bluuebunny/crossref_metadata_2025_split huggingface dataset:
BiœmuS: A new tool for neurological disorders studies through real-time emulation and hybridization using biomimetic Spiking Neural Network
Authors: Beaubois Romain , Cheslet Jérémy , Duenki Tomoya , Khoyratee Farad , Branchereau Pascal , Ikeuchi Yoshiho , Lévi Timothée 
Published: September 2023

AbstractCharacterization and modeling of biological neural networks has emerged as a field driving significant advancements in our understanding of brain function and related pathologies. As of today, pharmacological treatments for neurological disorders remain limited, pushing the exploration of promising alternative approaches such as electroceutics. Recent research in bioelectronics and neuromorphic engineering have led to the design of the new generation of neuroprostheses for brain repair.However, its complete development requires deeper understanding and expertise in biohybrid interaction. Here, we show a novel real-time, biomimetic, cost-effective and user-friendly neural network for bio-hybrid experiments and real-time emulation. Our system allows investigation and reproduction of biophysically detailed neural network dynamics while promoting cost-efficiency, flexibility and ease of use. We showcase the feasibility of conducting biohybrid experiments using standard biophysical interfaces and various biological cells as well as real-time emulation of complex models. We anticipate our system to be a step towards developing neuromorphicbased neuroprostheses for bioelectrical therapeutics by enabling communication with biological networks on a similar time scale, facilitated by an easy-to-use and accessible embedded real-time system. Our real-time device further enhances its potential for practical applications in biohybrid experiments.
A transcription factor module mediating C2photosynthesis
Authors: Dickinson Patrick J. , Triesch Sebastian , Schlüter Urte , Weber Andreas P.M. , Hibberd Julian M. 
Published: September 2023

ABSTRACTC4photosynthesis has arisen from the ancestral C3state in over sixty lineages of angio-sperms. It is widely accepted that an early step in C4evolution is restriction of glycine decarboxylase activity to bundle sheath cells to generate the so-called C2pathway. In C2Moricandiaspecies, changes to thecis-regulatory region controlling expression of the P-subunit ofGLYCINE DECARBOXYLASE(GLDP) in mesophyll cells enables this trait, but the mechanism underpinningGLDPexpression in the bundle sheath is not known. We identify a MYC-MYB transcription factor module previously associated with the control of glucosinolate bio-synthesis as the basis ofGLDPexpression in bundle sheath cells. In C3Arabidopsis thalianathis module drivesGLDPexpression in bundle sheath cells along with as yet unidentified factors driving expression in mesophyll cells. In the C2speciesMoricandia arvensis, GLDPexpression is lost from mesophyll cells and the MYC-MYB dependent expression in the bundle sheath is revealed. Evolution of C2photosynthesis is thus associated with a MYC-MYB based transcriptional network already present in the C3state. This work identifies a molecular genetic mechanism underlying the bundle sheath accumulation of glycine decarboxylase required for C2photosynthesis and thus a foundational step in the evolution of C4photosynthesis.
Changes in lipid metabolism track with the progression of neurofibrillary pathology in tauopathies
Authors: Olešová Dominika , Dobešová Dana , Majerová Petra , Brumarová Radana , Kvasnička Aleš , Kouřil Štěpán , Stevens Eva , Hanes Jozef , Fialová Ľubica , Michalicová Alena , Piešťanský Juraj , Friedecký David , Kováč Andrej 
Published: September 2023

AbstractBackgroundAbnormal aggregation of tau protein that leads to brain inclusions is a common feature of neurodegenerative disorders called tauopathies. Recent evidence suggests the involvement of lipid metabolic deregulations in the pathogenesis of tauopathies. However, the role of tau protein in the regulation of lipid metabolism is much less characterized and not well understood.MethodsWe used a transgenic rat model for tauopathy to reveal metabolic alterations induced by neurofibrillary pathology. Transgenic rats express a tau fragment truncated at the N-and C-terminals. For phenotypic profiling, we performed targeted metabolomic and lipidomic analysis of brain tissue, CSF, and plasma, based on the LC-MS platform. To monitor disease progression, we employed samples from transgenic and control rats aged 4, 6, 8, 10, 12, and 14 months. To study neuron-glia interplay in lipidome changes induced by pathological tau we used well well-established multicomponent cell model system. Univariate and multivariate statistical approaches were used for data evaluation.ResultsWe showed that tau has an important role in the deregulation of lipid metabolism. In the lipidomic study, pathological tau was associated with higher production of lipids participating in protein fibrillization, membrane reorganization, and inflammation. Interestingly, significant changes have been found in the early stages of tauopathy before the formation of high-molecular-weight tau aggregates and neurofibrillary pathology. Increased secretion of pathological tau proteinin vivoandin vitroinduced upregulated production of phospholipids and sphingolipids and accumulation of lipid droplets in microglia. During the later stages of tauopathy, we found a connection between the transition of tau into an insoluble fraction and changes in brain metabolism. The results showed that dysregulation of lipid composition by pathological tau leads to disruption of the microenvironment and further propagation of pathology.ConclusionOur results revealed that lipid metabolism is significantly affected during different stages of tau pathology and provide new evidence that supports the contribution of pathological tau proteins in individual lipid pathways. Our data suggests that biologically active membrane lipids such as phospholipids and sphingolipids could represent new potential next-generation therapeutic targets in tauopathies.
Deep unsupervised learning methods for the identification and characterization of TCR specificity to Sars-Cov-2
Authors: Miraoui Yanis 
Published: September 2023

