bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuronal, Affective, and Sensory Correlates of Targeted Helping Behavior in Male and Female Sprague Dawley Rats
Authors: Cox Stewart S. , Brown Brogan J. , Woods Samuel K , Brown Samantha J. , Kearns Angela M. , Reichel Carmela M.
Published: August 2022

Empathy is an innate ability to understand the emotional states of others along with the motivation to improve it. It has evolved over time into highly complex behaviors, the basis of which can be described using the Perception Action Model (PAM), where shared affect promotes an action that eliminates the distress of both the passive “Target” and, by extension, the active “Observer.” There are myriad biological variables that may modulate empathic behavior, including sex, sensory modalities, and neural activity. In the following studies, using our lab’s model of social contact-independent targeted helping, we first tested whether sex differences exist in helping behavior. Next, we explored sex differences in sensory and affective signaling, including the impact of direct visualization of a distressed conspecific and the type of ultrasonic vocalizations (USV) made between animal pairs during the task. Finally, we examined the neural activity of multiple cortical and subcortical regions of interest across time during targeted helping between males and females. We show both sexes exhibit similar helping behavior, but sensory and affective signaling differs between sexes. Further, changes in neural activity exhibited distinct sex-specific patterns across time. Our results indicate sex differences are not a ubiquitous presence in targeted helping. Instead, it is likely sex differences may be a convergent phenomenon in which the behavior is similar, but the underlying biological mechanisms are distinct. These results lay the groundwork for future studies to explore the similarities and differences that drive empathic behavior in both males and females.
Mapping the landscape of genetic dependencies in chordoma
Authors: Sharifnia Tanaz , Wawer Mathias J. , Goodale Amy , Lee Yenarae , Kazachkova Mariya , Dempster Joshua M. , Muller Sandrine , Levy Joan , Freed Daniel M. , Sommer Josh , Kalfon Jérémie , Vazquez Francisca , Hahn William C. , Root David E. , Clemons Paul A. , Schreiber Stuart L.
Published: August 2022

Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We applied genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirmed a known chordoma dependency, TBXT (T; brachyury), and identified a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, were also recovered. We found genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, had potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.
Does oxidative stress shorten telomeres in vivo? A meta-analysis
Authors: Armstrong Emma , Boonekamp Jelle
Published: August 2022

Telomere attrition is considered a hallmark of ageing. Untangling the proximate causes of telomere attrition may therefore reveal important aspects about the ageing process. In a landmark paper in 2002 Thomas von Zglinicki demonstrated that oxidative stress causes telomere attrition in cell culture. In the next 20 years, oxidative stress became firmly embedded into modern theories of ageing and telomere attrition. However, a recent surge of in vivo studies reveals an inconsistent pattern questioning the unequivocal role of oxidative stress in telomere dynamics, in living organisms. Here we report the results of the first formal meta-analysis on the association between oxidative stress and telomere dynamics in vivo, representing 37 studies, 4,834 individuals, and 18,590 correlational measurements. The overall correlation between oxidative stress markers and telomere dynamics was indistinguishable from zero. This result was independent of the type of oxidative stress marker, telomere dynamic, or taxonomic group. However, telomere measurement method affected the analysis with TRF but not qPCR-based studies showing a significant overall correlation. The correlation was more pronounced in short-lived species and during the adult life phase, when ageing becomes apparent. We then performed an additional meta-analysis of interventional studies (n=7) manipulating oxidative stress. This revealed a significant effect of treatment on telomere dynamics. Our findings indicate that oxidative stress may have a profound effect on telomere dynamics in living organisms fundamentally underpinning the process of ageing.
Development of a non-invasive method for testicular toxicity evaluation using a novel compact magnetic resonance imaging system
Authors: Yokota Satoshi , Miyaso Hidenobu , Hirai Toshinori , Suga Kousuke , Wakayama Tomohiko , Taquahashi Yuhji , Kitajima Satoshi
Published: August 2022

