bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems
Authors: Gao Cheng Frank , Vaikuntanathan Suriyanarayanan , Riesenfeld Samantha J. 
Published: June 2023

AbstractRNA velocity estimation is a potentially powerful tool to reveal the directionality of transcriptional changes in single-cell RNA-seq data, but it lacks accuracy, absent advanced metabolic labeling techniques. We developed a novel approach,TopicVelo, that disentangles simultaneous, yet distinct, dynamics by using a probabilistic topic model, a highly interpretable form of latent space factorization, to infer cells and genes associated with individual processes, thereby capturing cellular pluripotency or multifaceted functionality. Focusing on process- associated cells and genes enables accurate estimation of process-specific velocities via a master equation for a transcriptional burst model accounting for intrinsic stochasticity. The method obtains a global transition matrix by leveraging cell topic weights to integrate process- specific signals. In challenging systems, this method accurately recovers complex transitions and terminal states, while our novel use of first-passage time analysis provides insights into transient transitions. These results expand the limits of RNA velocity, empowering future studies of cell fate and functional responses.
EnhancingEscherichia coliAbiotic Stress Resistance through Ornithine Lipid Formation
Authors: Bedoya-Pérez Leidy Patricia , Aguilar-Vera Alejandro , Sánchez-Pérez Mishael , Utrilla José , Sohlenkamp Christian 
Published: June 2023

AbstractEscherichia coliis a common host for biotechnology and synthetic biology applications. During growth and fermentation, the microbes are often exposed to stress conditions, such as variations in pH or solvent concentrations. Bacterial membranes play a key role in response to abiotic stresses. Ornithine lipids (OLs) are a group of membrane lipids whose presence and synthesis have been related to stress resistance in bacteria. We wondered if this stress resistance could be transferred to bacteria not encoding the capacity to form OLs in their genome, such asE. coli. In this study, we engineered differentE. colistrains to produce unmodified OLs and hydroxylated OLs by expressing the synthetic operonolsFC. Our results showed that OL formation improved pH resistance and increased biomass under phosphate limitation. Transcriptome analysis revealed that OL-forming strains differentially expressed stress- and membrane-related genes. OL-producing strains also showed better growth in the presence of the ionophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP), suggesting reduced proton leakiness in OL-producing strains. Furthermore, our engineered strains showed improved heterologous violacein production at phosphate limitation and also at low pH. Overall, this study demonstrates the potential of engineering theE. colimembrane composition for constructing robust hosts with an increased abiotic stress resistance for biotechnology and synthetic biology applications.KeypointsTheE. colimembrane composition was engineered by producing ornithine lipidsOrnithine lipid production increase biomass yield under phosphate limitationEngineered strains show enhanced production phenotype under low pH stressTranscriptome analysis and CCCP experiments revealed reduced proton leakageGraphical abstract
Distinct endocannabinoids specifically signal to astrocytes and neurons
Authors: Noriega-Prieto Jose Antonio , Falcón-Moya Rafael , Eraso-Pichot Abel , Fundazuri Unai B , Guttipatti Pavan , Belisle Lindsey , Rodríguez-Moreno Antonio , van der Stelt Mario , Cheer Joseph , Marsicano Giovanni , Kofuji Paulo , Araque Alfonso 
Published: June 2023

AbstractThe endocannabinoid system is an essential intercellular signaling mechanism with a decisive role in many physiological functions of the brain. Endocannabinoids (eCBs), directly acting on presynaptic neuronal CB1 receptors (CB1Rs), can inhibit neurotransmitter release. In addition, they can potentiate adjacent synapses, inducing lateral regulation of synaptic transmission through astrocyte CB1Rs. In contrast to most, if not all, neurotransmitter systems, the eCB system involves two distinct ligands, Anandamide and 2-Arachidonoylglycerol (AEA and 2AG), and a single receptor (CB1R). The physiological meaning of this particularity remains unknown. Here we show that different eCBs are signaling both astrocytes and neurons, inducing distinct and contrasting synaptic regulation. Combining two-photon with a pharmacological and optogenetic approaches and transgenic mice for the synthesis enzyme of both eCBs, we have found that the absence of 2-AG synthesis abolished the inhibitory effect, which was mediated exclusively by neuronal mechanisms. However, the absence of AEA synthesis prevents the lateral potentiation mediated by astrocyte calcium mobilization. Together this indicates that 2-AG signals to neurons, decreasing neurotransmitter release, while AEA signals to astrocytes and induces lateral potentiation. Additionally, AEA synthesis is required for the synaptic potentiation induced by spike-timing-dependent plasticity, as well as astrocyte CB1R, indicating that distinct eCBs-signaling influences neuronal plasticity. We conclude that 2-AG and AEA induce distinct and contrasting synaptic regulation through CB1R in different cell types.
Different gametogenesis states uniquely impact longevity inCaenorhabditis elegans
Authors: Chaturbedi Amaresh , Lee Siu Sylvia 
Published: June 2023

