bluuebunny/crossref_metadata_2025_split huggingface dataset:
The recovery of plant community composition following passive restoration across spatial scales
Authors: Ladouceur Emma , Isbell Forest , Clark Adam T. , Harpole W. Stanley , Reich Peter B. , Tilman G. David , Chase Jonathan M. 
Published: April 2022

AbstractHuman impacts have led to dramatic biodiversity change which can be highly scale-dependent across space and time. A primary means to manage these changes is via passive (here, the removal of disturbance) or active (management interventions) ecological restoration. The recovery of biodiversity, following the removal of disturbance is often incomplete relative to some kind of reference target. The magnitude of recovery of ecological systems following disturbance depend on the landscape matrix, as well as the temporal and spatial scales at which biodiversity is measured.We measured the recovery of biodiversity and species composition over 27 years in 17 temperate grasslands abandoned after agriculture at different points in time, collectively forming a chronosequence since abandonment from one to eighty years. We compare these abandoned sites with known agricultural land-use histories to never-disturbed sites as relative benchmarks. We specifically measured aspects of diversity at the local plot-scale (α-scale, 0.5m2) and site-scale (γ-scale, 10m2), as well as the within-site heterogeneity (β-diversity) and among-site variation in species composition (turnover and nestedness).At our α-scale, sites recovering after agricultural abandonment only had 70% of the plant species richness (and ∼30% of the evenness), compared to never-ploughed sites. Within-site β-diversity recovered following agricultural abandonment to around 90% after 80 years. This effect, however, was not enough to lead to recovery at our γ-scale. Richness in recovering sites was ∼65% of that in remnant never-ploughed sites. The presence of species characteristic of the never disturbed sites increased in the recovering sites through time. Forb and legume cover declines in years since abandonment, relative to graminoid cover across sites.Synthesis.We found that, during the 80 years after agricultural abandonment, old-fields did not recover to the level of biodiversity in remnant never-ploughed sites at any scale. β-diversity recovered more than α-scale or γ-scales. Plant species composition recovered, but not completely, over time, and some species groups increased their cover more than others. Patterns of ecological recovery in degraded ecosystems across space and long time-scales can inform effective, targeted active restoration interventions and perhaps, lead to better outcomes.
A mathematical model that predicts human biological age from physiological traits identifies environmental and genetic factors that influence aging
Authors: Libert Sergiy , Chekholko Alex , Kenyon Cynthia 
Published: April 2022

AbstractWhy people age at different rates is a fundamental, unsolved problem in biology. We created a model that predicts an individual’s age from physiological traits that change with age in the large UK Biobank dataset, such as blood pressure, lung function, strength and stimulus- reaction time. The model best predicted a person’s age when it heavily-weighted traits that together query multiple organ systems, arguing that most or all physiological systems (lung, heart, brain, etc.) contribute to the global phenotype of chronological age. Differences between calculated “biological” age and chronological age (ΔAge) appear to reflect an individual’s relative youthfulness, as people predicted to be young for their age had a lower subsequent mortality rate and a higher parental age at death, even though no mortality data were used to calculate ΔAge. Remarkably, the effect of each year of physiological ΔAge on Gompertz mortality risk was equivalent to that of one chronological year. A Genome-Wide Association Study (GWAS) of ΔAge, and analysis of environmental factors associated with ΔAge identified known as well as new factors that may influence human aging, including genes involved in synapse biology and a tendency to play computer games. We identify a small number of readily measured physiological traits that together assess a person’s biological age and may be used clinically to evaluate therapeutics designed to slow aging and extend healthy life.
Predictable fluctuations in excitatory synaptic strength due to natural variation in presynaptic firing rate
Authors: Ren Naixin , Wei Ganchao , Ghanbari Abed , Stevenson Ian H. 
Published: April 2022

