bluuebunny/crossref_metadata_2025 huggingface dataset:
In depth profiling of the cancer proteome from the flowthrough of standard RNA- preparation kits for precision oncology
Authors: Mundt Madsen Filip , Nielsen Annelaura Bach , Wang Juanjuan , Duel Josephine Kerzel , Yde Christina Westmose , Eriksen Martina Amnitzbøll , Lassen Ulrik , Nielsen Finn Cilius , Rohrberg Kristoffer , Mann Matthias
Published: May 2023

Cancer is a highly heterogeneous disease, even within the same patient. Biopsies taken from different regions of a tumor may stand in stark molecular contrast to each other. Therefore, the ability to generate meaningful data from multiple platforms using the same biopsy is crucial for translating multi-omics characterizations into the clinic. However, it is generally a cumbersome and lengthy procedure to generate DNA, RNA and protein material from the same biopsy. The Qiagen AllPrep kit is an accessible, straightforward, and widely used kit in clinics worldwide to process biopsies and generate genomic and transcriptomic data from tumors. We aimed to determine if high-quality proteomics data could also be obtained from the remaining material. Here, we investigated procedures for generating deep and quantitatively accurate proteomic information in high throughput from Qiagen AllPrep flowthroughs. With a number of refinements, we obtain in excess of 10,000 quantified proteins, from 60 samples per day, achieving a substantial coverage of the total proteome. Additionally, we successfully characterize the tumors using phosphoproteomics. Combining a standard kit with in-depth proteomics will be an attractive approach for clinics seeking to implement multi-omics-based precision oncology.
Peripheral serotonergic neurons regulate gut motility and anxiety-like behavior
Authors: Zhang Hailong , Leitner Deborah R. , Hasegawa Yuko , Waldor Matthew K.
Published: May 2023

Serotonergic circuits in the central nervous system play important roles in regulating mood and behavior, yet the functions of peripheral serotonergic neurons are less understood. Here, we engineered mice lacking the serotonin-producing enzymeTph2in peripheral neurons but with intactTph2in central neurons. In contrast to mice lackingTph2in all neurons, mice lackingTph2in peripheral serotonergic neurons did not exhibit increased territorial aggression. However, similar to the total bodyTph2KO mice, the conditional KO animals, exhibited reduced gut motility and decreased anxiety-like behavior. These observations reveal that peripheral serotonergic neurons contribute to control of intestinal motility and anxiety-like behavior and suggest that therapeutics targeting this subset of peripheral neurons could be beneficial.
Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in Anza Borrego Desert
Authors: Stancheva Rosalina , Sethuraman Arun , Khadivar Hossein , Archambeau Jenna , Caughran Ella , Chang Ashley , Hunter Brad , Ihenyen Christian , Onwukwe Marvin , Palacios Dariana , Prairie Chloe La , Read Nicole , Tsang Julianna , Vega Brianna , Velasquez Cristina , Zhang Xiaoyu , Becket Elinne , Read Betsy
Published: May 2023

Here we describe the metagenome composition, community functional annotation, and diversity of prokaryotic microbial species derived from calcareous stromatolite formations discovered in the dry stream bed of the open-canopy, ephemeral San Felipe Creek in the Anza Borrego Desert. In this environment, resident microbes must be able to adapt to the harsh conditions of extreme heat, high UV light, desiccation and fluctuating solubilization/precipitation and hydration/evaporation. Metagenomic analysis revealed a community capable of carrying out complete nitrogen fixation and assimilatory nitrate reduction, forming biofilms and quorum sensing, and potentially forming thick-walled akinetes as desiccation-resistant stages. Nitrogen cycling is likely to play a fundamental role in mediating both the structure of the stromatolite microbial community and the mineral precipitation/dissolution. The viruses present in the stromatolites, particularlyNodulariaandMycobacteriumphages are also likely to impact community population dynamics and activity. Stromatolite community members possess different morphological and physiological strategies to cope with desiccation stress.

Metagenomic signatures were found for scytonemin, carotenoids, synthesis of potential microsporine-like amino acids; genes involved in microalgal desiccation tolerance, including those encoding aquaporins, chaperones, antioxidants; and enzymes responsible for the synthesis of trehalose, sucrose, and polyamines.

