bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific Deletion of Axin1 Leads to Activation of β-Catenin/BMP Signaling Resulting in Fibular Hemimelia Phenotype in Mice
Authors: Xie Rong , Yi Dan , Jie Qiang , Kang Qinglin , Zhang Zeng , Zhang Zhenlin , Xiao Guozhi , Chen Lin , Tong Liping , Chen Di 
Published: July 2022

AbstractAxin1 and Axin2 are key regulators of canonical Wnt signaling pathway. The roles of Axin1 and Axin2 in skeletal development and in disease development have not been fully defined. Here, we reported that Axin1 and Axin2 are essential for lower limb development. Specific deletion of Axin1 in limb mesenchymal cells leads to fibular hemimelia (FH)-like phenotype, associated with tarsal coalition. Further studies demonstrated that FH disease is associated with additional defects resembling to the proximal femoral focal deficiency (PFFD) in Axin1/Axin2 double knockout (KO) mice. We then provided in vivo evidence showing that Axin1 controls limb development through both canonical β-catenin and BMP signaling pathways. We demonstrated that inhibition of β-catenin or BMP signaling could significantly reverse the FH phenotype in mice. Together, our findings revealed that integration of Wnt and BMP signaling by Axin1 is required for lower limb development. Defects in Axin1 and Axin2 signaling could lead to the development of FH disease.
Control of neuronal terminal differentiation through cell context-dependent CFI-1/ARID3 functions
Authors: Li Yinan , Smith Jayson J. , Marques Filipe , Osuma Anthony , Huang Hsin-Chiao , Kratsios Paschalis 
Published: July 2022

SUMMARYARID3 transcription factors are expressed in the nervous system, but their functions and mechanisms of action are largely unknown. Here, we generatedin vivoa genome-wide binding map for CFI-1, the soleC. elegansARID3 ortholog. We identified 6,396 protein-coding genes as putative direct targets of CFI-1, most of which (77%) are expressed in post-mitotic neurons and encode terminal differentiation markers (e.g., neurotransmitter receptors, ion channels, neuropeptides). To gain mechanistic insights, we focused on two neuron types. In sensory neurons (IL2 class), CFI-1 exerts a dual role: it acts directly to activate, and indirectly to repress, distinct terminal differentiation genes. In motor neurons, however, CFI-1 acts directly as a repressor, continuously antagonizing three transcriptional activators (UNC-3/Ebf, LIN-39/Hox4-5, MAB-5/Hox6-8). By focusing on a glutamate receptor gene (glr-4/GRIK1), we found CFI-1 exerts its repressive activity through proximal binding to theglr-4locus. Further, the core DNA binding domain of CFI-1 is partially required forglr-4repression in motor neurons. Altogether, this study uncovers cell context-dependent mechanisms through which a single ARID3 protein controls the terminal differentiation of distinct neuron types.
Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion
Authors: Zhang Shu , Übelmesser Nadine , Barbieri Mariano , Papantonis Argyris 
Published: July 2022

SUMMARYMammalian chromosomes are folded by converging and opposing forces. Here, we tested the role of RNAPII across different scales of interphase chromatin folding in a cellular system allowing for its auxin-mediated degradation. We used Micro-C and computational modeling to characterize subsets of loops differentially gained or lost upon RNAPII depletion. Gained loops, extrusion of which was antagonized by RNAPII, almost invariably formed by engaging new or rewired CTCF anchors. Lost loops selectively concerned contacts between enhancers and promoters anchored by RNAPII. Surprisingly, promoter-promoter contacts were almost insensitive to polymerase depletion and sustained cohesin occupancy in its absence. Selective loss of enhancer-promoter contacts explains the repression of most genes. Together, our findings reconcile the role of RNAPII in transcription with that in setting-up regulatory 3D chromatin architectures genome-wide, while also revealing a direct impact on cohesin loop extrusion.
Searching for intra-locus sexual conflicts in the three-spined stickleback (Gasterosteus aculeatus) genome
Authors: Sylvestre Florent , Mérot Claire , Normandeau Eric , Bernatchez Louis 
Published: July 2022

