bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny
Authors: Diao Huitian , Chen Runqiang , Tsuda Shanel M. , Wang Dapeng , Frederick Megan A. , Kim Jihye , Karunadharma Pabalu P. , Martinez Gustavo , Getzler Adam J. , Toma Clara , Milner Justin J. , Venables Thomas C. , Martin Donna M. , Goldrath Ananda W. , Crotty Shane , Pipkin Matthew E. 
Published: August 2021

AbstractIndividual naive CD8 T cells activated in lymphoid organs differentiate into functionally diverse and anatomically distributed T cell phylogenies in response to intracellular microbes. During infections that resolve rapidly, including live viral vaccines1, distinct effector (TEFF) and memory (TMEM) cell populations develop that ensure long term immunity2. During chronic infections, responding cells progressively become dysfunctional and “exhaust”3. A diverse taxonomy of TEFF, TMEM and exhausted (TEX) CD8 T cell populations is known, but the initial developmental basis of this phenotypic variation remains unclear4–10. Here, we defined single-cell trajectories and identified chromatin regulators that establish antiviral CD8 T cell heterogeneity using unsupervised analyses of single-cell RNA dynamics11–13 and an in vivo RNAi screen14. Activated naive cells differentiate linearly into uncommitted effector-memory progenitor (EMP) cells, which initially branch into an analogous manifold during either acute or chronic infection. Disparate RNA velocities in single EMP cells initiate divergence into stem, circulating, and tissue-resident memory lineages that generate diverse TMEM and TEX precursor states in specific developmental orders. Interleukin-2 receptor (IL-2R) signals are essential for formation and transcriptional heterogeneity of EMP cells, and promote trajectories toward TEFF rather than TEX states. Nucleosome remodelers Smarca4 and Chd7 differentially promote transcription that delineates divergent TMEM lineages before cooperatively driving terminal TEFF cell differentiation. Thus, the lineage architecture is established by specific chromatin regulators that stabilize diverging transcription in uncommitted progenitors.
Maternal and paternal sugar consumption interact to modify offspring life history and physiology
Authors: Camilleri-Carter Tara-Lyn , Piper Matthew D.W. , Robker Rebecca L. , Dowling Damian K. 
Published: August 2021

AbstractIntergenerational effects on offspring phenotypes occur in response to variation in both maternal and paternal nutrition. Because the combined maternal and paternal effects are rarely considered together however, their relative contributions, and the capacity for interactions between parental diets to shape offspring life history and physiology are not understood. To address this, we altered sucrose levels of adult fruit flies (Drosophila melanogaster) prior to mating, across two generations, producing parent-parent and parent-offspring combinations that were either matched or mismatched in dietary sucrose. We then measured lifespan, fecundity, body mass, and triglyceride levels in parents and offspring. We reveal complex non-additive interactions, that involve diets of each parent and offspring to shape offspring phenotypes, but the effects were generally not consistent with an adaptive response to parental diet. Notably, we find that interacting parental flies (sires and dams) lived longer when their sucrose treatments were matched, but they produced shorter-lived offspring.
Kindlin-2 preserves integrity of the articular cartilage to protect against osteoarthritis
Authors: Wu Xiaohao , Lai Yumei , Chen Sheng , Zhou Chunlei , Tao Chu , Fu Xuekun , Li Jun , Huang Jian , Tong Wei , Tian Hongtao , Shao Zengwu , Liu Chuanju , Chen Di , Bai Xiaochun , Cao Huiling , Xiao Guozhi 
Published: August 2021

AbstractOsteoarthritis (OA) is an aging-related degenerative joint disease, which has no cure partly due to limited understanding of its pathological mechanism(s). Here we report that the focal adhesion protein Kindlin-2, but not Kindlin-1 or −3, is highly expressed in articular chondrocytes of the hyaline cartilage, which is dramatically decreased in the degenerated articular cartilage of aged mice and patients with OA. Inducible deletion of Kindlin-2 in chondrocytes at adult stage leads to spontaneous OA and much severe OA lesions in the mice receiving the surgery of destabilization of the medial meniscus. Mechanistically, Kindlin-2 deficiency promotes mitochondrial oxidative stress and activates Stat3 in articular chondrocytes, leading to Runx2-mediated chondrocyte hypertrophic differentiation and catabolism. In vivo, systemic pharmacological blockade of Stat3 activation or genetic ablation of Stat3 in chondrocytes reverses aberrant accumulation of Runx2 and ECM-degrading enzymes and limits OA deteriorations caused by Kindlin-2 deficiency. Furthermore, genetic inactivation of Runx2 in chondrocytes reverses structural changes and OA lesions caused by Kindlin-2 deletion without down-regulating p-Stat3 in articular chondrocytes. Of translational significance, intraarticular injection of Kindlin-2-expressing adeno-associated virus decelerates progression of aging- and instability-induced knee joint OA in mice. Collectively, we identify a novel pathway comprising of Kindlin-2, Stat3 and Runx2 in articular chondrocytes responsible for maintaining integrity of the articular cartilage and define a potential therapeutic target for OA.
A reference genome sequence resource for the sugar beet root rot pathogen Aphanomyces cochlioides
Authors: Botkin Jacob , Chanda Ashok K. , Martin Frank N. , Hirsch Cory D. 
Published: August 2021