The stromatolite ecosystem provides a diverse array of microniches where different functional guilds can develop complex metabolite exchange with the substrate supporting their life in extreme conditions. Metagenome analyses revealed several genes that might enable a specialized and unique group of endolithic cyanobacteria includingChroococcidiopsis, Hyella, Myxosarcina, andPleurocapsato derive metals and important nutrients from rocks, being potentially destructive for the calcareous formations. Our study revealed environmental adaptations of freshwater microbial communities in desert stream stromatolites which may provide valuable insights into Precambrian paleoenvironments, which are little known.
Hippocampome.org v2.0: a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits
Authors: Wheeler Diek W. , Kopsick Jeffrey D. , Sutton Nate , Tecuatl Carolina , Komendantov Alexander O. , Nadella Kasturi , Ascoli Giorgio A.
Published: May 2023

Hippocampome.orgis a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties.Hippocampome.orgv1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression. Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology,in vivofiring phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community.Hippocampome.orgv2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
Decentralized Mixed Effects Modeling in COINSTAC
Authors: Basodi Sunitha , Raja Rajikha , Gazula Harshvardhan , Romero Javier Tomas , Panta Sandeep , Maullin-Sapey Thomas , Nichols Thomas , Calhoun Vince D.
Published: May 2023

Performing group analysis on magnetic resonance imaging (MRI) data with linear mixed-effects (LME) models is challenging due to its large dimensionality and inherent multi-level covariance structure. In addition, as large-scale collaborative projects become commonplace in neuroimaging, data must increasingly be stored and analysed at different locations. In such settings, substantial overheads occur in terms of data transfer and coordination between participating research groups. In some cases, data cannot be pooled together due to privacy or regulatory concerns. In this work, we propose a decentralized LME model to perform a large-scale analysis of data from different collaborations without sharing or pooling. This method is efficient as it overcomes the hurdles of data privacy for sharing and has lower bandwidth and memory requirements for analysis than the centralized modeling approach. We evaluate our model using features extracted from structural magnetic resonance imaging (sMRI) data. Results highlight gray matter reductions in the temporal lobe/insula and medical front regions demonstrate the correctness of decentralized LME models. Our analysis also demonstrates that decentralized LME models achieve similar performance compared to the models trained with all the data in one location. We also implement the decentralized LME approach in COINSTAC, a decentralized platform for federating neuroimaging analysis, to demonstrate its value to the neuroimaging community.
Investigating the developmental onset of regenerative potential in the annelidCapitella teleta
Authors: Boyd Alicia A. , Seaver Elaine C.
Published: May 2023

An animal’s ability to regrow lost tissues or structures can vary greatly during its life cycle. The annelidCapitella teletaexhibits posterior, but not anterior, regeneration as juveniles and adults. In contrast, embryos display only limited replacement of specific tissues. To investigate when during developmentC. teletabecomes capable of regeneration, we assessed the extent to which larvae can regenerate. We hypothesized that larvae exhibit intermediate regeneration potential and demonstrate some features of juvenile regeneration, but do not successfully replace all lost structures. Both anterior and posterior regeneration potential of larvae were evaluated following amputation. Wound sites were analyzed for re-epithelialization, cell proliferation by EdU incorporation, stem cell and differentiation marker expression by in situ hybridization, presence of neurites and muscle fibers by immunohistochemistry and phalloidin staining respectively, and regrowth of structures. Wound healing occurred within 6 hours of amputation for both anterior and posterior amputations. Cell proliferation at both wound sites was observed for up to 7 days following amputation. In addition, the stem cell markervasawas expressed at anterior and posterior wound sites. However, growth of new tissue was observed only in posterior amputations. Neurites from the ventral nerve cord were also observed at posterior wound sites.De novo ashexpression in the ectoderm of anterior wound sites indicated neuronal cell specification, although the absence ofelavexpression indicated an inability to progress to neuronal differentiation. In rare instances, cilia and eyes reformed. Both amputations induced expanded expression of the myogenesis geneMyoDin pre-existing tissues. Our results indicate that amputated larvae complete early, but not late, stages of regeneration, indicating a gradual acquisition of regenerative ability inC. teleta.Furthermore, amputated larvae can metamorphose into burrowing juveniles, including those missing brain and anterior sensory structures. To our knowledge, this is the first study to assess regenerative potential of annelid larvae.
Breaking New Ground in Computational Psychiatry: Model-Based Characterization of Forgetting in Healthy Aging and Mild Cognitive Impairment
Authors: Hake Holly Sue , Leonard Bridget , Ulibarri Sara , Grabowski Thomas , Van Rijn Hedderik , Stocco Andrea
Published: May 2023

Computational models of memory used in adaptive learning settings trace a learner’s memory capacities. However, less work has been done on the implementation of these models in the clinical realm. Current assessment tools lack the reliable, convenient, and repeatable qualities needed to capture the individualized and evolving nature of memory decline. The goal of this project was to predict and track memory decline in subjectively- or mildly cognitively impaired (MCI) individuals by using a model-based, adaptive fact-learning system. Here we present data demonstrating that these tools can diagnose mild memory impairment with over 80% accuracy after a single 8-minute learning session. These findings provide new insights into the nature and progression of memory decline and may have implications for the early detection and management of Alzheimer’s disease and other forms of dementia.
Electroconvulsive stimuli reverse neuro-inflammation and behavioral deficits in a mouse model of depression
Authors: Rooney Alasdair G , Kilpatrick Alastair M , ffrench-Constant Charles
Published: May 2023

Background

Electroconvulsive therapy is a fast, safe, and effective treatment for severe clinical depression but there is an ongoing search for mechanistic insights.