In non-clinical animal studies for drug discovery, histopathological evaluation is the most powerful tool to assess testicular toxicity. However, histological analysis is extremely invasive; many experimental animals are needed to evaluate changes in the pathology and anatomy of the testes over time. As an alternative, small animal magnetic resonance imaging (MRI) offers a non-invasive methodology to examine testicular toxicity without radiation. The present study demonstrated the suitability of a new, ready-to-use compact MRI platform using a high-field permanent magnet to assist with the evaluation of testicular toxicity. To validate the utility of the MRI platform, male mice were treated with busulfan (40 mg/kg, intraperitoneal injection). Tenty-eight days after treatment, both testes in busulfan-treated and control mice (n = 3/group) were non-invasively scanned in situ by MRI at 1 tesla. On a T1-weighted, 3D gradient-echo MRI sequences (voxel size: 0.23 × 0.23 × 0.50 mm), the total testicular volume in busulfan-treated mice was significantly smaller than in controls. On T1-weighted images, the signal intensity of the testes was significantly higher in busulfan-treated mice than in controls. The mice were sacrificed, and the testes were isolated for histopathological analysis. The weight of the testes in busulfan-treated mice significantly decreased, similar to the results of the non-invasive analysis. Additionally, periodic acid-Schiff stain–positive effusions were observed in the interstitium of the busulfan-treated mouse testes, potentially explaining T1 shortening due to a high concentration of glycoproteinaceous content. The present data demonstrated a rapid evaluation of testicular toxicity in vivo by compact MRI.
Growth of Mesenchymal Stem Cells at the Surface of Silicone, Mineral and Plant-Based Oils
Authors: Peng Lihui , Gautrot Julien E.
Published: August 2022

Bioemulsions are attractive platforms for the expansion of adherent cells in bioreactors. Their design relies on the self-assembly of protein nanosheets at liquid-liquid interfaces, displaying strong interfacial mechanical properties and promoting integrin-mediated cell adhesion. However, most systems developed to date have focused on fluorinated oils, which are unlikely to be accepted for direct implantation of resulting cell products for regenerative medicine, and protein nanosheets self-assembly at other interfaces has not been investigated. In this report, the composition of aliphatic pro-surfactants palmitoyl chloride and sebacoyl chloride, on the assembly kinetics of poly(L-lysine) at silicone oil interfaces and characterisation of ultimate interfacial shear mechanics and viscoelasticity is presented. The impact of the resulting nanosheets on the adhesion of mesenchymal stem cells (MSCs) is investigated via immunostaining and fluorescence microscopy, demonstrating the engagement of the classic focal adhesion-actin cytoskeleton machinery. The ability of MSCs to proliferate at the corresponding interfaces is quantified. In addition, expansion of MSCs at other non-fluorinated oil interfaces, based on mineral and plant-based oils is investigated. Finally, the proof-of-concept of such non-fluorinated oil systems for the formulation of bioemulsions supporting stem cell adhesion and expansion is demonstrated.
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies
Authors: Doré Hugo , Guyet Ulysse , Leconte Jade , Farrant Gregory K. , Alric Benjamin , Ratin Morgane , Ostrowski Martin , Ferrieux Mathilde , Brillet-Guéguen Loraine , Hoebeke Mark , Siltanen Jukka , Corguillé Gildas Le , Corre Erwan , Wincker Patrick , Scanlan David J. , Eveillard Damien , Partensky Frédéric , Garczarek Laurence
Published: August 2022

The ever-increasing number of available microbial genomes and metagenomes provide new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, notably for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we first showed that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We then managed to identify clusters of adjacent genes that display specific distribution patterns in the field (CAGs) and are thus potentially involved in the adaptation to particular environmental niches. Several CAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine or phosphonates, which might be either directly used by cells, for e.g. the biosynthesis of proteins or DNA, or degraded into inorganic nitrogen and/or phosphorus forms. We also highlight the frequent presence of CAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas, which are absent in low-iron regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in these areas. In contrast, Prochlorococcus populations thriving in iron-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) into Fe(II). Together, this study provides insights into how these key members of the phytoplankton community might behave in response to ongoing global change.

Significance Statement

Picocyanobacteria face various environmental conditions in the ocean and numerous studies have shown that genetically distinct ecotypes colonize different niches. Yet the functional basis of their adaptation remains poorly known, essentially due to the large number of genes of yet unknown function, many of which have little or no beneficial effect on fitness. Here, by combining comparative genomics and metagenomics approaches, we have identified not only single genes but also entire gene clusters, potentially involved in niche adaptation. Although being sometimes present in only one or a few sequenced strains, they occur in a large part of the population in specific ecological niches and thus constitute precious targets for elucidating the biochemical function of yet unknown niche-related genes.
Strong effects of parasite genotype on drug susceptibility in the Indian subcontinent
Authors: Grace Cooper Alastair , Reis-Cunha João Luís , Jeffares Daniel C.
Published: August 2022