AbstractCurtailed reproduction affects lifespan and fat metabolism in diverse organisms, suggesting a regulatory axis between these processes. InCaenorhabditis elegans, ablation of germline stem cells (GSCs) leads to extended lifespan and increased fat accumulation, suggesting GSCs emit signals that modulate systemic physiology. Previous studies mainly focused on the germline-lessglp-1(e2141)mutant, however, the hermaphroditic germline ofC. elegansprovides an excellent opportunity to study the impact of different types of germline anomalies on longevity and fat metabolism. In this study, we compared the metabolomic, transcriptomic, and genetic pathway differences in three sterile mutants: germline-lessglp-1, feminizedfem-3, and masculinizedmog-3. We found that although the three sterile mutants all accumulate excess fat and share expression changes in stress response and metabolism genes, the germline-lessglp-1mutant exhibits the most robust lifespan increase, whereas the feminizedfem-3mutant only lives longer at specific temperatures, and the masculinizedmog-3mutant lives drastically shorter. We demonstrated that overlapping but distinct genetic pathways are required for the longevity of the three different sterile mutants. Our data showed that disruptions of different germ cell populations result in unique and complex physiological and longevity consequences, highlighting exciting avenues for future investigations.
Implementing midwifery twinning partnerships: challenges and facilitators. A rapid evidence summary
Authors: Edwards Deborah , Csontos Judit , Thomas Grace 
Published: June 2023

AbstractTwinning is a partnership method that focuses on mutual transfer of knowledge and skills between two parties, including organisations, clinical practices, universities, or individual health professionals. In midwifery, twinning is a particularly important tool that can help countries with high maternal and infant morbidity and mortality rates to make connections with countries where sickness and death rates related to birth are lower and the role of midwives is better developed. The aim of this rapid evidence summary is to explore the literature for midwifery twinning initiatives and the facilitators and challenges of twinning partnerships.Sixteen research reports and textual evidence were identified.Facilitators of successful implementation of twinning initiatives include having a clear vision and mission statement along with investing time and promoting a co-creational approach. Reciprocity along with the building of personal relationships. Strong leadership, commitment, values, mutual respect and personal rapport between the projects. Clear communication plans, workshops, peer exchange visits alongside regular virtual contact. Building on existing relationships, previous experience of international and cross-cultural work and being prepared to overcome cultural differences. Having a local project team and careful; matching and selection of twins and having an adaptable personality. Having funding available.Challenges include communication issues, cultural differences in communication, technological issues and economic considerations. Additionally misplaced expectations, such as difference in social expectations, or one twin partner expecting opportunities that are not agreed upon by the other poses challenges to the successful implementation of twinning initiatives.
Spatial differences in elemental stoichiometry and essential fatty acid content of food sources and consumers in a stream food web
Authors: Torres-Ruiz Monica , Wehr John D. , Perrone Alissa A. 
Published: June 2023

