bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping host-microbe transcriptional interactions by dual perturb-seq
Authors: Butterworth Simon , Kordova Kristina , Chandrasekaran Sambamurthy , Thomas Kaitlin K. , Torelli Francesca , Lockyer Eloise J. , Edwards Amelia , Goldstone Robert , Koshy Anita A. , Treeck Moritz 
Published: April 2023

SUMMARYIntracellular pathogens and other endosymbionts reprogram host cell transcription to suppress immune responses and recalibrate biosynthetic pathways. This reprogramming is critical in determining the outcome of infection or colonisation. Here, we combine pooled CRISPR knockout screening with dual host–microbe single-cell RNA-sequencing to identify the molecular mediators of these transcriptional interactions, a method we term dual perturb-seq. Applying dual perturb-seq to the intracellular pathogenToxoplasma gondii, we are able to identify previously uncharacterised effector proteins and directly infer their function from the transcriptomic data. We show thatTgGRA59 contributes to the export of other effector proteins from the parasite into the host cell and identify a novel effector,TgSOS1, that is necessary for sustained host STAT6 signalling and thereby contributes to parasite immune evasion and persistence. Together, this work demonstrates a novel tool that can be broadly adapted to interrogate host-microbe transcriptional interactions and reveal mechanisms of infection and immune evasion.
Experience Shapes Chandelier Cell Function and Structure in the Visual Cortex
Authors: Seignette Koen , Jamann Nora , Papale Paolo , Terra Huub , Porneso Ralph P. O. , de Kraker Leander , van der Togt Chris , van der Aa Maaike , Neering Paul , Ruimschotel Emma , Roelfsema Pieter R. , Montijn Jorrit S. , Self Matthew W. , Kole Maarten H. P. , Levelt Christiaan N. 
Published: April 2023

AbstractDetailed characterization of interneuron types in primary visual cortex (V1) has greatly contributed to understanding visual perception, yet the role of chandelier cells (ChCs) in visual processing remains poorly characterized. Using viral tracing we found that V1 ChCs predominantly receive monosynaptic input from local layer 5 pyramidal cells and higher-order cortical regions. Two-photon calcium imaging and convolutional neural network modelling revealed that ChCs are visually responsive but weakly selective for stimulus content. In mice running in a virtual tunnel, ChCs respond strongly to events known to elicit arousal, including locomotion and visuomotor mismatch. Repeated exposure of the mice to the virtual tunnel was accompanied by reduced visual responses of ChCs and structural plasticity of ChC boutons and axon initial segment length. Finally, ChCs only weakly inhibited pyramidal cells. These findings suggest that ChCs provide an arousal-related signal to layer 2/3 pyramidal cells that may modulate their activity and/or gate plasticity of their axon initial segments during behaviorally relevant events.
Thermoregulatory consequences of growing up during a heatwave or a cold snap
Authors: Persson Elin , Cuív Ciarán Ó , Nord Andreas 
Published: April 2023

AbstractChanges in environmental temperature during the developmental period can affect growth, metabolism, and temperature tolerance of the offspring. We know little about whether such changes remain to adulthood, which is important to understand the links between climate change, development, and fitness. We investigated if phenotypic consequences of the thermal environment in early life remained in adulthood in two studies on Japanese quail (Coturnix japonica). Birds were raised under simulated heatwave-, cold snap-or control conditions, from hatching until halfway through the growth period, and then in a common garden until reproductively mature. We measured biometric and thermoregulatory (metabolic heat production [MHP], evaporative water and heat loss [EWL, EHL] and body temperature) responses to variation in submaximal air temperature at the end of the thermal acclimation period and in adulthood. Warm birds had lower MHP than control birds at the end of the thermal acclimation period and, in the warmest temperature studied (40°C), also had higher evaporative cooling capacity compared to controls. No analogous responses were recorded in cold birds, though they had higher EWL than controls in all but the highest test temperature. None of the effects found at the end of the heatwave-or cold snap period remained until adulthood. This implies that chicks exposed to higher temperatures could be more prepared to counter heat stress as juveniles, but that they do not enjoy any advantages of such developmental conditions when facing high temperatures as adults. Conversely, cold temperature does not seem to confer any priming effects in adolescence.
Worldwide population genomics reveal long-term stability of the mitochondrial chromosome composition in a keystone marine plant
Authors: Khachaturyan Marina , Reusch Thorsten B. H. , Dagan Tal 
Published: April 2023