Intracellular parasites of the Leishmania donovani species complex cause visceral leishmaniasis (VL). For parasitic diseases, VL has a mortality rate second only to malaria, and is associated with poverty-stricken areas of the world: primarily Brazil, East Africa and the Indian subcontinent (ISC). Miltefosine (MIL) and the antimonal sodium stibogluconate (SSG) are drugs used in the treatment of leishmaniasis. However, treatment efficacy is variable, and the numbers of reports of parasite resistance to both drugs have risen since their introductions, particularly in the ISC. To assess the level of parasite genotype contribution to drug resistance, we utilised the sequencing and associated drug susceptibility data from Imamura et al. (2016) to estimate heritability and GWAS using LDAK. We obtained strong heritability results, with mainly SNP/indel variations associated with SSG and copy number variants associated with MIL resistance, respectively. However, GWAS results were inconclusive, suggesting that, although the parasite genotype directly influences drug resistance, the effect might be multifactorial.
Automated assembly of high-density carbon fiber electrode arrays for single unit electrophysiological recordings
Authors: Dong Tianshu , Chen Lei , Patel Paras R , Richie Julianna M , Chestek Cynthia A , Shih Albert J
Published: August 2022

Objective

Carbon fiber (CF) is good for chronic neural recording due to the small diameter (7 µm), high Young’s modulus, and low electrical resistance, but most high-density carbon fiber (HDCF) arrays are manually assembled with labor-intensive procedures and limited by the accuracy and repeatability of the operator handling. A machine to automate the assembly is desired.

Approach

The HDCF array assembly machine contains: 1) a roller-based CF extruder, 2) a motion system with three linear and one rotary stages, 3) an imaging system with two digital microscope cameras, and 4) a laser cutter. The roller-based extruder automatically feeds single CF as raw material. The motion system aligns the CF with the array backend then places it. The imaging system observes the relative position between the CF and the backend. The laser cutter cuts off the CF. Two image processing algorithms are implemented to align the CF with the support shanks and circuit connection pads.

Main results

The machine was capable of precisely handling 6.8 μm carbon fiber electrodes. Each electrode was placed into a 12 μm wide trenches in a silicon support shank. Two HDCF arrays with 16 CF electrodes populated on 3 mm shanks (with 80 μm pitch) were fully assembled. Impedance measurements were found to be in good agreement with manual assembled arrays. One HDCF array was implanted in the motor cortex in an anesthetized rat and was able to detect single unit activity.

Significance

This machine can eliminate the manual labor-intensive handling, alignment and placement of single carbon fiber during assembly, providing a proof-of-concepts towards fully automated HDCF array assembly and batch production.
E. faecalisacquires resistance to antimicrobials and insect immunity via common mechanisms
Authors: Wadhawan Ashima , Simoes da Silva Carolina J. , Nunes Catarina D. , Edwards Andrew M. , Dionne Marc S.
Published: August 2022

Enterococcus faecalisis a normal member of the gut microbiota and an opportunistic pathogen of many animals, including mammals, birds, and insects. It is a common cause of nosocomial infections, and is particularly troublesome due to extensive intrinsic and acquired antimicrobial resistance. Using experimental evolution, we generatedDrosophila-adaptedE. faecalisstrains, which exhibited immune resistance, resulting in increasedin vivogrowth and virulence. Resistance was characterised by mutations in bacterial pathways responsive to cell envelope stress.Drosophila-adapted strains exhibited changes in sensitivity to relevant antimicrobials, including daptomycin and vancomycin. Evolved daptomycin-resistant strains harboured mutations in the same signalling systems, with some strains showing increased virulence similar toDrosophila-adapted strains. Our results show that common mechanisms provide a route to resistance to both antimicrobials and host immunity inE. faecalisand demonstrate that the selection and emergence of antibiotic resistancein vivodoes not require antibiotic exposure.

One sentence summary

Host interaction can promote antimicrobial resistance and antimicrobial treatment can promote virulence inE. faecalis.
The olfactory bulb carries out concentration invariance calculations by itself and does it very quickly
Authors: Choi Yunsook , Cohen Lawrence B.
Published: August 2022

The olfactory bulb is known to carry out computations for the olfactory perception of concentration invariance of odor recognition, a perception that is essential for life as we know it. However it is not known whether these computations require the extensive feedback to the bulb from the many brain regions which send this feedback. We have measured the concentration dependence of the mitral cell output of the bulb before and after blocking this feedback by lidocaine infusion into the medial olfactory peduncle. Surprisingly we found that the concentration dependence of the mitral cell output was unaffected by the lidocaine block of feedback. Furthermore the computation is rapid; it is complete within a single 250 msec inhalation. The computations for concentration invariance are most likely carried out within the olfactory bulb itself and they are carried out quickly.
Soil depth governs microbial community assembly and enzymatic activity in extreme environments
Authors: Jing Xin , Classen Aimée T. , Li Daijiang , Lin Litao , Lu Mingzhen , Sanders Nathan J. , Wang Yugang , Feng Wenting
Published: August 2022