AbstractOur study characterizes spatial differences in food webs of two reaches of a New York 3rd-order stream differing in light availability. Food web components were analyzed using marker fatty acids (FAs). Food source nutritional quality for consumers and predators (insect larvae) was measured through stoichiometry of C, N and P and essential FAs. There were strong imbalances between detrital food sources (low N, P and essential FAs) and insects in both shaded and open reaches, and food sources and invertebrate consumers were differentially affected by light with respect to their elemental stoichiometry and essential FA content. Biochemical patterns indicated that invertebrates fed selectively on higher-quality sources (algae, bryophytes, epiphytic bacteria, transported matter) and less on lower-quality periphyton and benthic matter. In addition to confirming the importance of autochthonous food sources for stream invertebrates, this study has highlighted that local ecological processes driven by changes in light availability and canopy-derived nutrient-rich matter can alter the micro- and macronutrient content of primary producers and detrital matter. These changes tracked differently within each consumer and varied with types of nutrient. Invertebrates exhibited a greater degree of homeostasis with respect to N and P than their essential FAs, and across trophic levels.
Tree demographic strategies largely overlap across succession in Neotropical wet and dry forest communities
Authors: Schorn Markus E. , Kambach Stephan , Chazdon Robin L. , Craven Dylan , Farrior Caroline E. , Meave Jorge A. , Muñoz Rodrigo , van Breugel Michiel , Amissah Lucy , Bongers Frans , Hérault Bruno , Jakovac Catarina C. , Norden Natalia , Poorter Lourens , van der Sande Masha T. , Wirth Christian , Delgado Diego , Dent Daisy H. , DeWalt Saara J. , Dupuy Juan M. , Finegan Bryan , Hall Jefferson S. , Hernández-Stefanoni José L. , Lopez Omar R. , Rüger Nadja 
Published: June 2023

ABSTRACTSecondary tropical forests play an increasingly important role for carbon budgets and biodiversity conservation. Understanding successional trajectories is therefore imperative for guiding forest restoration and climate change mitigation efforts. Forest succession is driven by the demographic strategies – combinations of growth, mortality and recruitment rates – of the tree species in the community. However, our understanding of demographic diversity in tropical tree species stems almost exclusively from old-growth forests. Here, we assembled demographic information from repeated forest inventories along chronosequences in two wet (Costa Rica, Panama) and two dry (Mexico) Neotropical forests to assess whether the range of demographic strategies present in a community shifts across succession. We calculated demographic rates for >500 tree species while controlling for canopy status to compare demographic diversity in early successional (0-30 years), late successional (30-120 years) and old-growth forests. We quantified demographic diversity using two-dimensional hypervolumes of pairs of demographic rates and assessed whether shifts in demographic strategies were caused by intra-specific changes in demographic rates across succession or by species turnover. We expected that demographic strategies would shift from faster life-histories (fast growth, high mortality, high recruitment) in early successional forests to slower life histories (slow growth, low mortality, low recruitment) in old-growth forests and that shifts would be stronger in wet than in dry forests due to more pronounced differences in environmental conditions between early successional and old-growth forests. We also expected that demographic diversity would increase with succession. We found that demographic strategies largely overlapped across successional stages and that early successional stages already covered the full spectrum of demographic strategies found in old-growth forests. An exception was a group of species characterized by exceptionally high mortality rates that was confined to early successional stages in the two wet forests. Demographic diversity did not increase with succession. Our results suggest that current understanding of demographic strategies of tropical tree species, which has been generated mostly from long-term forest monitoring plots in old-growth forests, is largely representative of demographic diversity in general, and that demographic diversity recovers quickly during succession.
The Rapidly Evolving X-linkedmiR-506Family Finetunes Spermatogenesis to Enhance Sperm Competition
Authors: Wang Zhuqing , Wang Yue , Zhou Tong , Chen Sheng , Morris Dayton , Magalhães Rubens Daniel Miserani , Li Musheng , Wang Shawn , Wang Hetan , Xie Yeming , McSwiggin Hayden , Oliver Daniel , Yuan Shuiqiao , Zheng Huili , Mohammed Jaaved , Lai Eric C. , McCarrey John R. , Yan Wei 
Published: June 2023

