bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization and estimation of stroke infarct volumes in rodents
Authors: Weber Rebecca Z. , Bernardoni Davide , Rentsch Nora H. , Achón Buil Beatriz , Halliday Stefanie , Augath Mark-Aurel , Razansky Daniel , Tackenberg Christian , Rust Ruslan 
Published: July 2023

AbstractStroke volume is a key determinant of infarct severity and an important metric treatments evaluation. However, accurate estimation of stroke volume can be challenging, due to the often confined 2-dimensional nature of available data. Here, we introduce a comprehensive semi-automated toolkit to reliably estimate stroke volumes based on (1) whole brainsex-vivomagnetic resonance imaging (MRI) and (2) brain sections that underwent immunofluorescence staining. We located and quantified infarct areas from MRI three days (acute) and 28 days (chronic) after photothrombotic stroke induction in whole mouse brains. MRI Results were compared with measures obtained from immunofluorescent histologic sections of the same brains. Using our toolkit, we found that infarct volume determined by post-mortem MRI was highly correlated with a deviation of only 6.6% (acute) and 4.9% (chronic) to the measurements as determined in the histological brain sections indicating that both methods are capable of accurately assessing brain tissue damage.
Role of transporters and enzymes in metabolism and distribution of 4 chlorokynurenine and metabolites
Authors: Patel Waseema , Shankar Ravi G. , Smith Mark A. , Snodgrass H. Ralph , Pirmohamed Munir , Jorgensen Andrea , Alfirevic Ana , Dickens David 
Published: July 2023

Abstract4-chlorokynurenine (4-Cl-KYN) is in clinical development for potential CNS indications. We have sought to further understand the distribution and metabolism of 4-Cl-KYN as this information might provide a strategy to enhance the clinical development of this drug. We used excretion studies in rats,in vitrotransporter assays and pharmacogenetic analysis of clinical trial data to determine how 4-Cl-KYN and metabolites are distributed. Our data indicated that a novel acetylated metabolite (N-acetyl-4-Cl-KYN) did not affect the uptake of 4-Cl-KYN across the blood-brain barrier via LAT1. 4-Cl-KYN and metabolites were found to be renally excreted in rodents. In addition, we found that N-acetyl-4-Cl-KYN inhibited renal and hepatic transporters involved in excretion. Thus, this metabolite had the potential to limit the excretion of a range of compounds. Our pharmacogenetic analysis found that a SNP in N-acetyltransferase 8 (NAT8, rs13538) was linked to levels of N-acetyl-4-Cl-KYN relative to 4-Cl-KYN found in the plasma and that a SNP in SLC7A5 (rs28582913) was associated with the plasma levels of the active metabolite, 7-Cl-KYNA. Thus, we have a pharmacogenetics-based association for plasma drug level that could aid in the drug development of 4-Cl-KYN and have investigated the interaction of a novel metabolite with drug transporters.
Glycan-specific IgM is critical for human immunity toStaphylococcus aureus
Authors: Hendriks Astrid , Kerkman Priscilla F. , Varkila Meri R.J. , Haitsma-Mulier Jelle L.G. , Ali Sara , ten Doesschate Thijs , van der Vaart Thomas W. , de Haas Carla J.C. , Aerts Piet C. , Cremer Olaf L. , Bonten Marc J.M. , Nizet Victor , Liu George Y. , Codée Jeroen D.C. , Rooijakkers Suzan H.M. , van Strijp Jos A.G. , van Sorge Nina M. 
Published: July 2023

