bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcription factors regulating the fate and developmental potential of a multipotent progenitor in C. elegans
Authors: Soukup Evan M. , Bettinger Jill C. , Mathies Laura D.
Published: July 2022

Multipotent stem and progenitor cells have the capacity to generate a limited array of related cell types. The two C. elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all 143 cells of the somatic gonad, including complex tissues and specialized signaling cells. To screen for candidate regulators of cell fate and multipotency, we identified transcription factor genes with higher expression in SGPs than in their differentiated sister, the head mesodermal cell. We used RNA interference or genetic mutants to reduce the function of 183 of these genes and examined the worms at two developmental stages. Eight genes were identified that regulate the SGP fate, including the Ci/GLI homolog tra-1, which is the terminal regulator of sex determination. We show that tra-1 regulates SGP fate independently of its role in sex determination, supporting the idea that tra-1 retains ancestral functions. Four genes were necessary for SGPs to generate the correct number and type of descendant cells. We show that the E2F homolog, efl-3, regulates the cell fate decision between distal tip cells and the sheath/spermathecal precursor. We find that the FACT complex gene hmg-4 is required for the generation of the correct number of SGP descendants, and we define an earlier role for the nhr-25 nuclear hormone receptor-encoding gene, in addition to its previously described role in regulating the asymmetric division of SGPs. Overall, our data show that genes regulating cell fate are largely different from genes regulating developmental potential, demonstrating that these processes are genetically separable.
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels
Authors: Park Yein Christina , Reddy Bharat , Bavi Navid , Perozo Eduardo , Faraldo-Gómez José D.
Published: July 2022

The force-from-lipids hypothesis of cellular mechanosensation posits that membrane channels open and close in response to changes in the physical state of the lipid bilayer, induced for example by lateral tension. Here, we investigate the molecular basis for this transduction mechanism by studying the mechanosensitive ion channel MscS fromEscherichia coliand its eukaryotic homolog, MSL1 fromArabidopsis thaliana. First, we use single-particle cryo-EM to determine the structure of a novel open conformation of wild-type MscS, stabilized in a thinned lipid nanodisc. Compared with the closed state, the structure shows a reconfiguration of helices TM1, TM2 and TM3a, and widening of the central pore. Based on these structures, we examined how the morphology of the lipid bilayer is altered upon gating, using molecular dynamics simulations. The simulations reveal that closed-state MscS causes drastic protrusions in the inner leaflet of the lipid bilayer, both in the absence and presence of lateral tension, and for different lipid compositions. These deformations arise to provide adequate solvation to hydrophobic features of the protein surface in this conformation, and clearly reflect a high energy conformation for the membrane, particularly under tension. Strikingly, these protrusions are largely eradicated upon channel opening. An analogous computational study of open and closed MSL1 recapitulates these findings. The gating equilibrium of MscS channels thus appears to be dictated by two opposing conformational preferences, namely those of the lipid membrane and of the protein structure. We propose a membrane deformation model of mechanosensation, which posits that tension shifts the gating equilibrium towards the conductive state not because it alters the mode in which channel and lipids interact but because it increases the energetic cost of the morphological perturbations in the membrane induced by to the closed state.
Injectable hydrogel embedded with mesenchymal stem cells repairs severe spinal cord injury
Authors: Chen Xiangfeng , Lu Wujie , Zuo Yanming , Ye Jingjia , Li Xiaodan , Wu Zhonghan , Jin Shuang , Cai Wanxiong , Abdelrahman Zeinab , Zhang Tianfang , Gu Xiaosong , Yu Bin , Chen Zuobing , Wang Xuhua
Published: July 2022

Mesenchymal stem cell (MSC) transplantation was suggested as a promising approach to treat spinal cord injury (SCI). However, the heterogeneity of MSC and the lack of appropriate delivery methods impede its clinical application. To tackle these challenges, we first generated human MSCs derived from a single cell with a great homogeneity of batch quality and then developed a biocompatible injectable hydrogel to embed these cells to treat severe SCI. In a clinically relevant rat severe SCI model, we showed that the injection of MSCs with injectable hydrogel into the lesion site promoted robust functional recovery, while the intrathecal delivery of MSCs only resulted in limited therapeutic effects. Mechanistically, the hydrogel protected MSCs from the damage of harmful neuroinflammatory microenvironment in the spinal cord lesion. The hydrogel with the survived MSCs ameliorates the neuroinflammatory microenvironment of spinal cord lesion, preventing cavity formation and leads to the remnant of spared axons/tissues, which results in a better prognosis in the end.
Genomic signals of local adaptation and hybridization in Asian white birch
Authors: Nocchi Gabriele , Wang Jing , Yang Long , Ding Junyi , Gao Ying , Buggs Richard J. A. , Wang Nian
Published: July 2022