Methods

We used a mouse neuro-endocrine model of depression to examine behavioral, cellular, and molecular effects of electroconvulsive stimuli (ECS).

Results

The behavioral response to repeated ECS correlated with adult neurogenesis, more strongly in the ventral than dorsal hippocampus. Subsequent RNA-seq analysis targeting the ventral subgranular zone (SGZ) delineated ECS-responsive molecular pathways that were shared between naive and depressive-state conditions, and which may represent core biological responses to seizure induction. Other pathways responded to ECS preferentially in the depressive state, suggesting further state- specific mechanisms. By comparing gene set pathways reciprocally altered in depressed-state animals then reversed by ECS, we identified and validated neuro-inflammation as a candidate regulator of the antidepressant response. We further identified 56 novel candidate ‘antidepressant response’ genes in the ventral SGZ that may contribute to recovery, half of which have been implicated in human neuropsychiatric phenotypes.

Conclusions

Electroconvulsive stimuli reverse neuro-inflammation in a mouse model of depression. The results offer a detailed molecular characterization of potential SGZ antidepressant response-specific genes and pathways in brain regions implicated in depression.
Inactivating Negative Regulators of Cortical Branched Actin Enhances Persistence of Single Cell Migration
Authors: Fokin Artem I. , Boutillon Arthur , James John , Courtois Laura , Vacher Sophie , Simanov Gleb , Wang Yanan , Polesskaya Anna , Bièche Ivan , David Nicolas B. , Gautreau Alexis M.
Published: May 2023

The Rac1-WAVE-Arp2/3 pathway pushes the plasma membrane by polymerizing branched actin at the cell cortex and thereby powering membrane protrusions that mediate cell migration. Here, using knock-down (KD) or knock-out (KO), we combine the inactivation of the Arp2/3 inhibitory protein Arpin, the Arp2/3 subunit ARPC1A and the WAVE complex subunit, CYFIP2, that all enhance the polymerization of cortical branched actin (CBA). Inactivation of the 3 CBA negative regulators increases migration persistence of human breast MCF10A cells, and of endodermal cells in the zebrafish embryo, significantly more than any single or double inactivation. In the triple KO, but not triple KD cells, the “super-migrator” phenotype was associated with a heterogenous down-regulation of vimentin expression and a lack of coordination in collective behaviors, such as wound healing and acinus morphogenesis. Re-expression of vimentin in triple KO cells restored the normal persistence of single cell migration to a large extent, suggesting that vimentin down-regulation is one of the adjustments in gene expression through which the super-migrator phenotype is stably maintained in triple KO cells. Constant excessive production of branched actin at the cell cortex thus commits cells into a motile state through changes in gene expression.
Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates
Authors: Zupancic Jennifer M. , Smith Matthew D. , Trzeciakiewicz Hanna , Skinner Mary E. , Ferris Sean P. , Makowski Emily K. , Lucas Michael J. , McArthur Nikki , Kane Ravi S. , Paulson Henry L. , Tessier Peter M.
Published: May 2023

1.

Single-domain antibodies, also known as nanobodies, are broadly important for studying the structure and conformational states of several classes of proteins, including membrane proteins, enzymes, and amyloidogenic proteins. Conformational nanobodies specific for aggregated conformations of amyloidogenic proteins are particularly needed to better target and study aggregates associated with a growing class of associated diseases, especially neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. However, there are few reported nanobodies with both conformational and sequence specificity for amyloid aggregates, especially for large and complex proteins such as the tau protein associated with Alzheimer’s disease, due to difficulties in selecting nanobodies that bind to complex aggregated proteins. Here, we report the selection of conformational nanobodies that selectively recognize aggregated (fibrillar) tau relative to soluble (monomeric) tau. Notably, we demonstrate that these nanobodies can be directly isolated from immune libraries using quantitative flow cytometric sorting of yeast-displayed libraries against tau aggregates conjugated to quantum dots, and this process eliminates the need for secondary nanobody screening. The isolated nanobodies demonstrate conformational specificity for tau aggregates in brain samples from both transgenic tau mouse models and human tauopathies. We expect that our facile approach will be broadly useful for isolating conformational nanobodies against diverse amyloid aggregates and other complex antigens.
Inhibition of LRRK2 kinase activity rescues deficits in striatal dopamine dynamics in VPS35 p.D620N knock-in mice
Authors: Bu Mengfei , Follett Jordan , Tatarnikov Igor , Wall Shannon , Guenther Dylan , Deng Isaac , Wimsatt Genevieve , Milnerwood Austen , Moehle Mark S. , Khoshbouei Habibeh , Farrer Matthew J.
Published: May 2023