AbstractDifferences between sexes in trait fitness optima can generate intra-locus sexual conflicts that have the potential to maintain genetic diversity through balancing selection. However, these differences are unlikely to be associated with string selective coefficients and as a result are challenging to detect. Additionally, recent studies have highlighted that duplication on sexual chromosomes can create artefactual signals of inter-sex differentiation and increased genetic diversity. Thus, testing the relationship between intra-locus sexual conflicts and balancing selection requires a high-quality reference genome, stringent filtering of potentially duplicated regions, and dedicated methods to detect loci with low levels of inter-sex differentiation. In this study, we investigate intra-locus sexual conflicts in the three-spined stickleback using whole genome sequencing (mean coverage = 12X) of 50 females and 49 males from an anadromous population in the St. Lawrence River, Québec, Canada. After stringent filtering of duplications from the sex chromosomes, we compared three methods to detect intra-locus sexual conflicts. This allowed us to detect various levels of inter-sex differentiation, from stronger single locus effects to small cumulative or multivariate signals. Overall, we found only four genomic regions associated with confidence to intra-locus sexual conflict that displayed associations with long-term balancing selection maintaining genetic diversity. Altogether, this suggests that most intra-locus sexual conflicts do not drive long-term balancing selection and are most likely transient. However, they might still play a role in maintaining genetic diversity over shorter time scales by locally reducing the effects of purifying selection and the rates of genetic diversity erosion.
On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes
Authors: van der Gulik Peter T.S. , Egas Martijn , Kraaijeveld Ken , Dombrowski Nina , Groot Astrid T. , Spang Anja , Hoff Wouter D. , Gallie Jenna 
Published: July 2022

ABSTRACTAutomated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the mis-categorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, non-canonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions.
Contribution of hybridization to the evolution of a derived reproductive strategy in ricefishes
Authors: Flury J. M. , Meusemann K. , Martin S. , Hilgers L. , Spanke T. , Böhne A. , Herder F. , Mokodongan D. , Altmüller J. , Wowor D. , Misof B. , Nolte A.W. , Schwarzer J. 
Published: July 2022

AbstractTransitions between reproductive strategies are costly and involve major changes in life history, behaviour and morphology. Nevertheless, in Sulawesi ricefishes, pelvic-brooding evolved from transfer-brooding in two distantly related lineages within in the genera Adrianichthys and in Oryzias, respectively. Females of pelvic-brooding species carry their eggs attached to their belly until the fry hatches. Despite their phylogenetic distance, both pelvic-brooding lineages share a set of external morphological traits. A recent study found no direct gene-flow between pelvic-brooding lineages suggesting independent evolution of the derived reproductive strategy. It could, however, also be more complex. Pre-existing variation in an admixed population may enable the re-use of genetic variants when subjected to similar external selection pressure, resulting in similar phenotypes.We thus used a multi-species coalescent (MSC) model and D-statistics to identify gene-tree – species-tree incongruencies, to evaluate the evolution of pelvic-brooding with respect to inter-specific gene-flow not only between pelvic-brooding lineages, but between pelvic-brooding lineages and other Sulawesi ricefish lineages. We found a general network-like evolution in Sulawesi ricefishes and as previously reported, no gene-flow between the pelvic-brooding lineages. Instead, we found hybridization between the ancestor of pelvic-brooding Oryzias and the common ancestor of the four Oryzias species from Lake Poso, home of the pelvic-brooding Adrianichthys lineage. Further, indications of introgression were located within two confidence intervals of quantitative trait loci (QTL) associated with pelvic-brooding in O. eversi. We thus hypothesize that a mix of de novo mutations and (ancient) standing genetic variation shaped the evolution of pelvic-brooding.Significance statementThe evolution of pelvic-brooding in Oryzias eversi (Beloniformes:Adrianichthyidae), was recently described to be independent from another pelvic-brooding ricefish lineage (Adrianichthys) from Sulawesi. We confirmed these results, and detected no gene flow between the two distantly related pelvic-brooding lineages. Instead, we found ancient gene flow from another Orzyias lineage into the pelvic-brooding Oryzias lineage. One of the previously described QTL for pelvic brooding overlaps with a region of high introgression signal. Therefore, we assume that not only de novo mutations contributed to the evolution of pelvic-brooding in Orzyias, but that introduced ancient genetic variation was likely also recruited for the evolution of this derived brooding strategy.
Maternal immune activation alters social affective behavior and sensitivity to corticotropin releasing factor in male but not female rats
Authors: Rieger Nathaniel S. , Ng Alexandra J. , Lee Shanon , Brady Bridget H. , Christianson John P. 
Published: July 2022