Disentangling the numerous processes that affect patterns of genome-wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing dataset for 79 European and Russian white birches, we show a clear distinction betweenB. pendulaandB. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity ofB. platyphyllain north-western China and Central Russia is affected greatly by hybridization withB. pendula. Excluding these hybridized populations,B. platyphyllain China has a linear distribution from north-eastern to south-western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of co-variation between allele frequencies and environmental variables inB. platyphyllasuggest the role of natural selection in the distribution of diversity at 7,609 SNPs of which 3,767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1,633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in EurasianB. pendula. We use the 7,609 environmentally associated SNPs to estimate the risk of non-adaptedness for each sequencedB. platyphyllaindividual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.
Development of nanobodies as theranostic agents against CMY-2-like class C β-lactamases
Authors: Frédéric Cawez , Mercuri Paola Sandra , Yanez Francisco Morales , Maalouf Rita , Vandevenne Marylène , Kerff Frederic , Guérin Virginie , Mainil Jacques , Thiry Damien , Saulmont Marc , Vanderplasschen Alain , Lafaye Pierre , Aymé Gabriel , Bogaerts Pierre , Dumoulin Mireille , Galleni Moreno
Published: July 2022

Soluble single-domain fragments derived from the unique variable region of camelid heavy-chain antibodies (VHHs) against enzymes may behave as potent inhibitors. The immunization of alpacas with the CMY-2 β-lactamase led to the isolation of three VHHs that specifically recognized and inhibited CMY-2. The structure of the complex VHH cAbCMY-2(254)/CMY-2 was determined by X-ray crystallography. We showed that the epitope is close to the active site and that the CDR3 of the VHH protrudes in the catalytic site. The β-lactamase inhibition was found to follow a mixed profile with a predominant non-competitive component. The three isolated VHHs recognized overlapping epitopes since they behaved as competitive binder. Our study identified a binding site that can be targeted by a new class of β-lactamase’s inhibitors designed with the help of a peptidomimetic approach. Furthermore, the use of mono or bivalent VHH and rabbit polyclonal anti-CMY-2 antibodies enable the development of the first generation of ELISA test for the detection of CMY-2 produced by resistant bacteria.

IMPORTANCE

The still increasing antimicrobial resistance in human clinic or veterinary medicine is a major threat for modern chemotherapy. Beside the major caution in the use of current antibiotics, it is important to develop new classes of antibiotics. This work was focused on β-lactamases that are the enzymes involved in the hydrolysis of the major class of antibiotics, the β-lactam compounds. We selected camelid antibodies that inhibit CMY-2, a class C β-lactamase produced by bacteria isolated from the veterinary and human settings. We characterized the conformational epitope present in CMY-2 in order to create a new family of inhibitors based on the paratope of the antibody. Finally, we designed a primary version of a detection system based on an ELISA using VHH and polyclonal antibodies.
A modular platform for bioluminescent RNA tracking
Authors: Ng Kevin K. , Cole Kyle H. , Halbers Lila P. , Chan Christelle E.T. , Fuller Erin B. , Callicoatte Chelsea , Metcalfe Mariajose , Chen Claire C. , Barhoosh Ahfnan A. , Reid-McLaughlin Edison , Kent Alexandra D. , Steward Oswald , Lupták Andrej , Prescher Jennifer A.
Published: July 2022

A complete understanding of RNA biology requires methods for tracking transcriptsin vivo. Common strategies rely on fluorogenic probes that are limited in sensitivity, dynamic range, and depth of interrogation, owing to their need for excitation light and tissue autofluorescence. To overcome these challenges, we developed a bioluminescent platform for serial imaging of RNAs. Small RNA tags were engineered to recruit light-emitting luciferase fragments (termed RNA lanterns) upon transcription. Robust photon production was observed for RNA targets both in cells and in live animals. Importantly, only a single copy of the tag was necessary for sensitive detection, in sharp contrast to fluorescent platforms requiring multiple repeats. Overall, this work provides a foundational platform for visualizing RNA dynamics from the micro to the macro scale.
Synergizing exchangeable fluorophore labels for multi-target STED microscopy
Authors: Glogger M. , Wang D. , Kompa J. , Balakrishnan A. , Hiblot J. , Barth H.D. , Johnsson K. , Heilemann M.
Published: July 2022

Investigating the interplay of cellular proteins with optical microscopy requires multi-target labeling. Spectral multiplexing using high-affinity or covalent labels is limited in the number of fluorophores that can be discriminated in a single imaging experiment. Advanced microscopy methods such as STED microscopy additionally demand balanced excitation, depletion and emission wavelengths for all fluorophores, further reducing multiplexing capabilities. Non-covalent, weak-affinity labels bypass this “spectral barrier” through label exchange and sequential imaging of different targets. Here, we combine exchangeable HaloTag ligands, weak-affinity DNA hybridization and hydrophophic and protein-peptide interactions to increase labeling flexibility and demonstrate 6-target STED microscopy in single cells. We further show that exchangeable labels reduce photobleaching, facilitate long acquisition times and multi-color live-cell and high-fidelity 3D STED microscopy. The synergy of different types of exchangeable labels increase the multiplexing capabilities in fluorescence microscopy, and by that, the information content of microscopy images.
Host pathways associated with human bacterial infections extend to commensal Wolbachia-Drosophila endosymbiosis
Authors: Sharmin Zinat , Samarah Hani , Aldaya Bourricaudy Rafael , Serbus Laura Renee
Published: July 2022