Aim

A fundamental challenge in soil macroecology is to understand how microbial community structure shapes ecosystem functions along environmental gradients of land surface (i.e., horizontal dimension). However, little is known of microbial community structure-function relationships along environmental gradients of soil depth (i.e., vertical dimension) in extreme environments. A full understanding of the consequences of environmental change for microbial communities structure and subsequent changes in microbial functions could enable more accurate predictions of extreme environmental change effects. Here, we leveraged a 200-km desert soil salinity gradient that is created by a 12-year saline-water irrigation to evaluate how soil microbial community structure-function relationships change with soil salinity in the horizontal and vertical dimensions.

Location

The Tarim basin of Taklamakan desert.

Taxa

Soil bacteria and fungi.

Methods

We assessed the prime ecological processes controlling the assembly of microbial communities and the activity of enzymes relevant to carbon, nitrogen, and phosphorus cycling along soil salinity gradients across study sites (horizontal dimension) and soil depths (vertical dimension) by using the general linear model, hierarchical variance partitioning, and path model.

Results

Differences in soil depth (on the scale of meters) was as important as geographic distance (on the scale of kilometers) in shaping the structure of bacterial and fungal communities, while both the vertical and horizontal variability in enzymatic activity were largely attributed to the increase in the heterogeneity of soil properties, such as soil texture, water content, and pH.

Main conclusions

Our results suggest that dispersal limitation and environmental heterogeneity, not soil salinization, along soil depth governs microbial community assembly and enzymatic activity, respectively. This work highlights that conservation efforts of soil macroecology should consider soil depth as a key attribute in the face of ongoing salinization in arid ecosystems.
Structure-activity relationship of 2,4-D correlates auxin activity with the induction of somatic embryogenesis in Arabidopsis thaliana
Authors: Karami Omid , de Jong Hanna , Somovilla Victor J. , Acosta Beatriz Villanueva , Sugiarta Aldo Bryan , Wennekes Tom , Offringa Remko
Published: August 2022

2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxin activity. However, this hypothesis has never been thoroughly tested. Here we used a library of 40 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxin activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active auxins to not active. A halogen at the 4-position of the aromatic ring was important for auxin activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with two but not with one carbon. In the process, we also identified two 2,4-D analogues as efficient inducers of adventitious root formation and several possible anti-auxins. The auxin activity of the 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxin activity, indicating that the stress-related effects triggered by 2,4-D that are considered important for SE induction are down-stream of auxin signaling.
Cellular Harmonics for the Morphology-invariant Analysis of Molecular Organization at the Cell Surface
Authors: Mazloom-Farsibaf Hanieh , Zou Qiongjing , Hsieh Rebecca , Danuser Gaudenz , Driscoll Meghan
Published: August 2022

The spatiotemporal organization of membrane-associated molecules is central to the regulation of the vast signaling network that control cellular functions. Powerful new microscopy techniques enable the 3D visualization of the localization and activation of these molecules. However, quantitatively interpreting and comparing the spatial organization of molecules on the 3D cell surface remains challenging because cells themselves vary greatly in their morphology. Here, we introduce u-signal3D, a framework to assess the spatial scales of molecular organization at the cell surface in a cell-morphology invariant manner. We validated our framework by analyzing both synthetic polka dot patterns painted onto observed cell morphologies, as well as measured distributions of cytoskeletal and signaling molecules. To demonstrate the framework’s versatility, we further compared the spatial organization of cell surface signaling both within and between cell populations and powered an upstream machine-learning based analysis of signaling motifs. U-signal3D is open source and is available at https://github.com/DanuserLab/u-signal3D.
The centromere/kinetochore is assembled through CENP-C oligomerization
Authors: Hara Masatoshi , Ariyoshi Mariko , Sano Tomoki , Nozawa Ryu-suke , Shinkai Soya , Onami Shuichi , Jansen Isabelle , Hirota Toru , Fukagawa Tatsuo
Published: August 2022