ABSTRACTAphanomyces cochlioides, the causal agent of damping-off and root rot of sugar beet (Beta vulgaris L.), is a soil-dwelling oomycete responsible for yield losses in all major sugar beet growing regions. Currently, genomic resources for A. cochlioides are limited. Here we report a de novo genome assembly using a combination of long-read MinION (Oxford Nanopore Technologies) and short-read Illumina sequence data for A. cochlioides isolate 103-1, from Breckenridge, MN. The assembled genome was 76.3 Mb, with a contig N50 of 2.6 Mb. The reference assembly was annotated and was composed of 32.1% repetitive elements and 20,274 gene models. This high-quality genome assembly of A. cochlioides will be a valuable resource for understanding genetic variation, virulence factors, and comparative genomics of this important sugar beet pathogen.
Live imaging YAP signaling in mouse embryo development
Authors: Gu Bin , Bradshaw Brian , Zhu Min , Sun Yu , Hopyan Sevan , Rossant Janet 
Published: August 2021

AbstractYAP protein is a critical regulator of mammalian embryonic development. By generating a near-infrared fusion YAP reporter mouse line, we have achieved high-resolution live imaging of YAP localization during mouse embryonic development. We have validated the reporter by demonstrating its predicted responses to blocking LATs kinase activity or blocking cell polarity. By time lapse imaging preimplantation embryos, we revealed a mitotic reset behavior of YAP nuclear localization. We also demonstrated deep tissue live imaging in post-implantation embryos and revealed an intriguing nuclear YAP pattern in migrating cells. The YAP fusion reporter mice and imaging methods will open new opportunities for understanding dynamic YAP signaling in vivo in many different situations.
Orthogonal representation of task-related information in theta phase-based multiple place fields of single units in the subiculum
Authors: Lee Su-Min , Seol Jae-Min , Lee Inah 
Published: August 2021

AbstractThe subiculum is positioned at a critical juncture at the interface of the hippocampus with the rest of the brain. However, the exact roles of the subiculum in most hippocampal-dependent memory tasks remain largely unknown. One obstacle to make analytical comparisons of neural firing patterns between the subiculum and hippocampal CA1 is the broad firing fields of the subicular cells. Here, we used spiking phases in relation to theta rhythm to parse the broad firing field of a subicular neuron into multiple subfields to find the unique functional contribution of the subiculum while male rats performed a hippocampal-dependent visual scene memory task. Some of the broad firing fields of the subicular neurons were successfully divided into multiple subfields by using the theta-phase precession cycle. The resulting phase-based fields in the subiculum were more similar to those in CA1 in terms of the field size and phase-precession strength. The new method significantly improved the detection of task-relevant information in subicular cells without affecting the information content represented by CA1 cells. Notably, multiple fields of a single subicular neuron, unlike those in the CA1, could carry heterogeneous task-related information such as visual context and choice response. Our findings suggest that the subicular cells integrate multiple task-related factors by using theta rhythm to associate environmental context with action.
The impact of school closures on adolescent health-related outcomes during the COVID-19 pandemic: A natural experiment in South Korea
Authors: Lee Hanbin , Han Buhm 
Published: August 2021