AbstractMany controlled, in vitro studies have demonstrated how postsynaptic responses to presynaptic spikes are not constant but depend on short-term synaptic plasticity (STP) and the detailed timing of presynaptic spikes. However, the effects of short-term plasticity (depression and facilitation) are not limited to short, sub-second timescales. The effects of STP appear on long timescales as changes in presynaptic firing rates lead to changes in steady-state synaptic transmission. Here we examine the relationship between natural variations in the presynaptic firing rates and spike transmission in vivo. Using large-scale spike recordings in awake mice from the Allen Institute Neuropixels dataset, we first detect putative excitatory synaptic connections based on cross-correlations between the spike trains of millions of pairs of neurons. For the subset of pairs where a transient, excitatory effect was detected, we use a model-based approach to track fluctuations in synaptic efficacy and find that efficacy varies substantially on slow (∼1 minute) timescales over the course of these recordings. For many connections, the efficacy fluctuations are correlated with fluctuations in the presynaptic firing rate. To understand the potential mechanisms underlying this relationship, we then model the detailed probability of postsynaptic spiking on a millisecond timescale, including both slow changes in postsynaptic excitability and monosynaptic inputs with short-term plasticity. The detailed model reproduces the slow efficacy fluctuations observed with many putative excitatory connections, suggesting that these fluctuations can be both directly predicted based on the time-varying presynaptic firing rate and, at least partly, explained by the cumulative effects of STP.
Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans
Authors: Walker Alejandro R. , Shields Robert C. 
Published: April 2022

AbstractCRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. Strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and ‘openness’ of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.Impact StatementCRISPR-Cas is a widespread bacterial immune system that has been repurposed as a molecular biology tool. This study investigates the role of these systems in the biology and evolution of the dental caries pathogen Streptococcus mutans. CRISPR spacers, that encode immunity against foreign DNA, were extracted from over three hundred S. mutans isolates. Sequence analysis showed that the CRISPR spacers match against phage, mobile element, and bacterial DNA. This shows that S. mutans is actively acquiring immunity against horizontally acquired DNA. However, additional analysis revealed little to no impact of CRISPR-Cas systems on diversification of the S. mutans genome. This suggests that while these systems are actively acquiring CRISPR spacers to defend against foreign DNA, the overall impact on the S. mutans genome might be small.Data SummarySupporting data provided on the Github platform: https://github.com/theshieldslab/Streptococcus-mutans-CRISPR-Spacers-AnalysisThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
A genome-wide screen reveals that Dyrk1A kinase promotes nucleotide excision repair by preventing aberrant co-stabilization of cyclin D1 and p21
Authors: Bélanger François , Roussel Cassandra , Sawchyn Christina , Gezzar-Dandashi Sari , Ishimwe Aimé Boris Kimenyi , Mallette Frédérick Antoine , Wurtele Hugo , Drobetsky Elliot 
Published: April 2022

ABSTRACTNucleotide excision repair (NER) eliminates highly-genotoxic solar UV-induced DNA photoproducts that otherwise stimulate malignant melanoma development. Here, a genome-wide loss-of-function screen, coupling CRISPR/Cas9 technology with a flow cytometry-based DNA repair assay, was used to identify novel genes required for efficient NER in primary human fibroblasts. Interestingly, the screen revealed multiple genes encoding proteins, with no previously known involvement in UV damage repair, that significantly modulate NER uniquely during S phase of the cell cycle. Among these, we further characterized Dyrk1A, a dual specificity kinase that phosphorylates the proto-oncoprotein cyclin D1 on threonine 286 (T286), thereby stimulating its timely cytoplasmic relocalization and proteasomal degradation required for proper regulation of the G1-S phase transition and control of cellular proliferation. We demonstrate that in UV-irradiated HeLa cells, depletion of Dyrk1A leading to overexpression of cyclin D1 causes inhibition of NER uniquely during S phase and reduced cell survival. Consistently, expression/nuclear accumulation of nonphosphorylatable cyclin D1 (T286A) in melanoma cells strongly interferes with S phase NER and enhances cytotoxicity post-UV. Moreover, the negative impact of cyclin D1 (T286A) overexpression on repair is independent of cyclin-dependent kinase activity but requires cyclin D1-dependent co-stabilization of p21. Our data indicate that inhibition of NER during S phase might represent a previously unappreciated non-canonical mechanism by which oncogenic cyclin D1 fosters melanomagenesis.
Cell wound repair requires the coordinated action of linear and branched actin nucleation factors
Authors: Hui Justin , Nakamura Mitsutoshi , Dubrulle Julien , Parkhurst Susan M. 
Published: April 2022