Wolbachia bacteria are among the most successful endosymbionts in nature, carried by half of all insect species. Unlike human bacterial pathogens that kill host cells and tissues, Wolbachia endosymbionts are generally carried by insects with little adverse effect. The striking difference in outcome raises a basic question of what aspects of infection mechanisms are conserved across systems. In this study, 37 small molecule inhibitors were used to test whether 14 candidate host processes that affect the abundance of other intracellular bacteria also affect Wolbachia. Compounds that significantly affected the absolute abundance of the Wolbachia surface protein (wsp) gene in D. melanogaster were retested in D. simulans flies. 5 compounds that consistently increased wsp abundance in both systems were associated with the Imd pathway, Calcium signaling, Ras/mTOR signaling, and the Wnt pathway. By contrast, the only compound to suppress wsp abundance was a Ubiquitin-proteasome pathway inhibitor. The implicated host processes were retested for impact on Wolbachia using constitutive and inducible RNAi expression systems in D. melanogaster. These tests corroborated a function for the host target of rapamycin (tor) and armadillo (arm) genes in affecting bodywide wsp abundance. Prior studies have reported that Ras/mTOR and Wnt pathways interact with ATG6 (Beclin-1), representing a possible convergence point for signaling impacts on Wolbachia. ATG6 disruption tests, driven by inducible RNAi expression, also elevated wsp abundance. This work suggests that combined effects of the Wnt pathway, Ras/mTOR signaling, and autophagy normally support Wolbachia containment, moderating the Wolbachia-host endosymbiosis.

IMPORTANCE

Disease-related microbes have been intensively studied as a model for infection. An intrinsic complication of such studies is bacterial induction of cell stress and cell death. To expand our understanding of cellular infection mechanisms, we studied a bacterial endosymbiont of insects, called Wolbachia, that does not kill the cells it infects. We asked whether cellular processes involved in pathogen infection are also associated with Wolbachia infections. Chemical and genetic tests were used to investigate cellular effects on Wolbachia abundance within fruit flies. We identified a subset of cellular processes with robust, repeatable effects on Wolbachia infection: the Wnt pathway and the Ras/mTor pathway. The results also suggest that multiple cellular pathways act together, which collectively suppresses Wolbachia abundance in vivo. Active host containment may explain in part why Wolbachia is mostly regarded as a neutral endosymbiont, and not as a pathogen.
A New Software Tool for Computer Assisted In Vivo High-Content Analysis of Transplanted Fluorescent Cells in intact Zebrafish Larvae
Authors: Førde Jan-Lukas , Nerbø Reiten Ingeborg , Fladmark Kari Espolin , Kittang Astrid Olsnes , Herfindal Lars
Published: July 2022

Acute myeloid leukaemia and myelodysplastic syndromes are cancers of the bone marrow with poor prognosis in frail and older patients. To investigate cancer pathophysiology and therapies, confocal imaging of fluorescent cancer cells, and their response to treatments in zebrafish larvae, yields valuable information. While zebrafish larvae are well suited for confocal imaging, the lack of efficient processing of large datasets remains a severe bottleneck. To alleviate this problem, we present a software-tool to segment cells from confocal images and track characteristics such as volume, location in the larva and fluorescent intensity on a single-cell basis. Using this software-tool, we were able to characterize the responses of the cancer cell lines Molm-13 and MDS-L to established treatments. By utilizing the computer-assisted processing of confocal images as presented here, more information can be obtained while being less time-consuming and reducing the demand of manual data handling, when compared to a manual approach, thereby accelerating the pursuit of novel anti-cancer treatments.

Summary statement

We present a software tool for automatic cell segmentation of fluorescent cancer cells in zebrafish larvae to determine characteristics of the cancer cell population on a single-cell basis.
Mean-field approximations with adaptive coupling for networks with spike-timing-dependent plasticity
Authors: Duchet Benoit , Bick Christian , Byrne Áine
Published: July 2022