AbstractA large number of countries implemented school closure as a response to the COVID-19 pandemic in 2020. As existing studies mostly rely on retrospective or pre/post comparisons that are prone to unmeasured confounding, the effect of school closure on adolescent health is poorly understood. The South Korean government implemented school closure to prevent the spread of COVID-19. A difference-in-differences comparing changes in health-related outcomes between provinces with differing degrees of school closure was performed. The main analysis group consists of middle school students of age 14 to 16 who were hit hardest where up to 73% of total schooling was taken online in Seoul (the physical attendance was reduced from 170 days to 45 days). For sensitivity analysis, a placebo group of high school students of age 19 who attended all school-days physically was included to detect any violation of our identification strategy. In the main analysis group of boys that experienced reduced physical school-days, both total and vigorous physical activity were reduced (−0.35 [-0.54 -0.17] days/week for vigorous physical activity and -0.38 [-0.61 -0.16] days/week for total physical activity) while such effect was absent in the placebo group of boys that actually did not experience school closure (−0.08 [-0.49 0.32] days/week for vigorous PA and -0.16 [-0.67 0.34] days/week for total PA). In girls, vigorous physical activity decreased (−0.22 [-0.40 -0.04] days/week) but the total physical activity was nearly constant (0.03 [-0.18 0.25] days/week). Other outcomes were largely unchanged.
A highly efficient T-cell immunoassay provides assessment of B cell help function of SARS-CoV-2 specific memory CD4+T cells
Authors: Ansari Asgar , Sachan Shilpa , Jit Bimal Prasad , Sharma Ashok , Coshic Poonam , Sette Alessandro , Weiskopf Daniela , Gupta Nimesh 
Published: August 2021

SummaryThe B cell help function of CD4+T cells may serve as an immunologic correlate of protective adaptive immunity. The quantitative assessment of the B cell help potential of CD4+T cells is limited by the lack of suitable antigen-specific functional assays. Here, we describe a highly efficient antigen-specific T-B co-cultures for quantitative measurement of T-dependent B cell responses. UsingMycobacterium tuberculosisspecific setup, we show that early priming and activation of CD4+T cells is important for the mutualistic collaboration between antigen-specific T and B cells, which could be achieved by supplementing the co-cultures with autologous monocytes. We further show that monocyte-derived growth factors provide the impetus for productive T-B collaboration by conferring optimal survivability in the cultured cells. This study provides first evidence of C-type lectin domain family 11 member A (CLEC11A/SCGF) as an essential growth factor for B cell survival. Importantly, we demonstrate the successful translation of monocyte supplemented T-B co-cultures in qualitative assessment of SARS-CoV-2 specific memory CD4+T cells by quantifying several correlates of productive T-B cross-talk like plasma cell output, secreted antibody, antibody secreting cells and IL21 secreting T cells. Thus, the method described here can provides qualitative assessment of SARS-CoV-2 spike CD4+T cells after natural infection and can be applied to assess the B cell help function of memory CD4+T cells generated in response to COVID-19 vaccine.One sentence summaryQualitative assessment of antigen-specific CD4+T cells for T-dependent B cell responses.
DEVELOPMENTAL AND EVOLUTIONARY COMPARATIVE ANALYSIS OF A REGULATORY LANDSCAPE IN MAMMALS AND BIRDS
Authors: Hintermann Aurélie , Guerreiro Isabel , Bolt Christopher Chase , Lopez-Delisle Lucille , Gitto Sandra , Duboule Denis , Beccari Leonardo 
Published: August 2021

ABSTRACTModifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. However, how such 3D architectures and variations in CREs contribute to transcriptional evolvability remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. Here, we analysed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk partially rely on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CREs’ sequence, an observation supported by a genome-wide comparative approach.
Pitting corrosion prediction from cathodic data: application of machine learning
Authors: Boucherit Mohamed Nadir , Arbaoui Fahd 
Published: August 2021

Purpose
To constitute input data, the authors carried out electrochemical experiments. The authors performed voltammetric scans in a very cathodic potential region. The authors constituted an experimental table where for each experiment we note the current values recorded at a low polarization range and the pitting potential observed in the anodic region. This study aims to concern carbon steel used in a nuclear installation. The properties of the chemical solutions are close to that of the cooling fluid used in the circuit.

Design/methodology/approach
In a previous study, this paper demonstrated the effectiveness of machine learning in predicting the localized corrosion resistance of a material by considering as input data the physicochemical properties of its environment (Boucherit et al., 2019). With the present study, the authors improve the results by considering as input data, cathodic currents. The reason of such an approach is to have input data that integrate both the surface state of the material and the physicochemical properties of its environment.

Findings
The experimental table was submitted to two neural networks, namely, a recurrent network and a convolution network. The convolution network gives better pitting potential predictions. Results also prove that the prediction by observing cathodic currents is better than that obtained by considering the physicochemical properties of the solution.