The kinetochore is an essential protein complex for accurate chromosome segregation. The constitutive centromere-associated network (CCAN), a subcomplex of the kinetochore, associates with centromeric chromatin providing a platform for the kinetochore assembly. A CCAN protein, CENP-C, is thought to be a central hub for the centromere/kinetochore organization. However, the crucial role of CENP-C in centromeres remains to be elucidated. Here, we demonstrated that both the CCAN-binding domain and C-terminal Cupin domain of CENP-C are necessary and sufficient for chicken CENP-C function. Our structural and biochemical analyses revealed that the Cupin domain of chicken and human CENP-C is self-oligomerization domain, which is crucial for centromeric chromatin organization. CENP-C mutants lacking the oligomerization interface cause mislocalization of CCAN and cell death. Based on these results, we conclude that the CENP-C oligomerization plays a crucial role in centromere function via providing the robust centromeric chromatin in vertebrate cells.
Supraorbital whiskers act as wind-antennae in rat anemotaxis
Authors: Mugnaini Matias , Mehrotra Dhruv , Davoine Federico , Sharma Varun , Mendes Ana Rita , Gerhardt Ben , Concha-Miranda Miguel , Brecht Michael , Clemens Ann M.
Published: August 2022

We know little about mammalian anemotaxis, wind-sensing. Recently, however, Hartmann and colleagues showed whisker-based anemotaxis in rats. To investigate how whiskers sense airflow, we tracked whisker tips in anesthetized or cadaver rats under no airflow, low airflow and high (fan-blowing) airflow. Whisker tips showed little movement under no airflow conditions and all whisker tips moved during high airflow. Low airflow conditions – most similar to naturally occurring wind stimuli – engaged whisker tips differentially. Most whiskers moved little, the long supraorbital whisker showed maximal displacement and α, A1, β, and γ whiskers also showed movements. The long supraorbital whisker differs from other whiskers in its exposed dorsal position, upward bending, length and thin diameter.Ex vivoextracted long supraorbital whiskers also showed exceptional airflow displacement, suggesting whisker-intrinsic biomechanics mediate the unique airflow-sensitivity. Micro computed tomography revealed that the ring-wulst – the follicle structure receiving the most sensitive afferents – was more complete/ closed in supraorbital and other wind-sensitive whiskers than in non-wind-sensitive whiskers, suggesting specialization of the supraorbital for omni-directional sensing. We localized and targeted the cortical supraorbital whisker representation in simultaneous Neuropixels recordings with D/E-row whisker barrels. Responses to wind-stimuli were stronger in the supraorbital whisker representation than in D/E-row barrel cortex. We assessed the behavioral significance of whiskers in an airflow-sensing paradigm. We observed that rats spontaneously turn towards airflow stimuli in complete darkness. Selective trimming of wind-responsive whiskers diminished airflow turning responses more than trimming of non-wind-responsive whiskers. Lidocaine injections targeted to supraorbital whisker follicles also diminished airflow turning responses compared to control injections. We conclude that supraorbital whiskers act as wind antennae.

New and Noteworthy

Animals rely on sensory processing of airflow (anemotaxis) to guide navigation and survival. We examined mechanisms of rat anemotaxis by combining whisker tracking, biomechanical analysis, micro computed tomography of follicle structure, Neuropixels recordings in the barrel field, behavior of airflow turning and whisker interference by trimming and lidocaine injections. This diversity of methods led to a coherent pattern of results. Whiskers greatly differ in their airflow sensitivity and strongly wind-responsive whiskers – in particular long supraorbital whiskers – determine behavioral responses to airflow stimuli in rats.
Sex inclusion in transcriptome studies of daily rhythms
Authors: Obodo Dora , Outland Elliot H. , Hughey Jacob J.
Published: August 2022

Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US NIH began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
Not just flowering time: A resurrection approach shows floral attraction traits are changing over time
Authors: Bishop Sasha G.D. , Chang Shu-Mei , Baucom Regina S.
Published: August 2022

Contemporary anthropogenic changes in climate and landscape form a complex set of selective pressures acting on natural systems, yet, in many systems, we lack information about both whether and how organisms may adapt to these changes. In plants, research has focused on climate-induced changes in phenology and the resultant potential for disruption of plant-pollinator interactions, however there remains a paucity of knowledge regarding how other pollinator-mediated traits may be involved in adaptive response. Here, we use resurrection experiments to investigate the phenotypic basis of adaptation in a mixed-mating system plant, the common morning glory (Ipomoea purpurea). Specifically, we measure temporal and spatial changes in traits grouped into three categories relevant to plant-pollinator interactions - floral morphology, floral rewards, and floral phenology. We show a significant temporal increase in corolla size and shift to earlier flowering times, as well as a potential for increased investment in floral rewards, all of which are driven primarily by populations at more northern latitudes. Additionally, we find evidence for directional selection on floral morphology and phenology, and evidence of balancing selection acting on anther-stigma distance. Overall, these results show an adaptive response in line with greater investment in pollinator attraction rather than self-pollination and fine-scale spatial differences in adaptive potential.
Evolution of insecticide resistance via parallel amino acid substitutions in insect pests and their parasitoid wasps
Authors: Guo Lei , Huang Jia
Published: August 2022