Understanding the effect of spike-timing-dependent plasticity (STDP) is key to elucidate how neural networks change over long timescales and to design interventions aimed at modulating such networks in neurological disorders. However, progress is restricted by the significant computational cost associated with simulating neural network models with STDP, and by the lack of low-dimensional description that could provide analytical insights. Phase-difference-dependent plasticity (PDDP) rules approximate STDP in phase oscillator networks, which prescribe synaptic changes based on phase differences of neuron pairs rather than differences in spike timing. Here we construct mean-field approximations for phase oscillator networks with STDP to describe part of the phase space for this very high dimensional system. We first show that single-harmonic PDDP rules can approximate a simple form of symmetric STDP, while multi-harmonic rules are required to accurately approximate causal STDP. We then derive exact expressions for the evolution of the average PDDP coupling weight in terms of network synchrony. For adaptive networks of Kuramoto oscillators that form clusters, we formulate a family of low-dimensional descriptions based on the mean field dynamics of each cluster and average coupling weights between and within clusters. Finally, we show that such a two-cluster mean-field model can be fitted to synthetic data to provide a low-dimensional approximation of a full adaptive network with symmetric STDP. Our framework represents a step towards a low-dimensional description of adaptive networks with STDP, and could for example inform the development of new therapies aimed at maximizing the long-lasting effects of brain stimulation.
Optimizing multifunctional fluorescent ligands for intracellular labeling
Authors: Kumar Pratik , Vevea Jason D. , Tkachuk Ariana N. , Campbell Kirby , Watson Emma T. , Ayala Anthony X. , Grimm Jonathan B. , Chapman Edwin R. , Solecki David J. , Lavis Luke D.
Published: July 2022

Enzyme-based self-labeling tags enable covalent attachment of synthetic molecules to proteins inside living cells. A frontier of this field is designing multifunctional ligands that contain both fluorophores and affinity tags or pharmacological agents and can still efficiently enter cells. Self-labeling tag ligands with short linkers can enter cells readily but often show less activity due to steric issues; ligands with long linkers can be more potent but show lower cell permeability. Here, we overcome this tug-of-war between efficacy and cell-permeability by devising a rational strategy for making cell permeable multifunctional ligands for labeling HaloTag fusions. We found that the lactone–zwitterion equilibrium sconstant (KL–Z) of rhodamines inversely correlates with their distribution coefficients (logD7.4), suggesting that ligands based on dyes exhibiting lowKL–Zand high logD7.4values, such as Si-rhodamines, would efficiently enter cells. We designed cell-permeable multifunctional HaloTag ligands with a biotin moiety to purify mitochondria or a JQ1 appendage to translocate BRD4 from euchromatin to the nucleolus or heterochromatin. We discovered that translocation of BRD4 to constitutive heterochromatin in cells expressing HaloTag–HP1a fusion proteins can lead to apparent increases in transcriptional activity. These new reagents enable affinity capture and translocation of intracellular proteins in living cells and the use of Si-rhodamines and other lowKL–Z/high logD7.4dye scaffolds will facilitate the design of new multifunctional chemical tools for biology.

SIGNIFICANCE STATEMENT

Understanding cellular processes requires tools to measure and manipulate proteins in living cells. Self- labeling tags, such as the HaloTag and SNAP-tag, enable modification of cellular proteins with synthetic molecules. Creating ligands for these systems that have more than one chemical motif remains challenging, however, due to competing demands between cell permeability and functionality. We discovered that multifunctional ligands based on Si-rhodamines efficiently entered cells and enabled affinity purification of mitochondria or translocation of nuclear proteins; the performance of these molecules could be verified by fluorescence microscopy. These compounds should be useful for a variety of biological experiments and our general framework will allow the design of other multifunctional ligands to study living systems.
Molecular glue CELMoD compounds are allosteric regulators of cereblon conformation
Authors: Watson Edmond R. , Novick Scott J. , Matyskiela Mary E. , Chamberlain Philip P. , de la Peña Andres Hernandez , Zhu Jin-Yi , Tran Eileen , Griffin Patrick R. , Wertz Ingrid E. , Lander Gabriel C.
Published: July 2022

Cereblon (CRBN) is an ubiquitin ligase (E3) adaptor protein co-opted by CRBN E3 Ligase Modulatory Drugs (CELMoD) agents that target therapeutically-relevant proteins for degradation. Prior crystallographic studies defined the drug-binding site within CRBN’s Thalidomide Binding Domain (TBD), but the allostery of drug-induced neosubstrate binding remains unclear. We therefore performed cryo-EM analyses of the DDB1∼CRBN apo-complex, and compared these structures with DDB1∼CRBN in the presence of CELMoD compounds alone and complexed with neosubstrates. Association of CELMoD compounds to the TBD is necessary and sufficient for triggering CRBN allosteric rearrangement from an “open” conformation to the canonical “closed” conformation. Importantly, the neosubstrate Ikaros only stably associates with the closed CRBN conformation, illustrating the importance of allostery for CELMoD compound efficacy, and informing structure-guided design strategies to improve therapeutic efficacy.
Emergence of multiple set-points of cellular homeostatic tension
Authors: Ueda Yuika , Deguchi Shinji
Published: July 2022