Originality/value
The originality of the study lies in the use of cathodic currents as input data. These data contain implicit information on both the chemical environment of the material and its surface condition. This approach appears to be more efficient than considering the chemical composition of the solution as input data. The objective of this study remains, at the same time, to seek the optimal neuronal architectures and the best input data.
Face-to-face delivery this week; online the next: a reflection
Authors: Perera Ahesha , Rainsbury Liz , Bandara Saman 
Published: August 2021

Purpose
The purpose of this paper is to reflect on the effects of online learning on student engagement as a result of a shift from face-to-face to online learning during the COVID-19 lockdown in New Zealand.

Design/methodology/approach
The reflection expresses the accounting lecturers’ observations and experiences of student engagement in online learning during the COVID-19 lockdown focussing on the three facets of student engagement; social presence, cognitive presence and teaching presence.

Findings
The focus on social and teaching presence in online learning by Unitec academic staff had a positive impact on cognitive presence as student course success rates and course ratings were similar to rates achieved from face-to-face delivery despite a rapid transition to online learning.

Research limitations/implications
This reflection is based on the experiences of three academic staff in one tertiary organisation.

Practical implications
The findings of this study can be helpful for tertiary institutions that are planning to adopt blended learning in the future. Academic staff may revisit teaching pedagogies to design new strategies and institutions may develop blended learning guidelines and tools to support academics to embrace blended learning.

Social implications
The reflection shows the respect, support and care provided by academics to students building a sense of belongingness and supporting students’ mental well-being in a period of fear and anxiety about COVID-19.

Originality/value
This is a reflection on students’ online engagement during the COVID-19 pandemic, which has not been addressed previously in the academic literature.
Parameter optimization for solid fluidization exploitation of natural gas hydrate in South China Sea
Authors: Mao Liangjie , Cai Mingjie , Liu Qingyou , Zhang Ying 
Published: August 2021

PurposeThe purpose of this paper is to study the multi-phase flow behaviors in solid fluidization exploitation of natural gas hydrate (NGH) and its effect on the engineering safety.Design/methodology/approachIn this paper, a multi-phase flow model considering the endothermic decomposition of hydrate is established and finite difference method is used to solve the mathematical model. The model is validated by reproducing the field test data of a well in Shenhu Sea area. Besides, optimization of design parameters is presented to ensure engineering safety during the solid fluidization exploitation of NGH in South China Sea.FindingsTo ensure the engineering safety during solid fluidization exploitation of marine NGH, taking the test well as an example, a drilling flow rate range of 40–50 L/s, drilling fluid density range of 1.2–1.23 g/cm3 and rate of penetration (ROP) range of 10–20 m/h should be recommended. Besides, pre-cooled drilling fluid is also helpful for inhibiting hydrate decomposition.Originality/valueSystematic research on the effect of multiphase flow behaviors on the engineering safety is scare, especially for the solid fluidization exploitation of NGH in South China Sea. With the growing demand for energy, it is of great significance to ensure the engineering safety before the large-scale extraction of commercial gas from hydrate deposits. The result of this study can provide profound theoretical bases and valuable technical guidance for the commercial solid fluidization exploitation of NGH in South China Sea.
Online innovation and repurchase intentions in hotels: the mediating effect of customer experience
Authors: Amoako George Kofi , Doe Joshua Kofi , Neequaye Emmanuel Kotey 
Published: August 2021

PurposeThis study investigates how customer experience mediates the relationship between online innovation and repurchase intention in the hotel industry in Ghana.Design/methodology/approachData was collected from 167 clients from a two-star hotel in Accra, the capital city of Ghana. Structural equation modelling was used to analyse the relationship between the variables.FindingsResults from the analysis indicate that online innovation positively leads to higher repurchase intentions and better customer experience, affirming that customer experience leads to repurchase intentions. Thus, while online innovation leads to repurchase intentions, the strength of this repurchase intention depends on customer experience. Therefore, customer experience mediates the relationship between online innovation and repurchase intention in the hotel industry.Research limitations/implicationsThis study addressed only the customer's point of view; future studies could investigate the subject from the managers and other stakeholders' point of view to get a holistic view. Also, the sample size could be improved, and the study could be conducted in other African countries for comparison purposes.Practical implicationsThe study shows that online innovation does not automatically lead to increased positive repurchase intention. Hotel managers must, therefore, enforce good customer experience for better profitability.Originality/valueAs far as the researchers know, limited studies have been conducted into how customer experience mediates online innovation and repurchase intention in the hotel industry in Ghana using structural equation modelling. This makes this research unique in Ghana. This study makes an original contribution by measuring the real effect of innovation on repurchase intentions in the hotel industry in Ghana.