AbstractDespite rapid evolution across eutherian mammals, the X-linkedmiR-506family miRNAs are located in a region flanked by two highly conserved protein-coding genes (Slitrk2andFmr1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linkedmiR-506family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernable defects, but simultaneous ablation of five clusters containing nineteen members of themiR-506family led to reduced male fertility in mice. Despite normal sperm counts, motility and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linkedmiR-506family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that themiR-506family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.Significance StatementThe X-linkedmiR-506family has rapidly evolved in mammals, but their physiological significance remains elusive. Given their abundant and preferential expression in the testis and sperm, these X-linked miRNAs likely play a functional role in spermatogenesis and/or early embryonic development. However, the deletion of either individual miRNA genes or all of the five miRNA clusters encoding 38 mature miRNAs did not cause major fertility defects in mice. When these mutant males were subjected to conditions resembling polyandrous mating, the mutant sperm were much less competitive than the wild-type sperm, rendering the mutant males “functionally sub-fertile”. Our data suggest that themiR-506family of miRNAs regulates sperm competition and the reproductive fitness of the male.
Macrophage Migration Inhibitory Factor on Apoptotic Extracellular Vesicles Regulates Compensatory Proliferation
Authors: Essien Safia A. , Ahuja Ivanshi , Eisenhoffer George T. 
Published: June 2023

ABSTRACTApoptotic cells can signal to neighboring cells to stimulate proliferation and compensate for cell loss to maintain tissue homeostasis. While apoptotic cell-derived extracellular vesicles (AEVs) can transmit instructional cues to mediate communication with neighboring cells, the molecular mechanisms that induce cell division are not well understood. Here we show that macrophage migration inhibitory factor (MIF)-containing AEVs regulate compensatory proliferation via ERK signaling in epithelial stem cells of larval zebrafish. Time-lapse imaging showed efferocytosis of AEVs from dying epithelial stem cells by healthy neighboring stem cells. Proteomic and ultrastructure analysis of purified AEVs identified MIF localization on the AEV surface. Pharmacological inhibition or genetic mutation of MIF, or its cognate receptor CD74, decreased levels of phosphorylated ERK and compensatory proliferation in the neighboring epithelial stem cells. Disruption of MIF activity also caused decreased numbers of macrophages patrolling near AEVs, while depletion of the macrophage lineage resulted in a reduced proliferative response by the epithelial stem cells. We propose that AEVs carrying MIF directly stimulate epithelial stem cell repopulation and guide macrophages to cell non-autonomously induce localized proliferation to sustain overall cell numbers during tissue maintenance.
Influence of colour vision on attention to, and impression of, complex aesthetic images
Authors: Hiramatsu Chihiro , Takashima Tatsuhiko , Sakaguchi Hiroaki , Chen Xu , Tajima Satohiro , Seno Takeharu , Kawamura Shoji 
Published: June 2023

AbstractHumans exhibit colour vision variations due to genetic polymorphisms, with trichromacy being the most common, while some people are classified as dichromats. Whether genetic differences in colour vision affect the way of viewing complex images remains unknown. Here, we investigated how people with different colour vision focused their gaze on aesthetic paintings by eye-tracking while freely viewing digital rendering of paintings and assessed individual impressions through a decomposition analysis of adjective ratings for the images. Gaze concentrated areas among trichromats were more highly correlated than those among dichromats. However, compared to the brief dichromatic experience with the simulated images, there was little effect of innate colour vision differences. These results indicate that chromatic information is instructive as a cue for guiding attention, whereas the impression of each person is unaffected by colour-vision genetics and would be normalised to their own sensory experience through one’s own colour space.
Genetic Gains in IRRI’s Rice Salinity Breeding and Elite Panel Development as a Future Breeding Resource
Authors: Khanna Apurva , Ramos Joie , Sta. Cruz Ma Teresa , Catolos Margaret , Anumalla Mahender , Godwin Andres , Gregorio Glenn , Singh Rakesh Kumar , Dixit Shalabh , Ali Jauhar , Islam Md Rafiqul , Singh Vikas Kumar , Rahman Akhlasur , Khatun Hasina , Pisano Daniel Joseph , Bhosale Sankalp , Hussain Waseem 
Published: June 2023