AbstractStaphylococcus aureusis a major human pathogen but the immune factors that protect against it remain elusive. In particular, high opsonic IgG titers achieved in preclinicalS. aureusanimal immunization studies have consistently failed to translate to protection in human clinical trials. Here, we investigated the antibody responses to a conserved surface glycan, Wall Teichoic Acid (WTA). IgM and IgG antibodies specific to WTA were universally present in plasma from healthy individuals. Functionally, WTA-specific IgM outperformed IgG in opsonophagocytic killing ofS. aureusand conferred passive protection againstS. aureusinfectionin vivo. In the clinical setting, WTA-specific IgM responses, but not IgG responses, were significantly lower inS. aureusbacteremia patients compared to healthy individuals, correlated with mortality risk and showed impaired bacterial opsonization. Our findings can guide risk stratification of hospitalized patients and inform future design of antibody-based therapies and vaccines against seriousS. aureusinfection.
Putative staphylococcal enterotoxin possesses two common structural motifs for MHC-II binding
Authors: Rahman Shakilur , Saha Saradindu , Dasgupta Somdeb Bose , Das Amit Kumar 
Published: July 2023

AbstractStaphylococcus aureushas become a significant cause of health risks in humankind. Staphylococcal superantigens (SAgs) or enterotoxins are the key virulent factors that can exhibit acute diseases to severe life-threatening conditions. Recent literature reportsS. aureushas steadily gained new enterotoxin genes over the past few decades. In spite of current knowledge of the established SAgs, several questions on these putative enterotoxins are still remaining unanswered. Keeping that in mind, this study sheds light on a putative enterotoxin SEl26 to characterize its structural and functional properties.In-silicoanalyses indicate its close relation with the conventional SAgs, especially the zinc-binding SAgs. Additionally, important residues have been predicted that are vital for T-Cell receptor (TcR) and major histocompatibility complex class II (MHC-II) interaction and compared them with established SAgs. Besides, our biochemical analyses exhibited the binding of this putative enterotoxin with MHC-II, followed by regulating pro-inflammatory and anti-inflammatory cytokines.
Spatial predictive context speeds up visual search by biasing local attentional competition
Authors: Bouwkamp Floortje G. , de Lange Floris P. , Spaak Eelke 
Published: July 2023

AbstractThe human visual system is equipped to rapidly and implicitly learn and exploit the statistical regularities in our environment. Within visual search, contextual cueing demonstrates how implicit knowledge of scenes can improve search performance. This is commonly interpreted as spatial context in the scenes becoming predictive of the target location, which leads to a more efficient guidance of attention during search. However, what drives this enhanced guidance is unknown. First, it is under debate whether the entire scene (global context) or more local context drives this phenomenon. Second, it is unclear how exactly improved attentional guidance is enabled by target enhancement and distractor suppression. In the present MEG experiment, we leveraged Rapid Invisible Frequency Tagging (RIFT) to answer these two outstanding questions. We found that the improved performance when searching implicitly familiar scenes was accompanied by a stronger neural representation of the target stimulus, at the cost specifically of those distractors directly surrounding the target. Crucially, this biasing of local attentional competition was behaviorally relevant when searching familiar scenes. Taken together, we conclude that implicitly learned spatial predictive context improves how we search our environment by sharpening the attentional field.
Disentangling the Innate Immune Responses of Intestinal Epithelial Cells and Lamina Propria Cells toSalmonellaTyphimurium Infection in Chickens
Authors: Sutton Kate , Nash Tessa , Sives Samantha , Borowska Dominika , Mitchell Jordan , Vohra Prerna , Stevens Mark P. , Vervelde Lonneke 
Published: July 2023