Dysregulation of dopamine neurotransmission profoundly affects motor, motivation and learning behaviors, and is often observed during the prodromal phase of Parkinson’s disease (PD). However, the mechanism underlying these pathophysiological changes remains to be elucidated. Mutations in vacuolar protein sorting 35 (VPS35) and leucine-rich repeat kinase 2 (LRRK2) both lead to autosomal dominant PD, and VPS35 and LRRK2 may physically interact to govern the trafficking of synaptic cargos within the endo-lysosomal network in a kinase-dependent manner. To better understand the functional role of VPS35 and LRRK2 on dopamine physiology, we examined Vps35 haploinsufficient (Haplo) and Vps35 p.D620N knock-in (VKI) mice and how their behavior, dopamine kinetics and biochemistry are influenced by LRRK2 kinase inhibitors. We found Vps35 p.D620N significantly elevates LRRK2-mediated phosphorylation of Rab10, Rab12 and Rab29. In contrast, Vps35 haploinsufficiency reduces phosphorylation of Rab12. While striatal dopamine transporter (DAT) expression and function is similarly impaired in both VKI and Haplo mice, that physiology is normalized in VKI by treatment with the LRRK2 kinase inhibitor, MLi-2. As a corollary, VKI animals show a significant increase in amphetamine induced hyperlocomotion, compared to Haplo mice, that is also abolished by MLi-2. Taken together, these data show Vps35 p.D620N confers a gain-of-function with respect to LRRK2 kinase activation, and VPS35 and LRRK2 functionally interact to regulate DAT trafficking and striatal dopamine neurotransmission.
Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity
Authors: Yanuka-Golub Keren , Belkin Natalia , Weber Nurit , Mayyani Meor , Levy Yehuda , Reznik Itay J. , Rubin-Blum Maxim , Rahav Eyal , Kiro Yael
Published: May 2023

Submarine groundwater discharge (SGD) is a globally important process supplying nutrients and trace elements to the coastal environment, thus playing a pivotal role in sustaining marine primary productivity. Along with nutrients, groundwater also contains allochthonous microbes that are discharged from the terrestrial subsurface into the sea. Currently, little is known about the interactions between groundwater-borne and coastal seawater microbial populations, and their role upon introduction to coastal seawater populations. Here, we investigated seawater microbial abundance, activity and diversity in a site strongly influenced by SGD (in-situobservations), and through laboratory-controlled bottle incubations mimicking different mixing scenarios between SGD (either ambient or filtered through 0.1 µm/0.22 µm) and seawater. Our results demonstrate that the addition of <0.1 µm SGD stimulated heterotrophic activity and increased microbial abundance compared to control, whereas <0.22 µm filtration treatments induced primary productivity rates andSynechococcusgrowth. Amplicon sequencing of the 16S rRNA gene showed a strong shift from a SAR11-rich community in the reference SGD-unaffected coastal samples to aRhodobacteraceae-dominated one in the <0.1 µm treatment, in agreement with theirin-situenrichment in the SGD field site. These results suggest that despite the significant nutrient input, microbes delivered by SGD may affect the abundance, activity and diversity of intrinsic microbes in coastal seawater. Our results highlight the cryptic interplay between groundwater and seawater microbes in coastal environments, which has important implications for carbon cycling and climate.

Key Points:

Groundwater discharge into the coastal zone delivers both nutrients and allochthonous microbes.

Groundwater microbes interact with seawater populations, by which affecting the delicate autotroph-heterotroph balance.

Subterranean microbial processes are key drivers of food webs, potentially affecting biogenic carbon fluxes in the ocean and climate.
CRISPRδ: dCas13-mediated translational repression for accurate gene silencing in mammalian cells
Authors: Apostolopoulos Antonios , Tsuiji Hitomi , Shichino Yuichi , Iwasaki Shintaro
Published: May 2023

Current gene silencing tools based on RNA interference (RNAi) or, more recently, clustered regularly interspaced short palindromic repeats (CRISPR)⃩Cas13 systems, have critical drawbacks, such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR⃩Cas13). Thus, a more specific method of gene knockdown is needed. Here, we developed “CRISPRδ”, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13). Owing to its tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes during translation initiation and does not affect mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy regardless of the translation initiation mechanism: cap-dependent or internal ribosome entry site (IRES)-dependent translation. Strikingly, genome-wide ribosome profiling revealed the extremely high gene knockdown specificity of CRISPRδ. Moreover, fusion of a translational repressor to dCas13 ensured further improvement of the knockdown efficacy. Our method provides a framework for translational repression-based gene silencing in eukaryotes.
A real-time colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of highly pathogenic H5 clade 2.3.4.4b avian influenza viruses
Authors: Filaire Fabien , Sécula Aurélie , Lebre Laetitia , Croville Guillaume , Guerin Jean-Luc
Published: May 2023