Insecticides have become the primary selective force in many insect species; however, whether beneficial insects developed resistance remains unknown. We analyzed the sequences of hymenopteran GABAA receptor subunit geneRdl(resistance to dieldrin), which encodes the target of cyclodiene and phenylpyrazole insecticides. The resistance-conferring A2 S mutations were found in seven parasitoid wasps and similar amino acid replacements at homologous sites have been identified in four of their resistant hosts. Our findings indicate how parallel molecular evolution at a single amino acid site confers adaptation in both insects and their natural enemies, which may shape species interactions and community structure.
Coherently Remapping Toroidal Cells But Not Grid Cells are Responsible for Path Integration in Virtual Agents
Authors: Schøyen Vemund , Pettersen Markus Borud , Holzhausen Konstantin , Fyhn Marianne , Malthe-Sørenssen Anders , Lepperød Mikkel Elle
Published: August 2022

Animals employ a neural system to map physical environmental position to neural activity and encode allocentric location. Grid cells, proposedly a vital component of this system, form a population code of space by firing in characteristic tessellated triangles of locations. This population code remaps across environments and behavioural states, independently of specific sensory inputs, pointing to a substrate of standard computation across environments, which many speculate to be path integration. However, testing whether these cells are crucial for path integration is outside the scope of current experiments and calls for complementary methods, possibly given by computational models. Recently, normative artificial neural network models have shown that path integration and grid-cell-like activity can be found in recurrent neural networks (RNNs) trained to navigate in a simulated two-dimensional environment. Remarkably, the emergent spatial profile of these grid-like cells is similar to biological cell responses in that they set up a toroidal structure. Here, we extend the RNN normative model to multiple environments and show that cells that form the toroidal structure are crucial for path integration. However, cells selected through the grid cell score, a common defining property of grid cells, are much less important and comparable to randomly selected cells. Moreover, we show that the model can navigate multiple environments and that toroidal cells remap across environments in a biologically plausible way. Results demonstrate a causal relation between toroidal cells and path integration in virtual agents and propose a mechanism of remapping in grid cells based on remapping in place cells. The work is anticipated to impact both experimental and computational neuroscience and machine learning due to the methods employed and the evaluation of results. For example, we propose explicit experiments that can evaluate both the model’s validity and the role of grid cells in navigation. Moreover, the model may elucidate how high-dimensional data is mapped to low-dimensional structures, possibly providing a substrate for interpolation.
Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures
Authors: Díaz-Rovira Anna M. , Martín Helena , Beuming Thijs , Díaz Lucía , Guallar Victor , Ray Soumya S.
Published: August 2022

Machine learning protein structure prediction, such as RosettaFold and AlphaFold2, have impacted the structural biology field, raising a fair amount of discussion around its potential role in drug discovery. While we find some preliminary studies addressing the usage of these models in virtual screening, none of them focus on the prospect of hit-finding in a real-world virtual screen with a target with low sequence identity. In order to address this, we have developed an AlphaFiold2 version where we exclude all structural templates with more than 30% sequence identity. In a previous study, we used those models in conjunction with state of the art free energy perturbation methods. In this work we focus on using them in rigid receptor ligand docking. Our results indicate that using out-of-the-box Alphafold2 models is not an ideal scenario; one might think in including some post processing modeling to drive the binding site into a more realistic holo target model.
RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription
Authors: Abuhashem Abderhman , Chivu Alexandra G. , Zhao Yixin , Rice Edward J. , Siepel Adam , Danko Charles G. , Hadjantonakis Anna-Katerina
Published: August 2022

Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been predominantly studied in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we found that loss of Pol II pausing stalls pluripotent state transitions within the epiblast of the early mouse embryo. Using Nelfb−/− mice and a NELFB degron mouse pluripotent stem cell model, we show that embryonic stem cells (ESCs) representing the naïve state of pluripotency successfully initiate a transition program but fail to balance levels of induced and repressed genes and enhancers in the absence of NELF. We found an increase in chromatin-associated NELF during transition from the naïve to later pluripotent states. Overall, our work defines the acute and long-term molecular consequences of NELF loss and reveals a role for Pol II pausing in the pluripotency continuum as a modulator of cell state transitions.
Agility of facilities management organizations during the COVID-19 pandemic: lessons learnt for future pandemics
Authors: Ling Florence Yean Yng , Tam Jia Yi
Published: August 2022

Purpose

This study aims to investigate how agile facilities management (FM) organizations were during the COVID-19 pandemic in Singapore, examine the agile strategies adopted and extracted lessons learnt for managing facilities in future pandemics.