AbstractSalmonella entericaserovar Typhimurium (STm) is a major foodborne pathogen and poultry are a key reservoir of human infections. To understand the host responses to early stages ofSalmonellainfection in poultry, we infected 2D and 3D enteroids, the latter of which contains leukocytes, neurons, and mesenchymal cells that are characteristic of the lamina propria. We infected these enteroids with wild-type (WT STm), a non-invasive mutant lacking theprgHgene (ΔprgHSTm), or treated them with STm lipopolysaccharide (LPS) and analysed the expression of innate immune related genes by qPCR at 4 and 8 h. The localisation of ZO-1 expression was disrupted in WT STm infected enteroids but notΔprgHSTm or LPS treated enteroids, suggesting a loss of barrier integrity. The innate immune response to LPS was more pronounced in 2D enteroids compared to 3D enteroids and by 8 hpi, the response in 3D enteroids was almost negligible. However, when STm adhered to or invaded the enteroids, both 2D and 3D enteroids exhibited an upregulation of inflammatory responses. The presence of lamina propria cells in 3D enteroids resulted in the unique expression of genes associated with immune functions involved in regulating inflammation. Moreover, 2D and 3D enteroids showed temporal differences in response to bacterial invasion or adherence. At 8 hpi, innate responses in 3D but not 2D enteroids continued to increase after infection with WT STm, whereas the responses to the non-invasive strain decreased at 8 hpi in both 2D and 3D enteroids. In conclusion, STm infection of chicken enteroids recapitulated several observations fromin vivostudies ofSalmonella-infected chickens, including altered epithelial barrier integrity based on ZO-1 expression and inflammatory responses. Our findings provide evidence thatSalmonella-infected enteroids serve as effective models for investigating host-pathogen interactions and exploring the molecular mechanisms of microbial virulence although the 3D model mimics the host more accurately due to the presence of a lamina propria.
Genetic barriers more than ecological adaptations shapedSerratia marcescensdiversity
Authors: Sterzi Lodovico , Nodari Riccardo , Di Marco Federico , Ferrando Maria Laura , Saluzzo Francesca , Spitaleri Andrea , Allahverdi Hamed , Papaleo Stella , Panelli Simona , Rimoldi Sara Giordana , Batisti Biffignandi Gherard , Corbella Marta , Cavallero Annalisa , Prati Paola , Farina Claudio , Cirillo Daniela Maria , Zuccotti Gianvincenzo , Bandi Claudio , Comandatore Francesco 
Published: July 2023

AbstractBacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigated the genetic and ecological drivers underlying the evolution ofSerratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses revealed a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets revealed only a partial ecological separation of the clusters. Globally, two clusters only showed a peculiar gene composition and evident ecological adaptations. These results suggest that genetic isolation preceded ecological adaptations in the shaping of the species diversity, suggesting an evolutionary scenario for several bacterial species.
Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus
Authors: Ketaren Natalia E. , Mast Fred D. , Fridy Peter C. , Olivier Jean Paul , Sanyal Tanmoy , Sali Andrej , Chait Brian T. , Rout Michael P. , Aitchison John D. 
Published: July 2023

AbstractTo date, all major modes of monoclonal antibody therapy targeting SARS-CoV-2 have lost significant efficacy against the latest circulating variants. As SARS-CoV-2 omicron sublineages account for over 90% of COVID-19 infections, evasion of immune responses generated by vaccination or exposure to previous variants poses a significant challenge. A compelling new therapeutic strategy against SARS-CoV-2 is that of single domain antibodies, termed nanobodies, which address certain limitations of monoclonal antibodies. Here we demonstrate that our high-affinity nanobody repertoire, generated against wild-type SARS-CoV-2 spike protein (Mast, Fridy et al. 2021), remains effective against variants of concern, including omicron BA.4/BA.5; a subset is predicted to counter resistance in emerging XBB and BQ.1.1 sublineages. Furthermore, we reveal the synergistic potential of nanobody cocktails in neutralizing emerging variants. Our study highlights the power of nanobody technology as a versatile therapeutic and diagnostic tool to combat rapidly evolving infectious diseases such as SARS-CoV-2.
Urban colonization of invasive species on islands:Mus musculusandRattus rattusgenetics of establishment on Cozumel island
Authors: Borja-Martínez Gabriela , Vázquez-Domínguez Ella 
Published: July 2023

