRISPR/Cas9 gene editing methodology to assess the immune-modulatory capabilities of 573 putative cancer genes associated with altered cytotoxic activity in human cancers. Using KrasG12D- and BrafV600E-driven mouse lung cancer models, we identify Serpinb9 and Adam2 as our top immune suppressive and immune enhancing genes, respectively. Mechanistically, we show that Serpinb9 ablation in KrasG12D- and BrafV600E-mutant lung tumor cells greatly enhances the efficacy of cytotoxic T-cells in vitro and in vivo. ADAM2 is a cancer testis antigen broadly expressed in human cancers such as lung adenocarcinoma (13.9%), renal (74.7%), prostate (72.4%), uterine (28.6%) and invasive breast (9.5%) cancer. In our mouse models, we show that Adam2 expression is induced in KrasG12D- but not BrafV600E-driven murine lung tumors and that its expression is further enhanced by immunotherapy. We show that loss of Adam2 significantly decreases KrasG12D-lung tumor burden but blocks the efficacy of cytotoxic T-cells. Consistently, Adam2 overexpression dramatically increases tumor growth and enhances immunotherapy efficacy. Mechanistically, we find that Adam2’s oncogenic function depends on modulating the tumor immune microenvironment by restraining productive type I and type II interferon responses as well as cytokine signaling, reducing the presentation of tumor-associated antigen, and modulating surface expression of several immunoregulatory receptors within Kras-driven lung tumors. Adam2 expression also leads to reduced levels of immune checkpoint inhibitors such as Pd-l1, Lag3, Tigit and Tim3. This reduced exhaustion within the tumor microenvironment may explain why ex vivo expanded and adoptively transferred cytotoxic T-cells show enhanced cytotoxic efficacy against Adam2 overexpressing lung tumors. Together, our study highlights the power of integrating cancer genomic with in vivo CRISPR/Cas9 screens to uncover how cancer-associated genetic alterations control responses to immunotherapies.
A minimal growth medium for Pseudomonas azotoformans associated with insect gut
Authors: Cavallin Ismaela , Chouaia Bessem 
Published: March 2022

AbstractPseudomonas spp. can be found associated with several insect hosts. Some of these strains play a crucial role in helping their hosts overcome biotic challenges such as plant defence effectors. Defined media and optimally minimal media are instrumental in studying the physiology and metabolic pathways of microorganisms. In the case of the insect-associated Pseudomonas azotoformans isolated from Galeruca laticollis’ gut, we tested six previously designed defined/minimal media. To determine the optimal medium, we compared the bacterium’s growth performances on the different defined/minimal media to its growth performance on a rich medium using the Dynamic Time Warping Algorithm. The growth results at both 25°C and 30°C indicated the SMM as the optimal medium, with bacterial growth performances being the closest to a rich medium. Therefore, this medium would be highly suitable to study the catabolic pathways for the degradation of some xenobiotics in P. azotoformans.
Food security and disruptions of the global food supply chains during COVID-19: building smarter food supply chains for post COVID-19 era
Authors: Alabi Michael Omotayo , Ngwenyama Ojelanki 
Published: March 2022

PurposeThe COVID-19 pandemic has revealed the fragility of the complex global food supply chains (GFSCs) which has drastically affected the essential flow of food from the farms and producers to the final consumers. The COVID-19 outbreak has served as a great lesson for the food businesses and companies to re-strategize toward the post-COVID-19 era. This paper examines the impact of COVID-19 pandemic on food security and global food supply chains using the two countries (Canada and the United States) in North America as the case studies and provides appropriate strategy or framework to build smarter and resilience food supply chains for post-COVID-19 era.Design/methodology/approachThis paper is a general review of the impacts of COVID-19 pandemic on food security and disruptions of the GFSCs. This paper conducted a comprehensive literature review to have a complete understanding of the study, identify the research problem and missing gaps in literature and to formulate appropriate research questions. This study uses two countries from North America (Canada and the US) as case studies by analyzing the available open data from Statistics Canada and some recent studies conducted on food insecurity in the US. Finally, based on the findings, a proposed approach or framework was presented.FindingsThe findings from this study establishes that COVID-19 pandemic has greater impacts on the food security and GFSC due to disruption of the food supply chain leading to increase food insecurity in Canada and the US. The findings clearly show how the COVID-19 pandemic has disrupted the GFSC in the following ways – poor economy, shortage of farm worker, limitation to food accessibility, restriction in the transportation of farm commodities, changes in demand of consumers, shutdown of food production facilities, uncertainty of food quality and safety, food trade policies restriction, delays in transportation of food products, etc. The main findings of this study show that food and beverages sector needs to re-strategize, re-shape and re-design their food supply chains with post-COVID-19 resilience approach in mind. As a result, this study presents a proposed approach or framework to build a smarter and resilience GFSCs in the post-COVID-19 era. The findings in this study highlights the way the proposed framework provide solutions to the identified problems created by the COVID-19 pandemic in affecting the GFSC.Originality/valueThe contribution of this study towards the existing body of knowledge in food security and GFSC is in the form of a proposed approach or framework for building smarter and resilience GFSC that would assist the key players in the food industry to respond better and faster to the ongoing COVID-19 pandemic, including post-COVID-19 era.
Impact of cooperative entrepreneurship on territorial human development in Morocco – Spatial analysis
Authors: Ibourk Aomar , Raoui Soukaina 
Published: March 2022