Design/methodology/approach

Data were collected using a questionnaire coupled with in-depth interviews with FM professionals.

Findings

The FM sector experienced significant challenges such as increased operating cost and shortage of FM staff. FM organizations were assessed to be agile as they overcame challenges swiftly, made rapid changes to their service offerings as the situation evolved, engaged facility owners actively and adopted strategies that were flexible and responsive. They also adopted health-centric employee care.

Research limitations/implications

The research was conducted during the pandemic. The final verdict of FM organizations’ agility and the most effective practices may only be known when the COVID-19 pandemic ends.

Practical implications

Lessons learnt for FM to manage future pandemics were crystalized. These include reducing reliance on manpower, boosting technology adoption and personalized employee engagement.

Originality/value

This study added to knowledge by testing and confirming that the agility theory and its six metrics of agility comprising flexibility, velocity, responsiveness, collaboration, visibility and competence may be used by FM organizations to be agile in a crisis or disruption. Its originality is the discovery of a new construct – health-centric employee care – that is needed to further boost FM organizations’ agility performance in a pandemic. Health-centric employee care involves practices to reduce intra-staff transmission of the virus and individualized employee support to build resilience.
HR analytics: what’s holding users back?
Authors: Arora Meenal , Prakash Anshika , Mittal Amit , Singh Swati
Published: August 2022

Purpose

HR analytics is a process for systematic computational analysis of data or statistics. It discovers, interprets and communicates significant patterns in data to enable evidence-based HR research and uses analytical insights to help organizations achieve their strategic objectives. However, its adoption and utilization among HR professionals remain a subject of concern. This study aims to determine the reasons that facilitate or inhibit the acceptance of HR analytics among HR professionals in the banking, financial services and insurance (BFSI) sector.

Design/methodology/approach

A sample of 387 HR professionals in BFSI firms across India was collected through non-probabilistic purposive sampling. Structural equation modeling was applied to analyze the association between predetermined variables. In addition, the predictive relevance of “Data Availability” was analyzed using hierarchical regression.

Findings

The results revealed that data availability, hedonic motivation and performance expectancy positively influenced behavioral intention (BI). In contrast, effort expectancy, social influence and habit had an insignificant effect on BI. Also, facilitating conditions (FCs), habit, BI achieved a variance of 60% in HR analytics use. The use behavior of HR analytics was significantly influenced by FCs and BIs.

Practical implications

This study focuses on insights into the elements that influence HR analytics adoption, revealing additional light on success drivers and grey areas for failed adoption.

Originality/value

This research adds to the body of knowledge by identifying factors that hinder the adoption of HR analytics in Indian organizations and signifies the relevance of easy accessibility and availability of data for technology adoption.
Higher education in turbulent times: navigating the transition from un-sustainability in a world dominated by technology
Authors: Hume Therese
Published: August 2022

Purpose

The purpose of this paper is to reflect on the implications for higher education of a rapidly changing global context, where technologies play a role in the propagation of unsustainable patterns of change. Drawing from research on science and technology studies as well as existing work on (higher) education for sustainability, it seeks to expose the multidimensional nature of these patterns to raise a series of questions for educators, particularly those in engineering, computer science and other technical disciplines, and inform structured curricular and organisational interventions.

Design/methodology/approach

Theoretical perspectives on unsustainable patterns of technological change are explored with the objective of informing how the mitigation of their evolution could be addressed in educational settings. Key themes in the sustainability and higher education literature are then identified with the purpose of informing curricular and organisational intervention.

Findings

Countering unsustainable patterns of technological change requires the development of key sustainability competencies within more technical disciplines, informed by concepts in science and technology studies. This requires change at curricular, organisational and institutional levels to enable spaces for inter- and transdisciplinary learning to be created, so that skills may be developed.

Originality/value

This paper reflects on unsustainable patterns of technological change, identifying challenges for educators, in particular those in more technical disciplines.
Disclosure of key audit matters (KAMs) in financial reporting: evidence from an emerging economy
Authors: Rahaman Md Mustafizur , Hossain Md Moazzem , Bhuiyan Md. Borhan Uddin
Published: August 2022

Purpose

The new audit regulation for disclosure of key audit matters (KAMs) in financial reporting has been introduced in both developed and developing countries. This study investigates the influence of three distinctive sets of variables, namely industry features, firm characteristics and auditor attributes, on the extent, pattern and level of disclosure of KAMs by companies listed in Bangladesh, an emerging economy.