Stress fibers (SFs), a contractile actin bundle in nonmuscle mesenchymal cells, are known to intrinsically sustain a constant level of tension or tensional stress, a process called cellular tensional homeostasis. Malfunction in this homeostatic process has been implicated in many diseases such atherosclerosis, but its mechanisms remain incompletely understood. Interestingly, the homeostatic stress in individual SFs is altered upon recruitment of α-smooth muscle actin in particular cellular contexts to reinforce the preexisting SFs. While this transition of the set-point stress is somewhat a universal process observed across different cell types, no clear explanation has been provided as to why cells end up possessing different stable stresses. To address the underlying physics, here we describe that imposing a realistic assumption on the nature of SFs yields the presence of multiple set-points of the homeostatic stress, which transition among them depending on the magnitude of the cellular tension. We derive non-dimensional parameters that characterize the extent of the transition and predict that SFs tend to acquire secondary stable stresses if they are subject to as large a change in stiffness as possible or to as immediate a transition as possible upon increasing the tension. This is a minimal and simple explanation, but given the frequent emergence of force-dependent transformation of various subcellular structures in addition to that of SFs, the theoretical concept presented here would offer an essential guide to addressing potential common mechanisms governing complicated cellular mechanobiological responses.
Teaching the concept of decision-usefulness, and accounting as a technical, social and moral practice: the case of COVID-19 “case number” reporting
Authors: Sidaway Shannon I.L. , Juric Daniela , Deegan Craig
Published: July 2022

Purpose

The purpose of this paper is to demonstrate how teaching broader accounting concepts through real life non-financial case study information (such as COVID-19 case reporting) can assist students understanding accounting’s technical, social and moral perspectives. Accounting education and practice has traditionally focussed on the technical aspects of accounting and has situated accounting within a financial context.

Design/methodology/approach

This exploratory study uses content analysis of COVID-19 case and death numbers reported by several international health reporting agencies. This study does not set out to provide a detailed technical or comparative jurisdictional analysis of the decision-usefulness of COVID-19 information. Rather, this study looks at the “decision-usefulness” of the COVID-19 case and death number information, and provides examples that educators can draw upon for inspiration when showing how the qualitative characteristics of decision-useful information can be applied to non-financial information. This study also highlights, by use of a “novel data set”, the technical, social and moral aspects of accounting.

Findings

This study finds that the COVID-19 pandemic provides an opportunity for accounting education by positioning the qualitative characteristics of decision-useful information beyond a financial context. The exploration of accounting within this setting effectively demonstrates that accounting has “technical”, “social” and “moral” dimensions.

Originality/value

This paper fulfils an identified need to include teaching of decision-usefulness of non-financial information in the accounting curriculum to ensure that future professional accountants possess technical and professional competency skills.
Finite element modeling of reinforced concrete short columns subjected to shear in two perpendicular directions
Authors: Alraqad Marya , Allouzi Rabab , Alkloub Amer
Published: July 2022

Purpose

Short columns can cause serious damage when subjected to an earthquake due to their high stiffness with low ductility. These columns can be exposed to multidirectional shear forces, which encouraged this study to investigate the behavior of structural short columns under bi-directional shear.

Design/methodology/approach

Finite element analysis (FEA) using ABAQUS is conducted and calibrated based on experimental data tested by previous researchers who studied the uni-directional behavior of short columns subjected to cyclic shear displacements. Then, the calibrated column models are further investigated to study the influence of bidirectional cyclic shear. Two scenarios are investigated, namely “simultaneous” and “sequential,” to compare the performance in terms of shear strength reduction.

Findings

The results show that the shear strength reduction significantly appears when 1:1 simultaneous bi-directional cyclic shear is applied. However, the shear reduction is more significant when the sequential scenario is applied. The seismic forces or deformations applied in orthogonal directions should be combined to achieve the maximum seismic response of structures as specified in Federal Emergency Management Agency (FEMA) 356 Standard. Finally, the combinations presented in literature to consider bi-directional shear are investigated. Based on FE results, the effect of applied 1:0.30 bi-directional cyclic shear simultaneously does not result in significant effect on the considered columns properly design for seismic forces.

Originality/value

To investigate the effect of multidirectional shear forces on the shear strength capacity of short columns, the presented effect of multidirectional shear forces in literature to consider bi-directional shear are investigated.
Rise of the machines: Integrating technology with playback experiments to study cetacean social cognition in the wild
Authors: King Stephanie L. , Jensen Frants H.
Published: July 2022

Cetaceans represent an evolutionary peak in terms of their cognitive capacities, complex communication systems and their structured, multilevel societies. However, the difficulty of observing their behaviour underwater means that studying whale and dolphin sociality in the wild poses some significant methodological challenges.

Traditionally, playback experiments have been used to explore aspects of communication and cognition in whales and dolphins, particularly with trained animals under human care. However, while these studies have provided major breakthroughs in our understanding of cetacean social cognition, it is difficult to know whether these findings generalize to wild animals.

In recent years, new state‐of‐the‐art technology (drones and non‐invasive sound and movement tags) have revolutionized the field of marine mammal behaviour, providing unparalleled information on the fine‐scale behaviour of individuals in the wild. Here, we review the state of the field, combining published studies with our own extensive experience, to demonstrate how these new technologies fundamentally change the behavioural metrics that we are able to measure; allowing us to move from categorical observations to quantifying fine‐scale changes in movement, activity and vocal behaviour.