PurposeThis paper deals with the spatial impact of cooperative entrepreneurship on territorial human development in Morocco. Within the background of the new development model in Morocco, this study aims to explore how the social and solidarity economy (SSE) through the cooperative model can reduce territorial inequalities by promoting economic dynamics in territories with suboptimal human development.Design/methodology/approachThe empirical material is compiled from a database of 75 provinces in Morocco. After establishing a typology of the SSE in these territories, a test of the spatial effect of some indicators, such as the rate of urbanization and female employment, was undertaken. Moreover, a spatial impact study of the cooperatives' entrepreneurship and the local human development index will be carried out among the cooperatives' numbers and the share of their members.FindingsThis study's results indicate a diversity in the participation of the SSE in the regulation of territories. First, there is a heterogeneous relationship in the Moroccan space. Then, the cooperative model in Morocco shows that it plays a central role in readjusting social and spatial inequalities, pointing territories with suboptimal human development.Research limitations/implicationsAlthough our theoretical contribution covers the impact of the three components of the SSE on territorial human development in Morocco. The empirical work of this study is limited to only one component of the SSE which are the cooperatives. The future perspectives of this work are to follow the impact of the three components after the implementation of the new development model in Morocco.Practical implicationsThe main implication of this study is to map out the spatial role of cooperatives in territorial planning in Morocco. Policy makers still need to consolidate the implication of the cooperatives as a tool for promoting spatial equity, through the governance and the convergence between the different support and accompaniment programs for cooperatives in areas of human development deprivation.Originality/valueThe originality of this work comes from the exploration of the spatial dimension for the analysis of the role of the cooperatives for the promotion of a territorial human development. The SSE typologies described in the Moroccan provinces can allow actors to develop a business plan for the implementation of SSE initiatives.
Farmers' livelihood and adaptive capacity in the face of climate vulnerability
Authors: Akhtar Rulia , Masud Muhammad Mehedi , Rahman Muhammad Khalilur 
Published: March 2022

PurposeThe purpose of this study is to analyze the economic, social and environmental impacts of climate change on farmers' livelihoods and adaptive capacity while highlighting specific adaptation strategies in the local climate context.Design/methodology/approachData were collected using a survey questionnaire and analyzed using partial least square structural equation modeling (PLS-SEM). Respondents were selected from seven farmer organizations (Pertubuhan Peladang Kawasan) located in Kedah, Malaysia.FindingsThe study revealed that farmers perceive the economic, social and environmental impacts of climate change. These adverse effects of climate change have an impact on their livelihoods as well as their adaptive capacity. The findings also demonstrated that farmers' livelihoods mediate the relationship between economic and environmental impacts of climate change as well as the adaptive capacity of farmers.Originality/valueClimate change severely affects the agricultural sector as well as farmers' livelihoods. To minimize its effect, scientists and policymakers emphasize the improvement of farmers' adaptive capacity as well as appropriate adaptation methods. However, there is little research on how climate change affects the livelihoods of farmers in the context of Malaysia. Therefore, the results of the study will provide a new perspective for policymakers to formulate a better adaptation policy framework as well as select appropriate adaptation strategies for sustainable agricultural development.
Potential demand for Islamic banking: examining the Islamic consumer behavior as driving factor
Authors: Puteri Hesi Eka , Parsaulian Baginda , Azman Heru Aulia 
Published: March 2022

PurposeThis study aims to examine the impact of Islamic consumer behavior on the potential demand for Islamic banking by using the Islamic religiosity approach. By classifying the potential demand into the high, middle and low categories, this study attempts to examine whether the level of potential demand is influenced by aspects of social, cultural, psychological and personal considerations.Design/methodology/approachThis research was a quantitative study based on a survey on 18 regions in West Sumatera, Indonesia in 2019. Data were collected from 1818 respondents and analyzed by using multinomial logistic regression.FindingsThe findings reveal that the increasing factor of social and personal causes the tendency of the community to be in the high potential group as an Islamic bank customer by 1,661 times and 1,592 times as compared to in the low potential group. Psychological aspects also increase the probability of the community being in the medium demand potential as an Islamic bank customer.Research limitations/implicationsAlthough this study has attempted to elaborate on the consumers’ behavior variable with an Islamic religiosity perspective, theoretically this concept is not yet well established and still requires many applications in future research. Future studies are expected to enrich this analysis by examining more cases with communities that have different socio-demographic characteristics. This study also limits the exogenous variables used as predictors.Practical implicationsThis study aims to assist managers of Islamic banks to formulate strategies for developing Islamic banks based on Islamic consumer behavior because the facts showed that understanding of Islamic law and religious education in the family, Islamic lifestyle and also religious beliefs affected the potential demand for Islamic banks.Social implicationsFrom a policy perspective, this finding can be a consideration for Islamic banks, that the expansion of the market share of Islamic banks will be more appropriately directed to Muslim groups with indications of high adherence to Islamic values, those with Islamic lifestyles, and the Muslim community groups with Islamic understanding backgrounds and good religious education.Originality/valueThis study measures the impact of Islamic religiosity on the probability of people being in the high, medium or low potential group in adopting Islamic bank services, and these findings are important in the development of Islamic banking in Muslim-majority countries.