AbstractPrenatal infection increases risk for neurodevelopmental disorders such as autism in offspring. In the rodents, prenatal administration of the viral mimic Polyinosinic:polycytidylic acid (Poly I:C) allows for investigation of developmental consequences of gestational sickness on offspring social behavior and neural circuit function. Because maternal immune activation (MIA) disrupts cortical development and sociability, we examined social decision-making in a rat social affective preference (SAP) task. Following Poly I:C (0.5 mg/kg) on gestational day 12.5, male adult offspring (PN 50) exhibited atypical social interactions with stressed conspecifics whereas female SAP behavior was unaffected by maternal Poly I:C. Social responses to stressed conspecifics depend upon the insular cortex where corticotropin releasing factor (CRF) modulates synaptic transmission and SAP behavior. We characterized insular field excitatory postsynaptic potentials (fEPSP) in adult offspring of MIA or control treated dams. Male MIA offspring showed decreased sensitivity to CRF (300 nM) while female MIA offspring showed greater sensitivity to CRF compared to sham offspring. These sex specific effects appear to be behaviorally relevant as CRF injected into the insula of male and female rats prior to social exploration testing had no effect in MIA male offspring but increased social interaction in female MIA offspring. We examined the cellular distribution of CRF receptor mRNA but found no effect of maternal Poly I:C in the insula. Together these experiments reveal sex specific effects of prenatal infection on offspring social decision making and identify insular CRF signaling as a novel neurobiological substrate for autism risk.
Assessing the impact of social grants on household welfare using propensity score matching approach
Authors: Zwane Talent , Biyase Mduduzi , Rooderick September 
Published: July 2022

Purpose
This study aims to investigate the impact of social grants on rural household welfare in a village located in one of the poorest provinces in South Africa – KwaZulu Natal Province. Actually, since the inception of democratic rule, the South African government has turned to social grants to address the issues of poverty, income inequality and to improve household welfare. The coverage of social grants has increased substantially with more than 17 million (about 34% of the population) South Africans being recipients of social grants. Despite having relatively well-developed social security system, poverty levels in rural parts of South Africa remains very high.

Design/methodology/approach
This study uses a cross-sectional households survey data conducted in Hlokozi village. A propensity score matching technique, which accounts for non-random selection of households, is applied.

Findings
The results reveal that social grants have a significant and positive impact on rural household welfare. Specifically, the nearest neighbour matching estimates suggest that the causal effect for social grants on household welfare is the region of about R5,830. Consistent with the nearest neighbouring method, the results obtained using the Kernel matching method show that social grants are significant in improving rural household welfare.

Originality/value
While there are a number of studies that have shed some light on how social grant reduces poverty in South Africa, there are some gaps. Firstly, only a few studies have interrogated the impact of social grants on household welfare. Secondly, most of these studies have relied on descriptive analysis, and finally, besides poverty being high in rural areas, research on the impact of social grants on rural household welfare remains thin.
Whereof one cannot speak … a comment on Vollmer (2019)
Authors: Huber Christian 
Published: July 2022

Purpose
The purpose of this paper is to provide a conceptual reflection based on the author’s personal research experience, reading of the literature and contact with the academic education of emerging scholars.

Design/methodology/approach
In this reflection on the paper “Accounting for tacit coordination: The passing of accounts and the broader case for accounting theory” (Vollmer, 2019), the author argues that the silences of the qualitative empirical management accounting research process may preclude research from understanding the silences of accounting practitioners and shape the trajectory of the discipline as a whole.

Findings
The author presents a slightly exaggerated depiction of the qualitative empirical management accounting research process. From this, the author infers what impedes empirically studying unorthodox phenomena such as the silences of accounting practitioners.

Originality/value
The author offers a critical perspective on the author’s own research process, using accounting silences as way of reflecting on the potential and limitations of empirical research. Finally, the author makes tentative suggestions for opening up the standard research process.
Signalling in groups: New tools for the integration of animal communication and collective movement
Authors: Demartsev Vlad , Gersick Andrew S. , Jensen Frants H. , Thomas Mara , Roch Marie A. , Manser Marta B. , Strandburg‐Peshkin Ariana 
Published: July 2022

Abstract

Investigations of collective movement and animal communication have often followed distinct, though complementary, trajectories. Both subfields are deeply concerned with how information flows between individuals and shapes subsequent behaviour. Collective movement has largely focused on the dynamics of passive, cue‐mediated group coordination, while animal communication has primarily examined the content and function of active dyadic signal exchanges in sender–receiver frameworks. However, in many social groups, network‐wide signalling and collective movement decisions are tightly linked.

Here we discuss opportunities afforded by using multi‐sensor tracking tags to simultaneously monitor the fine‐scale movements and vocalisations of entire social groups. We highlight how such data can elucidate the role of vocal signals in individual and collective movement while illuminating the structures of entire vocal‐interaction sequences at previously unexamined timescales and across entire communication networks.

We identify practical and analytical challenges associated with these new tools and datasets, and present avenues for addressing them. We specifically address issues associated with the deployment and synchronisation of multiple tags, the processing and interpretation of resulting multidimensional datasets, and the benefits of combining tag‐based data collection with experimental approaches.