We discuss how conducting playback experiments alongside these new technologies combines rigorous experimental design with strong ecological validity and increased reproducibility and can be adapted for many social species, setting the standard for high‐calibre, field‐based experiments that explore animal social cognition in the wild.
The management of neovascular age‐related macular degeneration: A systematic literature review of patient‐reported outcomes, patient mental health and caregiver burden
Authors: Gale Richard P. , Finger Robert P. , Eldem Bora , Aslam Tariq , Barratt Jane , Daien Vincent , Kodjikian Laurent , Loewenstein Anat , Okada Mali , Wong Tien Yin , Sylvanowicz Michelle , Rodríguez Francisco J.
Published: July 2022

Purpose

The aim of this systematic literature review was to describe patient‐reported outcomes, mental health and caregiver burden in patients with neovascular age‐related macular degeneration (nAMD) treated with anti‐vascular endothelial growth factor (VEGF) agents in routine clinical practice.

Methods

Electronic searches were conducted in Embase and MEDLINE according to pre‐defined criteria.

Results

Of 856 records identified, 63 met inclusion criteria. Depression or depressive symptoms were reported in up to 42% of patients with nAMD. Of 25/63 (40%) studies evaluating quality of life (QoL) and using various tools, eight studies reported composite National Eye Institute Visual Functioning Questionnaire scores following anti‐VEGF treatment. Of these, seven reported a statistically significant improvement at the earliest time point measured (Month 3–12) and approximately 50% reported sustained QoL benefits at 12 months. In studies comparing the attributed or different regimens, the most important factor from the patient's perspective was the likelihood that a particular regimen would maintain vision. There was a preference towards treat and extend, which was associated with a perceived reduction in patient and caregiver burden, compared to fixed dosing.

Conclusions

A coordinated holistic approach to patient care is key to optimizing patient well‐being as well as visual outcomes. Further research regarding the patient‐reported impact of nAMD management outside the trial setting (particularly international longitudinal studies) is warranted. Standardization of QoL studies would assist in establishing whether sustained QoL improvement, rather than prevention of QoL decline, should be a realistic expectation of treatment of nAMD in the longer term.
Day‐to‐day variation in students’ academic success: The role of self‐regulation, working memory, and achievement goals
Authors: Blume Friederike , Irmer Andrea , Dirk Judith , Schmiedek Florian
Published: July 2022

Self‐regulation was found to be positively associated with school performance. Interrelations between self‐regulation, working memory (WM), and achievement goals, in particular mastery goals, have been established, as well as associations with academic outcomes. It stands to reason that self‐regulation, WM, achievement goals, and academic success are related on a daily level. However, previous research rarely considered this level of analysis. Here, we therefore addressed the relations of daily self‐regulation, WM, and achievement goals, and their relevance for daily and general academic success. Data were obtained through ambulatory assessments in 90 students before (Study 1; Mage = 9.83, SDage = 0.50) and 108 students after their transition to secondary school (Study 2; Mage = 10.12, SDage = 0.45) across 20 school days. Students reported about daily achievement goals prior to school, self‐regulation at school, and perceived academic success after school, as well as report card grades. Daily WM was assessed at school. Study 1 showed positive associations between daily mastery goals and self‐regulation, but not with WM. Together, daily performance‐approach goals and self‐regulation, but not other goals or WM uniquely contributed to daily perceived academic success. Study 2 showed positive associations between daily mastery goals and self‐regulation, but not with WM. Average daily mastery goals predicted daily WM. Together, daily mastery goals and self‐regulation, but not WM, uniquely contributed to daily perceived academic success. In both studies, average levels of WM, but not achievement goals or self‐regulation predicted report card grades. Results thus corroborate theoretical considerations on the importance of distinguishing self‐regulation processes at between‐ and within‐person levels.

Research Highlights

Analyses of intensive longitudinal data on daily self‐regulation, working memory, and achievement goal orientations in the school context of 9‐ to 11‐year‐olds.

In primary and secondary school, days with higher mastery goals and self‐regulation are days with higher academic success.

In primary and secondary school, days with higher mastery goals are days with higher self‐regulation.

In secondary school, students with higher average mastery goals show better daily WM performance.

Average working memory performance predicts report card grades beyond the influence of prior grades and achievement goal orientations.
Structural Transformation of Occupation Employment
Authors: Duernecker Georg , Herrendorf Berthold
Published: July 2022

We use census data to show that structural transformation reflects a fundamental reallocation of labour from goods to services, instead of a relabelling that occurs when goods‐producing firms outsource their in‐house service production. The novelty of our approach is that it categorizes labour by occupations, which are invariant to outsourcing. We find that the reallocation of labour from goods‐producing to service‐producing occupations is a robust feature in censuses from around the world and different time periods. To understand the underlying forces, we propose a tractable model in which uneven occupation‐specific technological change generates structural transformation of occupation employment.
Linkage between microbial functional genes and net N mineralisation in forest soils along an elevational gradient
Authors: Wang Jieying , He Liyuan , Xu Xiaofeng , Ren Chengjie , Wang Jun , Guo Yaoxin , Zhao Fazhu
Published: July 2022