AbstractHumans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouseMus musculusand the black ratRattus rattuson Cozumel island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our findings show that the constant introduction of individuals of different origins to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Moreover, we foundM. musculushas a particularly restricted distribution within the city of San Miguel Cozumel, whilst its genetic structure is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance in order to prevent these invasive species to disperse further.
Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination
Authors: Patiño-Guillén G. , Pešović J. , Panic M. , Savic-Pavicevic D. , Bošković F. , Keyser U.F. 
Published: July 2023

SummaryTranscription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilized T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discovered alternative transcription termination in the origin of replication sequence. Next, we employed circular DNA without transcription terminators to perform rolling circle transcription. This allowed us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
Transcriptomic analysis identifies synapse-enriched lncRNAs required for excitatory synapse development and fear memory
Authors: Samaddar Sarbani , Srinivasan Balakumar , Garg Kamakshi , Raj Nandu , Sultana Sania , Mukherjee Utsav , Banerjee Dipanjana , Liau Wei-Siang , Palakodeti Dasaradhi , Bredy Timothy W. , Banerjee Sourav 
Published: July 2023

SummaryRegulatory functions of lncRNAs in neurons have been majorly limited to the nucleus. The identity of synaptic lncRNAs and their functional role associated with synapse development and memory are poorly understood. We employed RNA-seq analysis of synaptoneurosomes to identify 94 synapse-enriched lncRNAs from the mouse hippocampus. We find Pvt1 to be a specific regulator of excitatory, but not inhibitory, synapse developmentin vivo. RNA-Seq from Pvt1 knockdown neurons identified down-regulated transcripts encoding pre- and post-synaptic proteins influencing synapse formation. This observation is congruent with reduction in mEPSC amplitude and frequency. We find a synapse-centric role for SynLAMP which is specifically transported to the synaptic compartment upon contextual fear conditioning (CFC) and regulate activity-dependent dendritic translation. CFC led to enhancement of interaction between SynLAMP and the translation repressor FUS, indicating SynLAMP to be a molecular decoy. SynLAMP RNAi partially occludes fear memory, suggesting an input-specific role of lncRNAs at the synapse.
Direct, quantitative, and comprehensive analysis of tRNA acylation using intact tRNA liquid-chromatography mass-spectrometry
Authors: Fricke Riley , Knudson Isaac , Schepartz Alanna 
Published: July 2023

AbstractAminoacyl-tRNA synthetases (aaRSs) provide the functional and essential link between the sequence of an mRNA and the protein it encodes. aaRS enzymes catalyze a two-step chemical reaction that acylates specific tRNAs with a cognate α-amino acid. In addition to their role in translation, acylated tRNAs contribute to non-ribosomal natural product biosynthesis and are implicated in multiple human diseases. From the standpoint of synthetic biology, the acylation of tRNAs with a non-canonical α-amino acid (ncAA) or more recently, a non-α-amino acid monomer (nαAA) is a critical first step in the incorporation of these monomers into proteins, where they can be used for fundamental and applied science. These endeavors all demand an understanding of aaRS activity and specificity. Although a number of methods to monitor aaRS functionin vitroorin vivohave been developed, many evaluate only the first step of the two-step reaction, require the use of radioactivity, or are slow, difficult to generalize, or both. Here we describe an LC-MS assay that rapidly, quantitatively, and directly monitors aaRS activity by detecting the intact acyl-tRNA product. After a simple tRNA acylation reaction workup, acyl- and non-acyl-tRNA molecules are resolved using ion-pairing reverse phase chromatography and their exact masses are determined using high-resolution time-of-flight mass spectrometry. The intact tRNA assay we describe is fast, simple, and quantifies reaction yields as low as 0.23%. The assay can also be employed on tRNAs acylated with flexizyme to detect products that are undetectable using standard techniques. The protocol requires basic expertise in molecular biology, mass spectrometry, and RNAse-free techniques.
Statistical Optimization of Hydrazone-Crosslinked Hyaluronic Acid Hydrogels for Protein Delivery
Authors: Mozipo Esther A. , Galindo Alycia N. , Khachatourian Jenna D. , Harris Conor G. , Dorogin Jonathan , Spaulding Veronica R. , Ford Madeleine R. , Singhal Malvika , Fogg Kaitlin C. , Hettiaratchi Marian H. 
Published: July 2023