ABSTRACTCells are subjected to a barrage of daily insults that often lead to its cortex being ripped open and requiring immediate repair. An important component of the cell’ s repair response is the formation of an actomyosin ring at the wound periphery to mediate its closure. Inhibition of linear actin nucleation factors and myosin result in a disrupted contractile apparatus and delayed wound closure. Here we show that branched actin nucleators function as a scaffold to assemble and maintain this contractile actomyosin cable. Removing branched actin leads to the formation of smaller circular actin-myosin structures at the cell cortex and slow wound closure. Removing linear and branched actin results in failed wound closure. Surprisingly, removal of branched actin and myosin results in the formation of parallel linear actin filaments that undergo a chiral swirling movement to close the wound. These results provide insight into actin organization in contractile actomyosin rings and uncover a new mechanism of wound closure.SummaryHui et al. find that branched actin is required during cell wound repair to serve as a scaffold to anchor the contractile actomyosin cable at the wound periphery. Inhibition of branched actin and myosin results in parallel linear filaments that swirl to close the wound, uncovering a new mechanism for cell wound repair.
DMT1 bridges endosomes and mitochondria to modulate mitochondrial iron translocation
Authors: Barra Jonathan , Crosbourne Isaiah , Wang Ling , Bossardi-Ramos Ramon , Jourd’heuil Frances , Nelson Iram , Adam Alejandro P. , Corr David T. , Jourd’heuil David , Barroso Margarida 
Published: April 2022

AbstractTransient “kiss-and-run” endosome-mitochondria interactions can mediate mitochondrial iron translocation (MIT) but the associated mechanisms are still elusive. We show that Divalent Metal Transporter 1 (DMT1) modulates MIT via endosome-mitochondria interactions in invasive MDA-MB-231, but not in non-invasive T47D breast cancer cells. CRISPR/Cas9-based DMT1 knockout (KO) stable cells were used to demonstrate that DMT1 regulates MIT, endosomal speed, and labile iron pool (LIP) levels only in MDA-MB-231. DMT1 silencing increases PINK1/Parkin mitophagy markers, the autophagy marker LC3B, as well as mitochondrial ferritin in MDA-MB-231, but not in T47D. Strikingly, re-expression of DMT1 in MDA-MB-231 DMT KO cells rescues all protein levels evaluated. DMT1 silencing decreases Tom20 colocalization with PMPCB, a DMT1 interactor that regulates mitophagy hyperactivation. In MDA-MB-231 both mitochondrial metabolism and invasion were impaired by DMT1 silencing and rescued by DMT1 re-expression. DMT1 acts as a bridge between endosomes and mitochondria to support higher MIT/lower LIP levels, which are necessary for sustaining mitochondrial bioenergetics and invasive cancer cell migration.SummaryCellular iron metabolism is tightly regulated, and cancer cells rely on mitochondrial iron for malignancy. Here, we report that the divalent metal transporter DMT1 serves as a bridge between endosomes and mitochondria regulating mitochondrial iron translocation in breast cancer cells.
Incomplete activation of developmentally required genes Alyref1 and Gabpb1 leads to preimplantation arrest in cloned mouse embryos
Authors: Ihashi Shunya , Hamanaka Mizuto , Kaji Masaya , Mori Miki , Imasato Yuma , Nakamura Misaki , Anzai Masayuki , Matsumoto Kazuya , Ikawa Masahito , Miyamoto Kei 
Published: April 2022