Finally, we argue that a comparative approach employing consistent methodologies across a range of environments, populations and systems is needed to shed light on the evolutionary ecology of communication and collective behaviour.
Monitoring vital signs: Wetland vegetation responses to hydrological resources in the Macquarie Marshes NSW, Australia
Authors: Mason Tanya J. , Honeysett Joel , Thomas Rachael F. , Popovic Gordana C. , Hosking Timothy , Shelly Darren J. , Bowen Sharon 
Published: July 2022

AbstractHuman intervention through damming, diversion and extraction of water resources has created regulated dryland river systems. As a result, connectivity between river channels and floodplain wetlands has diminished. Wetland function is fundamentally linked to water availability: flooding exchanges water, nutrients, sediments and biota with the floodplain. Water allocation for environmental flows may mitigate wetland degradation following river regulation by improving hydrological connectivity between rivers and floodplain wetlands. We report the results (2014–15 to 2018–19) of a vegetation monitoring program in the Macquarie Marshes in north western New South Wales. As part of the long‐term program, we monitored semi‐permanent wetland (Water Couch (Paspalum distichum) grassland or sedgeland dominated) and River Red Gum (Eucalyptus camaldulensis) forest/woodland communities along with environmental and water resource availability predictors. During the five‐year period, we found linear and nonlinear responses of functional group abundance and species richness to the water year and to time since last inundation. We also found differences in species assemblages in response to the flow and flooding regime, particularly water year and inundation duration. These results indicated that wetlands continued to express dry and wet phase responses. We also observed a depressed response to the large 2016–17 flood event by a subset of semi‐permanent wetland sites that had not been inundated in 3 years, compared with sites that were more recently inundated. This result indicated that environmental water management, along with protection of natural inundation events, may improve the resilience of floodplain wetlands: increased hydrological connectivity may promote a stronger wetland response when floods occur. Our results indicate that inundation, in part comprised of managed environmental flows, is a primary driver of species assemblage and functional group representation in semi‐arid floodplain wetlands.
Efficiency of diode laser and ultrasonic‐activated irrigation in retreatment of gutta percha and bioceramic sealer: An in vitro study
Authors: Almohareb Rahaf A. , Barakat Reem M. , Aljarallah Noor , Mudhish Halah , Almutairi Amjaad , Algahtani Fahda N. 
Published: July 2022

AbstractThis study was to determine the effectiveness of diode laser (LI) and ultrasonic (UI)‐activated irrigation with or without a surfactant as adjunct techniques during the retreatment of gutta‐percha and tricalcium silicate‐based sealer (BC) sealer. Forty‐two single‐rooted premolars were instrumented and filled with gutta‐percha and BC sealer, then retreated using NiTi retreatment rotary files. Teeth were randomly divided into three equal groups: Control (manual irrigation), UI and LI groups. Each group was subdivided into 2.5% NaOCl irrigant and ChlorCid™️ Surf subgroups. The amount of material removed following UI and LI was significantly greater than that of manual irrigation (p < 0.0001). However, there was no significant difference between the surfactant subgroups, irrespective of irrigation technique (p = 1.00, p = 0.535, p = 0.805). The use of UI and LI adjuncts to NiTi rotary retreatment techniques showed significant improvement in gutta‐percha with BC sealer removal. However, surfactants had no effect on the efficacy.
‘Enabling places’: Rethinking ‘community’ in ageing‐in‐community in Beijing, China
Authors: Li Yuan , Yu Jie , Rosenberg Mark W. 
Published: July 2022

AbstractObjective(s)To understand how community as ‘enabling places’ is experienced by older people and brings about enabling resources for supporting ageing in community (AIC).MethodsFrom a health geographical perspective, we conceptualize community as enabling places that are produced by the interaction of material, social, and symbolic resources. Focusing on a community‐based care centre (CBCC) in Beijing, China, we conducted semi‐structured interviews with 17 older persons to examine how a CBCC enabled AIC.ResultsThe CBCC site created three interdependent spaces and material/social/affective resources for enabling AIC: (1)living space (residential care beds) to create a sense of connection and safety; (2) a CBCC‐supported care space at home to create an atmosphere of trust and safety; and (3) a social space to create feelings of belonging and contribution. Variations in how the three resources interacted produced not only different spaces at the same site for various users but also different AIC experiences for the same user.ConclusionsCommunity is not simply a static research context or spatial container. Rather, community as an enabling place involves a dynamic process in which spatial/social/affective resources are encountered and interact. Older people's AIC experiences change as their encounters change in the three types of resources we described and thus their capacities for ageing well change correspondingly. Furthermore, the binary idea of community versus institution needs to be expanded to explore how home, community, and institution are related, in order to create enabling spaces for AIC.