AbstractMitochondrial genomes (mitogenomes) of flowering plants are comprised of multiple chromosomes. Their copy number and composition can be dynamic within and among individual plants due to uneven replication of the chromosomes and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitochondrial chromosome composition of the seagrassZostera marinais conserved among worldwide populations that diverged ca 350,000 years ago. Using long-read sequencing we characterized theZ. marinamitochondrial genome and inferred the repertoire of recombination-induced configurations of its eight chromosomes. To characterize the chromosome composition worldwide and study its evolution we examined the mitogenome inZ. marinameristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the chromosome copy number suggesting stable equal proportions among distantly related populations and a high conservation of the mitochondrial genome within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.Significance statementExtensive studies on evolution of plant mitochondria in individual plants revealed great variability of the mitogenome architecture across tissues, however, data on the mitochondrion evolution at the population level is still scarce. We show that the mitochondrial genome architecture in a keystone marine plant,Zostera marina, remained conserved over ca. 350,000 years worldwide. We suggest that the extreme conservation of theZ. marinamitochondria is a manifestation of streamlined mitochondria inheritance over plant generations, e.g., via a plant germline.
Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering
Authors: Barone Federico , Russo Elena Tea , Villegas Garcia Edith Natalia , Punta Marco , Cozzini Stefano , Ansuini Alessio , Cazzaniga Alberto 
Published: April 2023

AbstractTechnological advances in massively parallel sequencing have led to an exponential growth in the number of known protein sequences. Much of this growth originates from metagenomic projects producing new sequences from environmental and clinical samples. The Unified Human Gastrointestinal Proteome (UHGP) catalogue is one of the most relevant metagenomic datasets with applications ranging from medicine to biology. However, the lack of sequence annotation impairs its usability. This work aims to produce a family classification of UHGP sequences to facilitate downstream structural and functional annotation. This is achieved through the release of theDPCfam-UHGP50 datasetcontaining 10,778 putative protein families generated using DPCfam clustering, an unsupervised pipeline grouping sequences into multi-domain architectures. DPCfam-UHGP50 considerably improves family coverage at protein and residue levels compared to the manually curated repository Pfam. It is our hope that DPCfam-UHGP50 will foster future discoveries in the field of metagenomics of the human gut by the release of a FAIR-compliant database easily accessible via a searchable web server and Zenodo repository.
White matter plasticity during second language learning within and across hemispheres
Authors: Wei Xuehu , Gunter Thomas C. , Adamson Helyne , Schwendemann Matthias , Friederici Angela D. , Goucha Tomás , Anwander Alfred 
Published: April 2023

AbstractAdult second language (L2) learning is a challenging enterprise inducing neuroplastic changes in the human brain. However, it remains unclear how the structural language connectome and its subnetworks change during adult L2-learning. The current study investigated longitudinal changes in white matter (WM) language networks in each hemisphere, as well as their interconnection, in a large group of Arabic-speaking adults who learned German intensively for six months. We found a significant increase in WM-connectivity within bilateral temporal-parietal semantic and phonological subnetworks and right temporal-frontal pathways mainly in the second half of the learning period. At the same time, WM-connectivity between the two hemispheres decreased significantly. Crucially, these changes in WM-connectivity are correlated with L2 performance. The observed changes in subnetworks of the two hemispheres suggest a network reconfiguration due to lexical learning. The reduced interhemispheric connectivity may indicate a key role of the corpus callosum in L2-learning by reducing the inhibition of the language-dominant left hemisphere. Our study highlights the dynamic changes within and across hemispheres in adult language-related networks driven by L2 learning.SignificanceThe neuroplastic changes induced by learning a second language (L2) in adulthood open up new perspectives for understanding brain function. The current study shows structural changes in the language network of Arabic native speakers who learned German intensively in two phases of three months each. We found a marked change in the left-hemispheric lexical-semantic language system and the right fronto-temporal pathway, accompanied by a decrease in white matter connectivity in the corpus callosum during L2 learning, which occurred mainly in the second period of L2 acquisition. The reduced interhemispheric connectivity suggests that the inhibitory role of the corpus callosum, relevant for native language processing, is reduced by L2 learning. Our findings demonstrate a clear experience-dependent structural plasticity in the human brain during L2 learning.
Unlocking Trypanosome Biology: A Comprehensive Protein-Tagging Toolkit for Localization and Functional Analysis
Authors: Paterou Athina , Týč Jiří , Sunter Jack , Vaughan Sue , Gull Keith , Dean Samuel 
Published: April 2023

AbstractAfrican trypanosomes are medically important parasites that cause Sleeping sickness in humans and nagana in animals. In addition to their pathogenic role, they have emerged as valuable model organisms for studying fundamental biological processes. Protein tagging is a powerful tool for investigating protein localization and function. In a previous study, we developed two plasmids for rapid and reproducible protein tagging in trypanosomes, which enabled the localisation of all proteins in the trypanosome cell. However, the limited selection of fluorescent protein tags and selectable markers restricted the flexibility of this approach. Here, we present an expanded set of >100 vectors that utilizes universal primer annealing sequences, enabling protein tagging with a range of fluorescent and biochemical tags using five different selection markers. We evaluated the suitability of various fluorescent proteins for live cell imaging and determined their brightness and stability under different fixation conditions. Finally, we determined the optimal fluorescent protein for a set of specific experimental conditions demonstrating the utility of this toolkit.
Candida aurisundergoes adhesin-dependent and -independent cellular aggregation
Authors: Pelletier Chloe , Shaw Sophie , Alsayegh Sakinah , Brown Alistair J. P. , Lorenz Alexander 
Published: April 2023