SUMMARYDifferentiated cell nuclei can be reprogrammed after nuclear transfer (NT) to oocytes and the produced NT embryos can give rise to cloned animals. However, development of NT embryos is often hampered by recurrent reprogramming failures, including the incomplete activation of developmental genes, yet specific genes responsible for the arrest of NT embryos are not well understood. Here, we searched for developmentally important genes among the reprogramming-resistant H3K9me3-repressed genes, and identified Alyref and Gabpb1 by siRNA screening. Gene knockout of Alyref and Gabpb1 by the CRISPR/Cas9 system resulted in early developmental arrest in mice. Single embryo RNA-seq revealed that Alyref is needed for the formation of inner cell mass. The supplement of Alyref and Gabpb1 by mRNA injection supported efficient preimplantation development of cloned embryos. Thus, our study shows that the H3K9me3-repressed genes contain developmentally required genes and the incomplete activation of such genes results in preimplantation arrest of cloned embryos.
Kinesin-1 transports morphologically distinct intracellular virions during vaccinia infection
Authors: Xu Amadeus , Basant Angika , Schleich Sibylle , Newsome Timothy P , Way Michael 
Published: April 2022

AbstractIntracellular mature virions (IMV) are the first and most abundant infectious form of vaccinia virus to assemble during its replication cycle. IMV can undergo microtubule-based motility, but their directionality and the motor involved in their transport remain unknown. Here, we demonstrate that IMV, like intracellular enveloped virions (IEV), the second form of vaccinia, undergo anterograde transport and recruit kinesin-1. In vitro reconstitution of virion transport reveals that IMV and IEV move toward microtubule plus-ends with respective velocities of 0.66 and 0.56 μm/s. Quantitative imaging establishes IMV and IEV recruit an average of 65 and 115 kinesin-1 motor complexes respectively. In the absence of kinesin-1 there is a near-complete loss of in vitro motility and defects in the cellular spread of both virions. Our observations demonstrate kinesin-1 transports two morphologically distinct forms of vaccinia. Reconstitution of vaccinia-based microtubule motility in vitro provides a new model to investigate how motor number and regulation impacts transport of a bona fide kinesin-1 cargo.
Study on cooling inerting of an airborne fuel tank in flight
Authors: Liu Guannan , Wang Liqun , Wang Hongming , Huang Long , Peng Hao , Feng Shiyu 
Published: April 2022

Purpose
This study aims to seek a new economic and environmental protection fuel tank inerting method.

Design/methodology/approach
The principle that serves as the basis for the cooling inerting process is described, the workflow of the cooling inerting system is designed, the mathematical model of the cooling inerting system is established, and the important performance changes of cooling inerting in the flight package line and the influence of key parameters on it are simulated by using Modelica software.

Findings
The results show that the cooling inerting system can be turned on to quickly reduce the vapour concentration in the gas phase in the fuel space and reduce the temperature below the flammability limit. Within a certain range of pumping flow, the inerting effect is more obvious when the pumping flow is larger. Simply running the cooling inerting system on the ground can remain the tank in an inert state throughout the flight envelope.

Research limitations/implications
However, cooling inerting is suitable for models with fewer internal heat sources. An excessive number of internal heat sources will lead to inerting failure.