Soil net nitrogen (N) mineralisation, the difference between organic nitrogen mineralisation and mineral nitrogen immobilisation, changes with elevation, thereby determining plant productivity and soil N cycling along elevation gradients. However, it has yet to be established how different microbial functional genes influence the rate of soil net N mineralisation along such gradients. To address this deficiency in our current knowledge, we performed metagenomic sequencing to identify soil microbial functional genes encoding enzymes involved in N cycling at five forest sites along an elevational gradient spanning a range from 1503 to 3182 m above sea level. Our results indicate that the rate of net N mineralisation follows a unimodal pattern with increasing elevation, with a peak (0.18 mg kg−1d−1) being detected at the mid‐high elevation site. Further, we detected a significant correlation between the abundance of genes encoding enzymes involved in denitrification and ammonia assimilation pathways and net N mineralisation rate (p < 0.05). Moreover, we established that microbial species in the phylaCyanobacteria,AcidobacteriaandPlanctomycetes, harbouring keystone functional genes, play a predominant role in determining the rate of net N mineralisation. Our findings also revealed soil substrate content (ammonium nitrogen and nitrite nitrogen, soil organic carbon, and C:N ratio) and soil environment (soil temperature and soil moisture) to be the major drivers of net N mineralisation in soil via their regulatory effects on the composition of microbial communities and functional genes. Our characterisation of the microbial metagenomic basis of net N mineralisation in forest soils accordingly highlights the importance of the combined contributions of soil microbial functional genes, soil substrate, and environmental factors in determining the cycling of N in forest soils at different elevations.

Highlights

Net N mineralisation rate followed a unimodal pattern along an elevational gradient.

Denitrification and ammonia assimilation genes were correlated with net N mineralisation rate.

Cyanobacteriaplay a dominant role in determining net N mineralisation rate.

Soil substrate and environment determine microbial functional gene distribution.
Grazing and topography control nutrient pools in low Arctic soils of Southwest Greenland
Authors: van Soest Maud A. J. , Anderson N. John , Bol Roland , Dixon Liz R. , Haygarth Philip M.
Published: July 2022

Soil nutrient pools in the dry low Arctic are likely to be released under climatic change and this bioavailability has the potential to increase both terrestrial and aquatic productions. As well as the direct effect of warming, external disturbances such as nutrient deposition and grazing can also drive ecosystem change. This study in the low Arctic Kangerlussuaq area of southwest Greenland compared soil nutrient pools in terms of both topographic position on a catena and by soil depth in two small catchments with contrasting muskox abundance. We tested the hypotheses that there were differences between soil carbon (C), nitrogen (N) and phosphorus (P) across a soil catena (ridge ‐ slope ‐ valley) and by soil depth (litter ‐ 0–5 cm ‐ 25–30 cm) for the two sites (SS17b, muskox present, versus ‐ SS85, no muskox). Total C and N concentrations of soils were on average lower at SS17b compared to SS85. Moreover, the soil N concentration increased downslope in the catena with higher amounts in the valleys compared to the slopes and ridges. Soil P concentration (0.70 g P kg−1) was similar between catchments; however, litter P content was substantially different. The difference in soil nutrients between the two catchments was most likely due to the presence of muskox at SS17b, and hence grazing associated processes (defecation, altered microbiology and nutrient cycling). This study emphasises the heterogeneity of arctic landscapes and need for ecosystem specific research.

Highlights

Soil nutrient pools in two low‐arctic catchments in Greenland were compared.

Grazing and dung inputs by muskox affect soil nutrient pools in Greenland.

Soil P stores in Kangerlussuaq are similar to intensively managed farmland in Europe.

The heterogeneity of arctic landscapes and need for ecosystem‐specific research are emphasised.
Effect of biochar on soil properties and infiltration in a light salinized soil: Experiments and simulations
Authors: Li Yi , Liu Chuncheng , Liang Zhijie , Wang Xiaofang , Fan Xiangyang , Liu De Li , Biswas Asim
Published: July 2022