AbstractThe T-cell receptor (TCR) is one of the key players in the immune response to the Sars-Cov-2 virus. In this study, we used deep unsu-pervised learning methods to identify and characterize TCR speci-ficity. Our research focused on developing and applying state-of-the-art modelling techniques, including AutoEncoders, Variational Au-to Encoders and transfer learning with Transformers, to analyze TCR data. Through our experiments and analyses, we have achieved promis-ing results in identifying TCR patterns and understanding TCR speci-ficity for Sars-Cov-2. The insights gained from our research provide valuable tools and knowledge for interpreting the immunological re-sponse to the virus, ultimately contributing to the development of effective vaccines and treatments against the viral infection.
Single-Molecule Reaction-Diffusion
Authors: Xu Lance W.Q. , Jazani Sina , Kilic Zeliha , Pressé Steve 
Published: September 2023

AbstractWe propose to capture reaction-diffusion on a molecule-by-molecule basis from the fastest acquirable timescale, namely individual photon arrivals. We illustrate our method on intrinsically disordered human proteins, the linker histone H1.0 as well as its chaperone prothymosinα, as these diffuse through an illuminated confocal spot and interact forming larger ternary complexes on millisecond timescales. Most importantly, single-molecule reaction-diffusion, smRD, reveals single molecule properties without trapping or otherwise confining molecules to surfaces. We achieve smRD within a Bayesian paradigm and term our method Bayes-smRD. Bayes-smRD is further free of the average, bulk, results inherent to the analysis of long photon arrival traces by fluorescence correlation spectroscopy. In learning from thousands of photon arrivals continuous spatial positions and discrete conformational and photophysical state changes, Bayes-smRD estimates kinetic parameters on a molecule-by-molecule basis with two to three orders of magnitude less data than tools such as fluorescence correlation spectroscopy thereby also dramatically reducing sample photodamage.
Spatial distribution and functional integration of displaced ipRGCs
Authors: Duda Sabrina , Block Christoph T. , Pradhan Dipti R. , Arzhangnia Yousef , Greschner Martin , Puller Christian 
Published: September 2023

AbstractThe mammalian retina contains many distinct types of ganglion cells, which form mosaics to evenly tile the retina with cells of each type at each position of the visual field. It is well known that displaced retinal ganglion cells (dRGCs) exist with cell bodies in the inner nuclear layer, along with regularly placed RGCs with cell bodies in the ganglion cell layer. A prominent example of dRGCs are M1-type intrinsically photosensitive ganglion cells (ipRGCs) which exist in various species including humans and non-human primates. Little is known, however, about their spatial relationship with regularly placed ipRGCs.Here, we identified mouse ipRGC types M1, M2, and M4/sONɑ by immunohistochemistry and light microscopy to anatomically investigate the distribution of displaced and regularly placed cells. Reconstruction of immunolabeled dendritic mosaics from M1 and sONɑ RGCs indicated that dRGCs tiled the retina evenly with their regularly placed RGC partners. Multi-electrode array recordings revealed conventional receptive fields of displaced sONɑ RGCs which fit into the functional mosaic of their regularly placed counterparts. We further analyzed the RGC distributions across complete retinas. The analysis of regularly placed M1 ipRGCs and ɑRGCs revealed distinct density gradients where ∼16% and ∼8% occurred as dRGCs, respectively. The density distributions of dRGCs showed type-specific patterns which followed neither the global density distribution of all ganglion cells nor the local densities of corresponding cell types.Our study shows that the displacement of ganglion cell bodies into the inner nuclear layer occurs in a type-dependent manner, where dRGCs are positioned to form complete mosaics with their regularly placed RGC partners. Our data suggest that dRGCs and regularly placed RGCs serve the same functional role within their corresponding population of ganglion cells.Significance statementWe applied large-scale anatomical and electrophysiological experiments in mice to show that displaced intrinsically photosensitive retinal ganglion cells (ipRGCs) complete the mosaics of their regularly placed counterparts with their dendritic trees and receptive fields. Therefore, displaced ipRGCs likely serve the same functional role as corresponding regularly placed cells. The density distributions of displaced ipRGCs showed distinct, type-specific patterns. Interestingly, they followed neither the global density distribution of all ganglion cells nor the local densities of corresponding cell types.
Phenotypic and genomic characterization ofBacillus sensu latofor their biofertilization effect and plant growth promotion features in soybean plants
Authors: Torres P. , Altier N. , Beyhaut E. , Martin N. , Fresia P. , Garaycochea S. , Abreo E. 
Published: September 2023