Originality/value
This study provides theoretical support for the feasibility of cooling inerting. Cooling inerting does not require engine air, and the cooling is mainly accomplished with air, which places a small load on the cooling system and has a much lower cost than the airborne hollow fibre film inerting technology widely used at present. It is a promising new inerting technology.
Trade credit from agrochemical vendors as an alternative source of finance for cabbage producers in the Bono East Region of Ghana
Authors: Amrago Ernest Christlieb , Mensah Nicholas Oppong 
Published: April 2022

PurposeThe purpose of this study is to examine trade credit from agrochemical vendors as an alternative source of finance for cabbage producers in the Bono East Region of Ghana. The determinants of trade credit supply and impact on cabbage producer’s profitability are investigated.Design/methodology/approachThe study sample size is 260. The perception index, probit regression, negative binomial regression and the propensity score matching (PSM) was employed to assess the perception of trade credit, factors influencing trade credit supply and the impact of trade credit supply on the cabbage producer’s profitability and agrochemical vendor’s welfare respectively.FindingsThe perception index analysis revealed that the agrochemical vendors, in general, had a positive perception of trade credit. Different groups of factors influence trade credit supply. Further along, the number of times trade credit was used by the cabbage producers was influenced by several factors. On the PSM result, trade credit use had a significant positive impact on the cabbage producer’s profitability. In detail, all the matching estimations revealed that profitability increased above Gh¢ 4,000.00 (US$ 692.04). Likewise, the robustness check result (Inverse Probability Weighted Regression Adjustment (IPWRA)), was no different from the matching estimations. Generally, the result indicates that the impact of trade credit supply on the agrochemical vendor's welfare using total household expenditure, total savings and income as proxy variables for welfare were positive.Originality/valueTrade credit has encountered less attention in the agricultural finance discourse; however, this study makes an imperative contribution on the same. Specifically, the study reveals the determinants of trade credit supply from agrochemical vendors and a positive impact of trade credit use on the cabbage producer’s profitability, a result which has not been investigated in the trade credit literature.
Evaluating lean techniques to improve success factors in the construction phase
Authors: Noorzai Esmatullah 
Published: April 2022

Purpose
This paper aims to develop a decision-making model to analyze and select the most appropriate lean technique (LT), considering success factors to improve site management and reduce waste in the construction phase.

Design/methodology/approach
A comprehensive literature review identified six LTs and the 11 most critical factors affecting the efficiency of the construction phase. Then, the appropriateness of these LTs to improve the identified factors were assessed using the analytic hierarchy process. At last, a sensitivity analysis of the results was performed to validate the findings.

Findings
The results show that the most effective LT to improve success factors in the construction phase is “Daily Huddle Meetings”, and the most critical factor with the greatest impact on LT selection is determined to be “Efficient Construction Management”.

Originality/value
Few studies have evaluated the suitability of LTs in terms of construction success factors (CSFs). Hence, given the vital role of the construction phase in the whole project life cycle and the impact of LTs in improving the productivity of this phase, this research investigates the correlation between LTs and CSFs to promote efficient site management.
Bi-objective green in-house transportation scheduling and fleet size determination in mixed-model assembly lines with mobile robots
Authors: Zhou Binghai , Zhang Jihua , Fei Qianran 
Published: April 2022

PurposeFacing the challenge of increasing energy cost and requirement of reducing the emissions, identifying the potential factors of them in the manufacturing factories is an important prerequisite to control energy consumption. This paper aims to present a bi-objective green in-house transportation scheduling and fleet size determination problem (BOGIHTS&FSDP) in automobile assembly line to schedule the material delivery tasks, which jointly take the energy consumption into consideration as well.Design/methodology/approachThis research proposes an optimal method for material handling in automobile assembly line. To solve the problem, several properties and definitions are proposed to solve the model more efficiently. Because of the non-deterministic polynomial-time-hard nature of the proposed problem, a Multi-objective Discrete Differential Evolution Algorithm with Variable Neighborhood Search (VNS-MDDE) is developed to solve the multi-objective problem.FindingsThe performances of VNS-MDDE are evaluated in simulation and the results indicate that the proposed algorithm is effective and efficient in solving BOGIHTS&FSDP problem.Originality/valueThis study is the first to take advantage of the robot's interactive functions for part supply in automobile assembly lines, which is both the challenge and trend of future intelligent logistics under the pressure of energy and resource. To solve the problem, a VNS-MDDE is developed to solve the multi-objective problem.