The sustainable development of agriculture in Xinjiang Province, China has been threatened by soil salinization. Biochar can be an effective amendment to improve salt‐affected soils. An appropriate amount of biochar application and incorporation depth are key factors for amending performance. However, few studies have investigated the effects of differing biochar application amounts on saline soil properties, including soil water infiltration, using a combination of experiments and simulations. In this study, acidulated biochar was applied at rates of 0, 10, 25, 50 and 100 t ha−1 to a farmland topsoil to investigate the impacts of biochar on Xinjiang saline soil's physical and chemical properties and infiltration characteristics. The soil's physical and chemical properties that were investigated included soil pH, soil organic carbon content, soil salt content, saturated hydraulic conductivity (Ks), soil water retention curves, and infiltration characteristics including cumulative infiltration (CI) and wetting front (Zf). HYDRUS‐1D was applied to predict soil water movement under different biochar incorporation depths. Results showed that the rate of change of soil pH, soil organic carbon content, soil salt content and Ks were −0.009, 0.102 g kg−1, 0.045 g kg−1 and 0.035 cm day−1, respectively, per ton of biochar applied. Soil water retention curves showed that biochar enhanced soil water retention capacity and available soil water content (AWC) in the silt clay loam soil. The Philip model was a good (R2 > 0.80) fit to soil water infiltration and indicated that biochar amendment promoted infiltration rates. The van Genuchten model was good for describing soil hydraulic parameters (R2 > 0.99) and could be used for HYDRUS‐1D simulations (R2 > 0.99, RRMSE <6.8% and NSE >0.98). The optimum biochar application amount for the light salinised soil in Xinjiang was recommended as 25 t ha−1 incorporated to 30 cm depth based on the AWC, soil salt content and incorporation depths. The study provides a reference for future field experiment design.

Highlights

Effects of biochar on salt‐affected soil studied using a combination of experiments and simulations.

Acidulated biochar amendment of saline soils can reduce pH and increase SOC.

Biochar incorporation depth was considered to affect soil water infiltration.

The biochar application amount at 25 t ha−1 incorporated to 30 cm depth was recommended
Diel light cycles affect phytoplankton competition in the global ocean
Authors: Tsakalakis Ioannis , Follows Michael J. , Dutkiewicz Stephanie , Follett Christopher L. , Vallino Joseph J.
Published: July 2022

Aim

Light, essential for photosynthesis, is present in two periodic cycles in nature: seasonal and diel. Although seasonality of light is typically resolved in ocean biogeochemical–ecosystem models because of its significance for seasonal succession and biogeography of phytoplankton, the diel light cycle is generally not resolved. The goal of this study is to demonstrate the impact of diel light cycles on phytoplankton competition and biogeography in the global ocean.

Location

Global ocean.

Major taxa studied

Phytoplankton.

Methods

We use a three‐dimensional global ocean model and compare simulations of high temporal resolution with and without diel light cycles. The model simulates 15 phytoplankton types with different cell sizes, encompassing two broad ecological strategies: small cells with high nutrient affinity (gleaners) and larger cells with high maximal growth rate (opportunists). Both are grazed by zooplankton and limited by nitrogen, phosphorus and iron.

Results

Simulations show that diel cycles of light induce diel cycles in limiting nutrients in the global ocean. Diel nutrient cycles are associated with higher concentrations of limiting nutrients, by 100% at low latitudes (−40° to 40°), a process that increases the relative abundance of opportunists over gleaners. Size classes with the highest maximal growth rates from both gleaner and opportunist groups are favoured by diel light cycles. This mechanism weakens as latitude increases, because the effects of the seasonal cycle dominate over those of the diel cycle.

Main conclusions

Understanding the mechanisms that govern phytoplankton biogeography is crucial for predicting ocean ecosystem functioning and biogeochemical cycles. We show that the diel light cycle has a significant impact on phytoplankton competition and biogeography, indicating the need for understanding the role of diel processes in shaping macroecological patterns in the global ocean.
A Critical Review of Molybdenite 187Re Parent‐187Os Daughter Intra‐Crystalline Decoupling in Light of Recent In SituMicro‐Scale Observations
Authors: Zimmerman Aaron , Yang Gang , Stein Holly J. , Hannah Judith L.
Published: July 2022

Two recent advances in instrumentation convey rhenium and osmium elemental and isotopic distribution in molybdenite at the micro‐scale: (1) NanoSIMS imaging which reveals heterogeneities that could preclude micro‐scale geochronology (spot dating), and (2) reaction‐cell LA‐ICP‐MS/MS which partially resolves overlapping masses of isobaric 187Re and 187Os which otherwise confound micro‐scale analyses. The results from each of these measurement principles led respective researchers to conclude that no apparent parent‐daughter decoupling occurs, at least in their chosen samples. This contradicts 20 years of prior macro‐ to micro‐scale Re‐Os molybdenite data. Given these contradictions, we compare their results to our macro‐scale isotope dilution (ID) N‐TIMS measurement results of NIST Reference Material 8599, Henderson molybdenite. We document the homogeneity of the NIST molybdenite, including model age variability, precision of ID N‐TIMS measurement results and statistical treatment. We demonstrate that parent‐daughter decoupling cannot be precluded by visual inspection of NanoSIMS isotopic maps. In addition, we prove mathematically that quantifying reaction‐cell reacted 187Os by LA‐ICP‐MS/MS is far too imprecise to preclude parent‐daughter decoupling at an extent that hinders high‐precision geochronology, although full 2‐D ablation of a molybdenite crystal surface may yield an accurate Re‐Os age. Nevertheless, LA‐ICP‐MS/MS is useful for documenting the spatial extent of heterogeneous parent‐daughter distribution within individual crystals and supports whole crystal ID N‐TIMS.