Highly pathogenic avian influenza viruses (HPAIV) are a major threat to the global poultry industry and public health due to their zoonotic potential. Since 2016, Europe and France have faced major epizootics caused by clade 2.3.4.4b H5 HPAIV. To reduce sample-to-result times, point-of-care testing is urgently needed to help prevent further outbreaks and the propagation of the virus. This study presents the design of a novel real-time colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of clade 2.3.4.4b H5 HPAIV. A clinical validation of this RT-LAMP assay was performed on 198 pools of clinical swabs sampled in 52 poultry flocks during the H5 HPAI 2020-2022 epizootics in France. This RT-LAMP assay allowed the specific detection of HPAIV H5Nx clade 2.3.4.4b within 30 minutes with a sensitivity of 86.11%. This rapid, easy-to-perform, inexpensive, molecular detection assay could be included in the HPAIV surveillance toolbox.
An automated interface for sedimentation velocity analysis in SEDFIT
Authors: Schuck Peter , To Samuel C. , Zhao Huaying
Published: May 2023

Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
Wnt/β-catenin signaling controls mouse eyelid growth by mediating epithelial-mesenchymal interactions
Authors: Zhu Xuming , Senoo Makoto , Millar Sarah E. , Ma Gang
Published: May 2023

Eyelid closure is required for the development of multiple ocular tissues. Interactions between the epithelium and underlying mesenchyme play a pivotal role in regulating eyelid development. However, the molecular mechanisms underlying these interactions remain unclear. Wnt signaling pathways regulate the development of ocular tissues, but their functions in eyelid development are not fully defined. In this study, we find that deletion of β-catenin in supraorbital mesenchyme abolishes eyelid growth by causing decreased proliferation in supraorbital epithelium and underlying mesenchyme. Inhibition of Wnt secretion by deletingWlsin supraorbital epithelium results in failure of eyelid developing, similar to the effects of deleting mesenchymal β-catenin, suggesting that mesenchymal Wnt/β- catenin signaling is controlled by epithelial Wnt ligands during eyelid development. We also found that deletion ofp63results in formation of hypoplastic eyelids and reduced expression of several Wnt ligands in eyelid epithelium, indicating that expression of Wnt ligands in eyelid development is at least partially regulated by p63. Taken together, our data indicate that Wnt/β-catenin signaling controls eyelid growth by orchestrating epithelial- mesenchymal interactions.
Carotenoid assembly regulates quinone diffusion and theRoseiflexus castenholziireaction center-light harvesting complex architecture
Authors: Xin Jiyu , Shi Yang , Zhang Xin , Yuan Xinyi , Xin Yueyong , He Huimin , Shen Jiejie , Blankenship Robert E. , Xu Xiaoling
Published: May 2023

Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in Roseiflexus castenholzii, a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LHαβ subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome c and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.
In vivo Ontogeny of human forebrain neural progenitor cell grafts in adult rats: an immunohistological study
Authors: Liu Chunhua , Lin Aiping , Xing Qi , Zhang Di , Meng Wei , Wu Rui , Shi Heng , Huang Wenhao , Huang Xiaofen , Qin Dajiang , Wang Xiaoyun , Zhong Xiaofen , Guo Yiping
Published: May 2023

A thorough understanding of the cell behaviors of the human neural grafts is fundamental to exploit them to achieve cell therapy for recovering brain functions. Here by using immunohistological staining, we trace the cell fate of the intrastriatal human neural progenitor cell (NPC) grafts up to 9 months in adult rats, with multiple examining time points to provide a unified working time frame for future transplantation study. Lots of Nestin+/Sox2+ human cells continuously migrate along the white matter tracts into distal brain parenchyma even long time after transplantation, providing a potential for curing diffuse brain damage. Further analysis reveals a significant heterogeneity of the long-term sustained neural stem cells (NSC)/NPCs that progressing throughout different stages, mimicking the neural development of human forebrain. More importantly, the initial GFAP expression in human grafts marks the NSC progression instead of terminal astrocyte differentiation. The distally migrating human cells continuously show the capability to produce new neurons, albeit at a low efficiency in the intact brain. Further investigations in neural disease models are needed. Such study would benefit neural cell therapy with regarding to the optimization of the transplantation strategy and choosing of acting mode by neural grafts (e.g. via cell replacement orex vivogene therapy).
Date milk enriched with vitamin D: nutrient content and acceptability as a food additive for preschoolers 48-59 months
Authors: Jufri Nurnashriana , Marliyati Sri Anna , Anwar Faisal , Ekayanti Ikeu
Published: May 2023