SummaryBacillus sensu latowere screened for their capacity to mineralize organic phosphorus (P) and promote plant growth, improving nitrogen (N) and phosphorus nutrition of soybean plants. Isolates were first identified based on their genomic sequences through TYGS and ANII. ILBB95, ILBB510 and ILBB592 were identified asPriestia megaterium, ILBB139 asBacillus wiedmannii, ILBB44 as a member of a sister clade ofB. pumilus(together with a human pathogenic strain), ILBB15 asPeribacillus butanolivoransand ILBB64 asLysinibacillussp. These strains were evaluated for their capacity to mineralize organic P as sodium phytate and solubilize inorganic P forms in liquid medium. Thesein vitroassays allowed the strains to be ranked according to their P mobilization potential, with ILBB15 and ILBB64 showing the highest orthophosphate production from phytate, ILBB592 the lowest and ILBB510 nil. In addition, features related to their rhizocompetence and plant growth promotion were evaluatedin vitroandin silico.Finally, plant bioassays were deployed to assess the effect of the co-inoculation ofBacillus s.l.strains and rhizobial inoculant on nodulation, plant growth and nutrition.In plantabioassays showed thatB. pumilusILBB44 andP. megateriumILBB95 increased P absorbed in plants grown on a poor substrate of sand and vermiculite and also on the richer mix of sand, vermiculite and peat.Priestia megateriumILBB592 increased rhizobial nodulation and N content in plants grown on sand, vermiculite and peat mixture only. ILBB15 reduced plant growth and nutrition on both substrates. Genomes of ILBB95 and ILBB592 were characterized by genes related with plant growth and biofertilization whereas ILBB15 was differentiated by genes related to bioremediation.Priestia megateriumILBB592 can be described as nodule-enhancing rhizobacteria (NER) and together with ILBB95, can be envisaged as prospective PGPR with the capacity to exert a positive effect on N and P nutrition of soybean plants.
Screening of the Pandemic Response Box identifies anti-microsporidia compounds
Authors: Huang Qingyuan , Chen Jie , Pan Guoqing , Reinke Aaron W. 
Published: September 2023

AbstractMicrosporidia are fungi obligate intracellular pathogens, which infect most animals and cause microsporidiosis. Despite the serious threat that microsporidia pose to humans and agricultural animals, few drugs are available for the treatment and control of microsporidia. To identify novel inhibitors, we took advantage of the model organismCaenorhabditis elegansinfected with its natural microsporidianNematocida parisii. We used this system to screen the Pandemic Response Box, a collection of 400 diverse compounds with known antimicrobial activity. After testing these compounds in a 96-well format at high (100 μM) and low (40 μM) concentrations, we identified four inhibitors that restored the ability ofC. elegansto produce progeny in the presence ofN. parisii. All four compounds reduced the pathogen load of bothN. parisiiandPancytospora epiphaga, aC. elegans-infecting microsporidia related to human-infecting species. One of these compounds, a known inhibitor of a viral protease, MMV1006203, inhibited invasion and prevented the firing of spores. A bis-indole derivative, MMV1593539, decreased spore viability. An albendazole analog, MMV1782387, inhibited proliferation ofN. parisii. We tested albendazole as well as 5 other analogs and observed that MMV1782387 was amongst the strongest inhibitors ofN. parisiiand displayed the least host toxicity. Our study further demonstrates the effectiveness of theC. elegans-N. parisiisystem for discovering microsporidia inhibitors and the compounds we identified provide potential scaffolds for anti-microsporidia drug development.
KLF7 is a general inducer of human pluripotency
Authors: Arboit Mattia , Zorzan Irene , Pellegrini Marco , Martini Paolo , Carbognin Elena , Martello Graziano 
Published: September 2023