AbstractCandida aurisis a fungal pathogen of humans responsible for nosocomial infections with high mortality rates. High levels of resistance to antifungal drugs and environmental persistence mean these infections are difficult to treat and eradicate from a healthcare setting. Understanding the life cycle and the genetics of this fungus underpinning clinically relevant traits, such as antifungal resistance and virulence, is of the utmost importance to develop novel treatments and therapies. Epidemiological and genomic studies have identified five geographical clades (I-V), which display phenotypic and genomic differences. Aggregation of cells, a phenotype primarily of clade III strains, has been linked to reduced virulence in mouse andGalleria mellonellainfection models. The aggregation phenotype has thus been associated with conferring an advantage for (skin) colonisation rather than for systemic infection. However, strains with different clade affiliations were compared to infer the effects of different morphologies on virulence. This makes it difficult to distinguish morphology-dependent causes from clade-specific or even strain-specific genetic factors. Here, we identify two different types of aggregation: one induced by antifungal treatment which is a result of a cell separation defect; and a second which is controlled by growth conditions and only occurs in strains with the ability to aggregate. The latter aggregation type depends on an ALS-family adhesin which is differentially expressed during aggregation in an aggregativeC. aurisstrain. Finally, we demonstrate that macrophages cannot clear aggregates, suggesting that aggregation might after all provide a benefit during systemic infection and could facilitate long-term persistence in the host.Author SummaryCandida aurisis a single-celled fungus, a yeast, that can cause severe infections in hospital patients. This fungus is difficult to treat because it is resistant to many antifungal drugs. Therefore, to understand the processes that enhance the virulence of this yeast with a view to developing new treatments. Previous studies have found thatC. auriscan form aggregates, or clumps of cells, which may play a role in how the fungus infects people. In this study, we identified two different types of aggregation inC. auris, one triggered by antifungal treatment, and another controlled by growth conditions. This discovery allowed us to study aggregate formation in the same genetic background. In doing so, we found that a certain protein, an ALS-family adhesin, is involved in the aggregation process. Surprisingly, we also discovered that aggregates may promote infection by making it harder for the immune system to clear the yeast. This new understanding could help researchers develop better ways to fightC. aurisinfections.
A Human Breast Cell Atlas Mapping the Homeostatic Cellular Shifts in the Adult Breast
Authors: Reed Austin D. , Pensa Sara , Steif Adi , Stenning Jack , Kunz Daniel J. , He Peng , Twigger Alecia-Jane , Kania Katarzyna , Barrow-McGee Rachel , Goulding Iain , Gomm Jennifer J. , Jones Louise , Marioni John C. , Khaled Walid T. 
Published: April 2023

AbstractOne of the barriers for breast cancer prevention and treatment is our poor understanding of the dynamic cellular shifts that naturally occur within the breast and how these changes contribute to tumour initiation. In this study we report the use of single cell RNA sequencing (scRNAseq) to compile a Human Breast Cell Atlas (HBCA) assembled from 55 donors that had undergone reduction mammoplasties or risk reduction mammoplasties. The data from more than 800,000 cells identified 41 cell subclusters distributed across the epithelial, immune, and stromal compartments. We found that the contribution of these different clusters varied according to the natural history of the tissue. Breast cancer risk modulating factors such as age, parity, and germline mutation affected the homeostatic cellular state of the breast in different ways however, none of the changes observed were restricted to any one cell type. Remarkably, we also found that immune cells fromBRCA1/2carriers had a distinct gene expression signature indicative of potential immune exhaustion. This suggests that immune escape mechanisms could manifest in non-cancerous tissues during very early stages of tumour initiation. Therefore, the Atlas presented here provides the research community with a rich resource that can be used as a reference for studies on the origins of breast cancer which could inform novel approaches for early detection and prevention.
Exploring the potential of copper oxide biogenic synthesis: a review article on the biomedical and dental implementations
Authors: Mahmood Rana I. , Mohammed-Salih Harraa S. , Ghazi Ata’a , Abdulbaqi Hikmat J. , Al-Obaidi Jameel R. 
Published: April 2023