AbstractHydrazone-crosslinked hydrogels are attractive protein delivery vehicles for regenerative medicine. However, each regenerative medicine application requires unique hydrogel properties to achieve an ideal outcome. The properties of a hydrogel can be impacted by numerous factors involved in its fabrication. We used design of experiments (DoE) statistical modeling to efficiently optimize the physicochemical properties of a hyaluronic acid (HA) hydrazone-crosslinked hydrogel for protein delivery for bone regeneration. We modified HA with either adipic acid dihydrazide (HA-ADH) or aldehyde (HA-Ox) functional groups and used DoE to evaluate the interactions of three input variables, the molecular weight of HA (40 or 100 kDa), the concentration of HA-ADH (1-3% w/v), and the concentration of HA-Ox (1-3% w/v), on three output responses, gelation time, compressive modulus, and hydrogel stability over time. We identified 100 kDa HA-ADH3.0HA-Ox2.33as an optimal hydrogel that met all of our design criteria, including displaying a gelation time of 3.7 minutes, compressive modulus of 62.1 Pa, and minimal mass change over 28 days. For protein delivery, we conjugated affinity proteins called affibodies that were specific to the osteogenic protein bone morphogenetic protein-2 (BMP-2) to HA hydrogels and demonstrated that our platform could control the release of BMP-2 over 28 days. Ultimately, our approach demonstrates the utility of DoE for optimizing hydrazone-crosslinked HA hydrogels for protein delivery.Graphical Abstract
Applying bag of words approach to determine remote sensing technology acceptance among smallholder plantations
Authors: Diana Shinta Rahma , Farida Farida 
Published: July 2023

PurposeTechnology acceptance is a measure of that technology’s usefulness. Oil palm is one of the biggest contributors to Indonesia’s revenues, thus fueling its economy. Using remote sensing would allow a plantation to monitor and forecast its production and the amount of fertilizer used. This review aims to provide a policy recommendation in the form of a strategy to improve the added value of Indonesia’s oil palm and support the government in increasing oil palm production. This recommendation needs to be formulated by determining the users’ acceptance of remote sensing technology (state-owned plantations, private plantation companies and smallholder plantations).Design/methodology/approachThis review’s methodology used sentiment analysis through text mining (bag of words model). The study’s primary data were from focus group discussions (FGDs), questionnaires, observations on participants, audio-visual documentation and focused discussions based on group category. The results of interviews and FGDs were transcribed into text and analyzed to 1) find words that can represent the content of the document; 2) classify and determine the frequency (word cloud); and finally 3) analyze the sentiment.FindingsThe result showed that private plantation companies and state-owned plantations had extremely high positive sentiments toward using remote sensing in their oil palm plantations, whereas smallholders had a 60% resistance. However, there is still a possibility for this technology’s adoption by smallholders, provided it is free and easily applied.Research limitations/implicationsBasically, technology is applied to make work easier. However, not everyone is tech-savvy, especially the older generations. One dimension of technology acceptance is user/customer retention. New technology would not be immediately accepted, but there would be user perceptions about its uses and ease. At first, people might be reluctant to accept a new technology due to the perception that it is useless and difficult. Technology acceptance is the gauge of how useful technology is in making work easier compared to conventional ways.Practical implicationsTherefore, technology acceptance needs to be improved among smallholders by intensively socializing the policies, and through dissemination and dedication by academics and the government.Social implicationsThe social implications of using technology are reducing the workforce, but the company will be more profitable and efficient.Originality/valueRemote sensing is one of the topics that people have not taken up in a large way, especially sentiment analysis. Acceptance of technology that utilizes remote sensing for plantations is very useful and efficient. In the end, company profits can be allocated more toward empowering the community and the environment.