AbstractGenetic gain is a crucial parameter to check the breeding program’s success and help optimize future breeding strategies for enhanced genetic gains. In this work, IRRI’s historical data from the Philippines and Bangladesh of the salinity breeding program was used to estimate the genetic gains and identify the best lines based on higher breeding values for yield as a future genetic resource. Two-stage mixed-model approach accounting for experimental design factors and pedigrees was adopted to obtain the breeding values for yield and estimate genetic trends under the salinity conditions. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha for the Philippines and 0.31% per annum with a yield advantage of 14.02 kg/ha for Bangladesh datasets was observed. For the released varieties, genetic gain was 0.12% per annum with a yield advantage of 2.2 kg/ha/year and 0.14% per annum with a yield advantage of 5.9 kg/ha/year, respectively. Further, based on higher breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of >2400 kg/ha in the Philippines and >3500 kg/ha in Bangladesh with a selection accuracy >0.4 were selected for formulating the elite breeding panel as a future breeding resource. Conclusively, higher genetic gains are pivotal in IRRI’s rice salinity breeding program, which requires a holistic breeding approach with a major paradigm shift in breeding strategies to enhance genetic gains.Key MessageEstimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains.
Salmonellamanipulates the host to drive pathogenicity via induction of interleukin 1β
Authors: Zigdon Mor , Sawaed Jasmin , Zelik Lilach , Binyamin Dana , Ben-Simon Shira , Asulin Nofar , Levin Rachel , Modilevsky Sonia , Naama Maria , Telpaz Shahar , Rubin Elad , Awad Aya , Sawaed Wisal , Harshuk-Shabso Sarina , Nuriel-Ohayon Meital , Werbner Michal , Koren Omry , Winter Sebastian E , Apte Ron N , Voronov Elena , Bel Shai 
Published: June 2023

AbstractAcute gastrointestinal infection with intracellular pathogens likeSalmonellaTyphimurium triggers the inflammasome and the release of the proinflammatory cytokine interleukin 1β (IL-1β). However, the role of IL-1β in intestinal defense againstSalmonellaremains unclear. Here, we show that IL-1β production is detrimental duringSalmonellainfection. Mice lacking IL-1β (IL-1β-/-) failed to recruit neutrophils to the gut during infection, which reduced tissue damage and prevented depletion of short-chain fatty acid-producing commensals. Changes in epithelial cell metabolism that typically support pathogen expansion, such as switching energy production from fatty acid oxidation to fermentation, were absent in infectedIL-1β-/-mice which inhibitedSalmonellaexpansion. Additionally, we found that IL-1β induces expression of complement anaphylatoxins and suppresses the complement-inactivator Carboxypeptidase N (CPN1). Disrupting this process via IL-1β loss completely prevented mortality inSalmonella-infectedIL-1β-/-mice and led to chronic infection. Thus,Salmonellaexploits IL-1β signaling to outcompete commensal microbes and establish gut colonization. Moreover, our findings identify the intersection of IL-1β signaling and the complement system as key host factors involved in controlling mortality during invasive Salmonellosis.
Corrosion of Al-Li alloy melt on oxide refractories
Authors: Han Wan , Hu Xiaojun 
Published: June 2023

Purpose
When smelting Al-Li alloy, the material inevitably comes into contact with various oxide-refractories. These refractories are subjected to varying degrees of melt-corrosion at high temperatures. The purpose of this study is to find stable oxide refractories at casting temperature.

Design/methodology/approach
Four materials were selected for evaluation, and their corrosion by the Al-Li alloy at casting temperature and different holding times was measured. Subsequently, scanning electron microscopy and energy-dispersive spectroscopy were used to study the interfaces. Stable refractory materials were selected by comparing the thicknesses of the reaction layers.

Findings
The thickness of the Al-Li/ZrO2 reaction layer varies linearly with the square root of the holding duration. Therefore, the growth of the reaction layer is controlled by diffusion. The reaction layer of Al-Li/Al2O3 is thinner, and its growth is also controlled by diffusion. However, there were no obvious reaction layers between the Al-Li alloy and MgO or Y2O3. By comparing these reaction-layer thicknesses, the order of stability was found to be ZrO2 < Al2O3 < MgO and Y2O3.

Originality/value
These results provide a scientific basis for the optimal selection of refractory materials for Al-Li alloy smelting.