ABSTRACTPluripotency is the capacity to give rise to all differentiated cells of the body and the germ line and is governed by a self-reinforcing network of transcription factors. The forced expression of only some of these factors enables the reprogramming of somatic cells to pluripotency. In murine cells, several kruppel-like factors (KLFs) have been identified as stabilisers and inducers of pluripotency. Human somatic cells are routinely reprogrammed by expression of KLF4 in combination with OCT4, SOX2 and cMYC (OSKM). An extensive transcriptome analysis revealed, however, that KLF4 is barely expressed in conventional human pluripotent stem cells (PSCs). Here we show that KLF7 is robustly expressed in conventional human PSCs and it allows transcription factor-mediated somatic reprogramming. Moreover, we find that KLF7 is highly expressed in naive PSCs and its forced expression in conventional hPSCs induces upregulation of naive markers and boosts efficiency of chemical resetting to naive PSCs, overall suggesting that KLF7 is a general human pluripotency factor and an inducer of pluripotency.
Methylosome and SMN complexes are dispensable for snRNP assembly in Arabidopsis
Authors: Goretti Daniela , Collani Silvio , Nardeli Sarah Muniz , Schmid Markus 
Published: September 2023

ABSTRACTThe role of RNA splicing as modulator of the molecular responses to stress is well described. In contrast, its importance in the acclimation of plants to changes in ambient temperatures started to emerge only recently. Here, we analyzed the role of temperature in spliceosome assembly, a key step often neglected in studies focusing on splicing. Taking advantage of mutants showing temperature-dependent phenotypes we conducted a comprehensive study of the role that the methylosome and SMN complexes have in plant snRNP assembly. Genetic analyses, as well asin vivoandin vitroevidence suggest a mechanism for snRNP assembly in plants that differs remarkably from vertebrate animals. The SMN complex in plants is apparently reduced to a single protein, GEMIN2, that is not essential for plant development. Similarly, the methylosome has a less crucial role in spliceosome assembly than previously thought. Our results highlight how an evolutionary conserved molecular process like RNA splicing has nevertheless evolved plant specific characteristics.
Buyer–seller interactions and customer satisfaction – the moderating role of COVID-19 protocols: a study of small apparel fashion enterprises in the regional shopping malls in Ghana
Authors: Yeboah Solomon Tawiah , Haider Yasmeen , Amoako George 
Published: September 2023

PurposeThe study explored the relationship between buyer–seller interactions and customer satisfaction in the small apparel fashion enterprises in the emerging markets. The moderating role of COVID-19 protocols implementations on buyer–seller interactions and customer satisfaction was further examined.Design/methodology/approachBuyer–seller interactions affecting customer satisfaction were divided into three constructs, namely, interactions relating to the overall customers shopping experience, smooth payment process and in-store interactions, and the COVID-19 protocols implementations were used as a moderator. A convenient sampling strategy was adopted to survey 450 customers of apparel fashion enterprises within the four regions in Ghana, of which 397 were validly used for the analysis. Existing questionnaires were adapted to collect data from the respondents. The data collected was therefore analysed using SPSS and SmartPLS programme to ascertain the nature of the relationships among the variables.FindingsThe study found that, in-store interactions, shopping experience and smooth payment processes directly influence customer satisfaction. However, the implementation of COVID-19 protocols failed to moderate the relationship between buyer–seller interactions and customer satisfaction.Research limitations/implicationsThe limitations of the study involve its context-specific, focusing on the small apparel and fashion market. Also, future researchers can re-examine the model in other geographical jurisdictions, focusing on small apparel owners’ competencies and other variables that position buyer–seller interactions as precursors of customer satisfaction in the small apparel fashion industry. The theoretical and managerial relevance of the findings are also discussed.Originality/valueThe paper extends the domain of buyer–seller interactions and customer satisfaction phenomena within the apparel fashion industry. Its examination of the impact of COVID-19 protocols’ implementation on customer satisfaction provides an insight into managers regarding how the applications can affect customers in a typical shopping environment.
An impetus for the research paradigm of corporate citizenship and customer loyalty: imprints from scale construction
Authors: Gulati Twinkle , Shankar Siddharatha 
Published: September 2023

PurposeThe purpose of this research is to construct a logical, consistent and validated instrument to appraise the effect of corporate citizenship on customer loyalty, all-inclusive of possible factors.Design/methodology/approachTo attain this intent, a literature review is organized at the onset and then statements are created, improved and confirmed. In total, 384 customer-filled forms have been analyzed in parts, initially with exploratory factor analysis (EFA) and thereafter with confirmatory factor analysis (CFA).FindingsEFA outcomes obtain 26 items and three dimensions: corporate citizenship and customer acquisition, corporate citizenship and customer inclination, and corporate citizenship and customer patronization. The comprehensiveness, solidness, and judiciousness of the same have been tested by CFA.Research limitations/implicationsThis investigation would function as an impetus that can further evolve the empirical paradigm of corporate citizenship and customer loyalty by significantly impacting theory and practice.Practical implicationsIt presents the pragmatic perspectives of customers about modern-age citizenship endeavors for marketers, thus attuning their socially responsible marketing movements with upright citizenship actions.Originality/valueSince the discipline of corporate citizenship has received inadequate empirical understanding from the marketing outlook, possibly because of the lack of a confirmed and consistent instrument from the customers' angle, this developed scale can fill up that space.