Design/methodology/approach

The study uses qualitative and quantitative research approaches to investigate the pattern of disclosure of KAMs and their determinants. With a sample of 447 firm-year observations from companies listed on the Dhaka Stock Exchange over 2018–2020, the study reveals industry-level, firm-level and auditor-specific characteristics that affect KAMs' communication in the new audit reporting model.

Findings

The findings suggest that significant differences exist between firms in the number and types of KAMs reported and the extent of their disclosure. The study findings also observed variations both within and across different industry sectors. Highly regulated firms disclose a greater number of KAMs, while environmentally sensitive firms are found to provide a greater detail of the issues presented as KAMs. Further, both firm size and age positively impact the number of KAMs disclosed and the extent of the disclosure provided. Big-4-affiliated auditors do not issue a significantly higher number of KAMs but deliver extensive details to their KAMs description, compared to non-Big-4 auditors. In addition, while auditors, in general, tend to issue boilerplate KAMs, Big-4 associates are found to disclose more new KAMs. However, audit fees and auditor rotation do not influence KAMs disclosure.

Research limitations/implications

This study is based on two years of publicly available data. However, future studies could consider in-depth interviews to explore the motivation behind KAMs' disclosure in Bangladesh and other developing countries with similar cultural and contextual values.

Practical implications

These findings have substantial policy considerations for improving firms' audit quality and, thus, their financial reporting quality, with implications for national and international standard-setters, regulators and other stakeholders.

Originality/value

This study is one of the earliest endeavours to investigate KAMs in a context of an emerging country, such as Bangladesh, which adopted KAMs' disclosure in 2018.
Less workplace parking with fully autonomous vehicles?
Authors: Tscharaktschiew Stefan , Reimann Felix
Published: August 2022

Purpose

Recent studies on commuter parking in an age of fully autonomous vehicles (FAVs) suggest, that the number of parking spaces close to the workplace demanded by commuters will decline because of the capability of FAVs to return home, to seek out (free) parking elsewhere or just cruise. This would be good news because, as of today, parking is one of the largest consumers of urban land and is associated with substantial costs to society. None of the studies, however, is concerned with the special case of employer-provided parking, although workplace parking is a widespread phenomenon and, in many instances, the dominant form of commuter parking. The purpose of this paper is to analyze whether commuter parking will decline with the advent of self-driving cars when parking is provided by the employer.

Design/methodology/approach

This study looks at commuter parking from the perspective of both the employer and the employee because in the case of employer-provided parking, the firm’s decision to offer a parking space and the incentive of employees to accept that offer are closely interrelated because of the fringe benefit character of workplace parking. This study develops an economic equilibrium model that explicitly maps the employer–employee relationship, considering the treatment of parking provision and parking policy in the income tax code and accounting for adverse effects from commuting, parking and public transit. This study determines the market level of employer-provided parking in the absence and presence of FAVs and identifies the factors that drive the difference. This study then approximates the magnitude of each factor, relying on recent (first) empirical evidence on the impacts of FAVs.

Findings

This paper’s analysis suggests that as long as distortive (tax) policy favors employer-provided parking, FAVs are no guarantee to end up with less commuter parking.

Originality/value

This study’s findings imply that in a world of self-driving cars, policy intervention related to work commuting (e.g. fringe benefit taxation or transport pricing) might be even more warranted than today.
The dynamics of value propositions through social media engagement in maritime transport networks: Maersk vs Mediterranean Shipping Company
Authors: D'agostini Enrico
Published: August 2022

Purpose

This study explores the levels of Facebook engagement of the two largest Europe-based shipping lines, Maersk and Mediterranean Shipping Company (MSC), to discover the marketing orientation of the topics advertised and to ascertain whether they tend to be about brand recognition, new transport services, or value propositions for stakeholders.

Design/methodology/approach

The Facebook posts of Maersk and MSC were analysed using social media text mining and social network analysis (SNA); in- and out-degree centrality analysis was performed to determine the key terms in their posts. NetMiner software was used to collect the respective data on Maersk and MSC. The inquiry period was set between May 2020 and February 2021.

Findings

The results indicated a divergence in their post contents, with higher engagement and a wider, more active follower base for MSC than for Maersk. Maersk primarily posts about logistics services and supply chain solutions. MSC communicates about new and large container vessels. Both companies seek greater brand recognition and information sharing through social media.

Originality/value

These results can be used by the stakeholders to evaluate whether Maersk and MSC truly deliver on their respective value propositions communicated online through their social media engagement. It can also help Maersk and MSC gauge the level of effectiveness of their communication with stakeholders and modify their digital engagement strategy accordingly.