Products that combine liquid milk and date flesh are still minimal. Milk is an excellent source of protein and dates are a food ingredient that is rich in vitamins and minerals that are suitable for growth as well as phytochemical components which function to enhance the sensory properties of dates so that they can be used as a flavor enhancer in various dairy products such as cookies, yogurt, ice cream, and cakes. The purpose of this study was to create a vitamin D-enriched date milk product as an alternative nutritional supplement for preschool children aged 48-59 months. The study used a completely randomized design with three percentage addition of date flesh treatments, namely F1 (10%), F2 (15%), and F3 (20%). The results showed that the formulas significantly differed between the water, protein, and carbohydrate contents (P < 0.05). In contrast, the energy, ash, fat, zinc, iron, and calcium content were not statistically significant (P > 0.05). Kruskal-Wallis analysis product acceptance data showed only color and aroma attributes that were quite different between formulas (P < 0.05). In contrast, taste, thickness, mouthfeel, aftertaste, and overall characteristics were not statistically different (P > 0.05). Formula F2 (15%) was selected based on the hedonic rating and ranking tests. Formula F2 (15%) can be accepted quite well, with the percentage that consumes drinks without residue as much as 60% and those who can finish at least ½ portion of drinks as much as 93.3%.
Halogen bonds, chalcogen bonds, pnictogen bonds, tetrel bonds and other σ-hole interactions: a snapshot of current progress
Authors: Brammer Lee , Peuronen Anssi , Roseveare Thomas M.
Published: May 2023

We report here on the status of research on halogen bonds and other σ-hole interactions involvingp-block elements in Lewis acidic roles, such as chalcogen bonds, pnictogen bonds and tetrel bonds. A brief overview of the available literature in this area is providedviaa survey of the many review articles that address this field. Our focus has been to collect together most review articles published since 2013 to provide an easy entry into the extensive literature in this area. A snapshot ofcurrentresearch in the area is provided by an introduction to the virtual special issue compiled in this journal, comprising 11 articles and entitled `Halogen, chalcogen, pnictogen and tetrel bonds: structural chemistry and beyond.'
The determinants of job satisfaction amongst specific migrant construction workers
Authors: Rotimi Funmilayo Ebun , Rotimi James Olabode Bamidele , Silva C.W. Chathurani , Olatunji Oluwole Alfred , Ramanayaka Chamil Erik D.
Published: May 2023

Purpose

Migrant construction workers, significant in many developed economies, face several challenges, which place them at a higher risk of job dissatisfaction compared to locals. Therefore, this study investigates the determinants of job satisfaction amongst a specific group of migrant construction workers, who hold temporary work visas (TWVs) in New Zealand (NZ).

Design/methodology/approach

An explanatory research approach was used to investigate the determinants of job satisfaction identified through the literature review. Data were collected through a structured survey administered to 200 Chinese migrants on TWVs (short stays) working on selected major projects in the Auckland region. Data analysis involved T-test and structural equation modelling (SEM) of 102 valid questionnaire responses.

Findings

The study highlights the importance of providing opportunities for knowledge advancement and career progression for migrant construction workers to improve their job satisfaction. The results found that Chinese migrant construction workers are generally satisfied with their jobs and would extend their stay if job opportunities are provided. The results confirm that remuneration and opportunities for knowledge advancement and career progression lead to increased job satisfaction, while loneliness decreases job satisfaction. The opportunities for knowledge advancement and career progression triggered more satisfaction than remuneration.

Originality/value

The research result provides a useful knowledge base for understanding the determinants of job satisfaction amongst Chinese migrant construction workers with TWVs. These findings have implications for employment management practices within the construction industry and could enhance immigration information policies and other recruitment agencies' approaches to sourcing overseas workers for the NZ construction industry.
Stakeholder collaboration to mitigate constraints to delivering low-carbon buildings: insights from high-rise high-density cities
Authors: Hewa Welege Nandun Madhusanka , Pan Wei , Kumaraswamy Mohan
Published: May 2023

Purpose

Despite carbon reduction commitments, many constraints hinder the delivery of low-carbon buildings (LCBs) in high-rise high-density cities. The collaborative commitment of relevant stakeholders is vital to effectively address and mitigate these constraints. Hence, this study aims to comprehensively explore the required stakeholder collaboration attributes to address and mitigate the “common” constraints of delivering LCBs by focussing on several high-rise high-density cities.