PurposeIn the developing field of nano-materials synthesis, copper oxide nanoparticles (NPs) are deemed to be one of the most significant transition metal oxides because of their intriguing characteristics. Its synthesis employing green chemistry principles has become a key source for next-generation antibiotics attributed to its features such as environmental friendliness, ease of use and affordability. Because they are more environmentally benign, plants have been employed to create metallic NPs. These plant extracts serve as capping, stabilising or hydrolytic agents and enable a regulated synthesis as well.Design/methodology/approachOrganic chemical solvents are harmful and entail intense conditions during nanoparticle synthesis. The copper oxide NPs (CuO-NPs) synthesised by employing the green chemistry principle showed potential antitumor properties. Green synthesised CuO-NPs are regarded to be a strong contender for applications in the pharmacological, biomedical and environmental fields.FindingsThe aim of this study is to evaluate the anticancer potential of CuO-NPs plant extracts to isolate and characterise the active anticancer principles as well as to yield more effective, affordable, and safer cancer therapies.Originality/valueThis review article highlights the copper oxide nanoparticle's biomedical applications such as anticancer, antimicrobial, dental and drug delivery properties, future research perspectives and direction are also discussed.
HRM challenges in Slovakia generated by the Covid-19 pandemic
Authors: Szeiner Zsuzsanna , Juhász Tímea , Hevesi Endre , Poór József 
Published: April 2023

PurposeThe article analyzes the challenges Slovak businesses and organizations are facing in relation to the Covid-19 pandemic and the resulting human resource management solutions they apply.Design/methodology/approachThe authors present a part of their research conducted in six Central Eastern European (CEE) countries. Based on timely data, the article presents socioeconomic characteristics of Slovakia and the results of the research “HRM Challenges in Times of the Covid-19 Crisis” conducted among employers in Slovakia. The survey method encompassed 247 Slovakian organizations.FindingsThe year 2020 was an extraordinary one for businesses, governments, and individuals alike. According to the results of this research, Slovak organizations were not prepared for the Covid-19 crisis. Respondents who had a pandemic action plan at the time of the breakout were hardly found. Measures taken to preserve human health directly impacted the way how work is done and organized. This poses significant challenges for both employers and employees. In general, small organizations used cost and staff reduction tools. On the other hand, some of the respondents, mainly large organizations have been using future-oriented solutions, e.g. organizational development.Originality/valueIn this research the authors analyzed the experiences of a Central European country, namely Slovakia. However, the experiences gained and collected here can be useful in the international arena as well.
Community mobilisation and collaboration through innovative approaches to overcome significant disasters: an analysis of the biggest earthquake in Turkish history
Authors: Temel Serdal , Durst Susanne 
Published: April 2023

PurposeThis commentary aims to provide an overview of how innovation in community mobilisation and collaboration can help address natural disasters quickly and more effectively. This is done using the example of the earthquake that hit Turkey and Syria and caused considerable damage, the full extent of which cannot yet be assessed.Design/methodology/approachThis commentary was prepared by two researchers who collected a number of examples and assessed their contribution to earthquake mitigation.FindingsThis commentary confirms that applying digital technologies and other innovative approaches to disaster management can mobilise people and contribute to more effective disaster management, especially in disasters where every minute counts.Originality/valueThis commentary explains the role of active mobilisation of civil society using digital technologies and other innovative approaches during one of humanity's largest earthquakes. As far as the authors are aware, this issue has not yet been discussed in this way in contemporary literature.
Which of the book recommendation sections is the most similar to the user selections in LibraryThing?
Authors: Momeni Atefeh , Pashootanizadeh Mitra , Kaedi Marjan 
Published: April 2023

Purpose
This study aims to determine the most similar set of recommendation books to the user selections in LibraryThing.

Design/methodology/approach
For this purpose, 30,000 tags related to History on the LibraryThing have been selected. Their tags and the tags of the related recommended books were extracted from three different recommendations sections on LibraryThing. Then, four similarity criteria of Jaccard coefficient, Cosine similarity, Dice coefficient and Pearson correlation coefficient were used to calculate the similarity between the tags. To determine the most similar recommended section, the best similarity criterion had to be determined first. So, a researcher-made questionnaire was provided to History experts.

Findings
The results showed that the Jaccard coefficient, with a frequency of 32.81, is the best similarity criterion from the point of view of History experts. Besides, the degree of similarity in LibraryThing recommendations section according to this criterion is equal to 0.256, in the section of books with similar library subjects and classifications is 0.163 and in the Member recommendations section is 0.152. Based on the findings of this study, the LibraryThing recommendations section has succeeded in introducing the most similar books to the selected book compared to the other two sections.

Originality/value
To the best of the authors’ knowledge, itis for the first time, three sections of LibraryThing recommendations are compared by four different similarity criteria to show which sections would be more beneficial for the user browsing. The results showed that machine recommendations work better than humans.