Design/methodology/approach

A list of 21 “significant and common” constraints was identified through a systematic literature review followed by a questionnaire survey covering five economies (Hong Kong, Singapore, Australia, Qatar and the UAE). Nineteen influential stakeholders/stakeholder categories were identified through the literature, and their ability to influence the 21 constraints was mapped and identified through a two-round Delphi survey of 15 experienced professionals. The Delphi survey findings were analysed through social network analysis (SNA) methods to assess the stakeholder engagement and collaboration attributes.

Findings

The SNA results revealed the ability of stakeholders to influence the constraints, required collaborative stakeholder networks to address the constraints, significance of stakeholders according to the SNA centrality measures, core and periphery stakeholders and individual co-affiliation networks of core stakeholders.

Originality/value

While achieving the planned primary target of exploring stakeholder collaboration and their significance through SNA, this study also presents a useful sequential methodological approach for future researchers to conduct similar studies in different contexts. The findings also provide a foundation for accelerating the delivery of LCBs by strengthening stakeholder collaboration.
Governing FinTech for performance: the monitoring role of female independent directors
Authors: Arena Claudia , Catuogno Simona , Naciti Valeria
Published: May 2023

Purpose

The use of digital technologies in the financial service industry has brought new complexities to the corporate governance in banks. Relying on the agency perspective of the shareholder, debtholder and societal governance in banks, this research examines the impact of financial technology innovation (FinTech) on banks' performance by enlightening the monitoring role of female independent directors.

Design/methodology/approach

Relying on a sample of Italian banks observed during the period 2016–2020, the authors hand-collected data on the use of FinTech by considering (1) the in-house provisions of FinTech solutions, (2) the collaboration with external FinTech firms and (3) a combination of both measures. The authors run a panel data regression analysis with fixed effects, measuring bank performance through bank competitiveness and bank riskiness.

Findings

The authors find that FinTech increases bank competitiveness in gathering money from depositors and that independent women on board mitigate the negative relationship between FinTech and the riskiness of banks' assets, ameliorating the conflicting interests among shareholders, debtholder and societal governance.

Originality/value

This study emphasizes the complexities of bank governance when dealing with FinTech in the wider perspective of equity governance, debt governance and the societal governance spotlighting the importance of appointing female directors in independent positions to enhance the bright sides of financial innovation. The authors enrich the literature on FinTech with a finer understanding of the drivers and implications of in-house provisions of FinTech solutions versus the collaboration with external FinTech firms.
Knowing how satisfied/dissatisfied is far from enough: a comprehensive customer satisfaction analysis framework based on hybrid text mining techniques
Authors: Yang Tong , Wu Jie , Zhang Junming
Published: May 2023

Purpose

This study aims to establish a comprehensive satisfaction analysis framework by mining online restaurant reviews, which can not only accurately reveal consumer satisfaction but also identify factors leading to dissatisfaction and further quantify improvement opportunity levels.

Design/methodology/approach

Adopting deep learning, Cross-Bidirectional Encoder Representations Transformers (BERT) model is developed to measure customer satisfaction. Furthermore, opinion mining technique is used to extract consumers’ opinions and obtain dissatisfaction factors. Furthermore, the opportunity algorithm is introduced to quantify attributes’ improvement opportunity levels. A total of 19,133 online reviews of 31 restaurants in Universal Beijing Resort are crawled to validate the framework.

Findings

Results demonstrate the superiority of Cross-BERT model compared to existing models such as sentiment lexicon-based model and Naïve Bayes. More importantly, after effectively unveiling customer dissatisfaction factors (e.g. long queuing time and taste salty), “Dish taste,” “Waiters’ attitude” and “Decoration” are identified as the three secondary attributes with the greatest improvement opportunities.

Practical implications

The proposed framework helps managers, especially in the restaurant industry, accurately understand customer satisfaction and reasons behind dissatisfaction, thereby generating efficient countermeasures. Especially, the improvement opportunity levels also benefit practitioners in efficiently allocating limited business resources.

Originality/value

This work contributes to hospitality and tourism literature by developing a comprehensive customer satisfaction analysis framework in the big data era. Moreover, to the best of the authors’ knowledge, this work is among the first to introduce opportunity algorithm to quantify service improvement benefits. The proposed Cross-BERT model also advances the methodological literature on measuring customer satisfaction.
Who is cooperative in negotiations? The impact of political skill on cooperation, reputation and outcomes
Authors: Tasa Kevin , Bahmani Mehran
Published: May 2023

Purpose

The purpose of this study is to predict cooperation in negotiation through the lens of individual differences. Specifically, this paper examines how a social competence variable called “political skill” relates to cooperation and subsequent effects on negotiation process, outcomes and negotiator reputation. The authors demonstrate how political skill fits in the evolving literature focusing on individual differences in negotiation by comparing political skill to a wide range of other individual difference measures.

Design/methodology/approach

This study was conducted by assessing individual difference measures at the beginning of graduate-level negotiation courses and tracking negotiation behaviors and outcomes over several months. This approach was chosen to minimize the potential for short, time-limited interactions to mask existing relationships. It also allowed the authors to include multiple negotiation interactions, which takes a broader view of negotiation performance, and assess negotiator reputation by allowing it to emerge over time.

Findings

The results of this study show that political skill, self-rated at the beginning of this study, is significantly related to a negotiator’s overall use of cooperative behavior as rated by peers. Political skill also showed a significant relationship with reputation for cooperativeness and aggregate outcomes in negotiations. These results control for other individual difference measures such as personality, implicit negotiation beliefs, social value orientation and negotiation self-efficacy.

Originality/value

Using a method that allows the effects of an individual difference to materialize over time, this study empirically establishes the connection between political skill and negotiation reputation, process and outcomes. The methodological contributions of this study explore the relations between self-rated individual difference variables, peer-rated cooperative behaviors and objective coded negotiation outcomes in evaluating political skill in negotiation.
An impact analysis of macroeconomic factors on South Asia’s renewable energy output
Authors: Khan Imran , Gunwant Darshita Fulara
Published: May 2023

Purpose

South Asia is one of the fastest-growing regions in the world. With its fast economic development, the energy requirement for the region has rapidly grown. As the region relies mainly on nonrenewable energy sources and is suffering from issues like pollution, the high cost of energy imports, depleting foreign reserves, etc. it is searching for those factors that can help enhance the renewable energy generation for the region. Thus, taking these issues into consideration, this paper aims to investigate the impact of macroeconomic factors that can contribute to the enhancement of renewable energy output in South Asia.

Design/methodology/approach

An autoregressive distributed lag methodology has been applied to examine the long-term effects of remittance inflows, literacy rate, energy imports, government expenditures and urban population growth on the renewable energy output of South Asia by using time series data from 1990 to 2021.

Findings

The findings indicated that remittance inflows have a negative and insignificant long-term effect on renewable electricity output. While it was discovered that energy imports, government spending and urban population growth have negative but significant effects on renewable electricity output, literacy rates have positive and significant effects.

Originality/value

Considering the importance of renewable energy, this is one of the few studies that has included critical macroeconomic variables that can affect renewable energy output for the region. The findings contribute to the body of knowledge that a high literacy level is crucial for promoting renewable energy output, while governments and policymakers should prioritize reducing energy imports and ensuring that government expenditures on renewable energy output are properly used. SAARC, the governing body of the region, also benefits from this study while devising the renewable energy output policies for the region.
SME owners and accountants' perceptions of financial information in small- and medium-sized entities: a Sri Lanka case study
Authors: Wijekoon Nisansala , Sharma Umesh , Samkin Grant
Published: May 2023

Purpose

This paper aims to examine the perceptions of owners and accountants of small- and medium-sized entities (SMEs) on the users and their financial information needs of SME financial reporting.

Design/methodology/approach

Postal questionnaire surveys with owners and accountants of SMEs were used to identify users and their financial information needs. In total, 1,498 questionnaires were sent to SME owners and accountants. A total of 358 questionnaires were returned, generating 323 useable questionnaires. The management branch of stakeholder theory is used for the study which asserts that company management is expected to meet the expectations of those stakeholders who are more powerful than others.

Findings

The users of Sri Lanka SME financial information were limited to owners, banks and Department of Inland Revenue. Users and financial information needs of owners varied in relation to the size of the SME. Financial information are useful for making capital investment and planning decisions for owners regardless of the size of the SME. By sharing information with outside parties, disclosures can diminish information asymmetries between the firms and its stakeholders. The top three reasons for which owners use SME financial information are for planning purposes, estimating income tax liabilities, and taking marketing and pricing decisions.

Research limitations/implications

Since the study focuses only on the views of owner-managers and accountants of SMEs, the holistic understanding of uses of SME financial information by other user groups cannot be achieved.

Practical implications

The results of this study provide international and local standard setters with an indication of future direction for SME financial reporting.

Social implications

This paper extends existing knowledge on users and their financial information needs of SMEs in developing countries. Consequently, the findings of this paper make a valuable contribution to the work of practitioners such as local and international standards-setters and regulators who may be considering developing/revising financial reporting framework for SMEs either worldwide or in developing countries.

Originality/value

Although SME financial reporting has attracted enormous attention in the recent accounting literature, academic research into SME financial reporting is scant. This paper extends existing knowledge on users and their financial information needs of SMEs in developing countries. The general purpose financial reporting model and the accounting standard IFRS for SMEs in particular would not be applicable to Sri Lankan SMEs unless it modifies to reflect the financial information needs of users of Sri Lankan SME financial information.