bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Classification of Lysin Motif Receptor-Like Kinases in Lotus japonicus
Authors: Ruman Hafijur , Kawaharada Yasuyuki 
Published: November 2022

Abstract
Lysin motif receptor-like kinases (LysM-RLKs) are a plant-specific receptor protein family that sense components from soil microorganisms, regulating innate immunity and symbiosis. Every plant species possesses multiple LysM-RLKs in order to interact with a variety of soil microorganisms; however, most receptors have not been characterized yet. Therefore, we tried to identify LysM-RLKs from diverse plant species and proposed a new classification to indicate their evolution and characteristics, as well as to predict new functions. In this study, we have attempted to explore and update LysM-RLKs in Lotus japonicus using the latest genome sequencing and divided 20 LysM-RLKs into 11 clades based on homolog identity and phylogenetic analysis. We further identified 193 LysM-RLKs from 16 Spermatophyta species including L. japonicus and divided these receptors into 14 clades and one out-group special receptor based on the classification of L. japonicus LysM-RLKs. All plant species not only have clade I receptors such as Nod factor or chitin receptors but also have clade III receptors where most of the receptors are uncharacterized. We also identified dicotyledon- and monocotyledon-specific clades and predicted evolutionary trends in LysM-RLKs. In addition, we found a strong correlation between plant species that did not possess clade II receptors and those that lost symbiosis with arbuscular mycorrhizal fungi. A clade II receptor in L. japonicus Lys8 was predicted to express during arbuscular mycorrhizal symbiosis. Our proposed new inventory classification suggests the evolutionary pattern of LysM-RLKs and might help in elucidating novel receptor functions in various plant species.
Engaging Citizens in Government Contracting: A Theoretical Approach for the Role of Social Service Nonprofits
Authors: Park Gowun , Brunjes Benjamin M 
Published: November 2022

AbstractOutsourcing may lead public administrators to regard service recipients as customers to be satisfied rather than as citizens demanding access and empowerment. This research investigates the extent to which social service nonprofits might bridge the gap between citizenship and customer service to advance shared values and reinforce public institutions. Due to unique institutional and organizational features, such as value-driven commitments, restrictions to financial distribution, and special knowledge of under-represented groups, social service nonprofit contractors may offer distinct advantages over for-profit firms in contract management. We begin by analyzing the conflicting and complementary aspects of citizenship and customer service in democracy and identify the advantages of nonprofit contractors. Then, using the lenses of transaction cost economics and agency theory, we explore how nonprofits can mitigate contract risks while bolstering citizenship. We present several suggestions to guide public agencies and future scholarship on reasserting the importance of public values in modern governance.
RADIATION DETECTOR FOR THE ISRAELI FIRST RESPONDERS—METHODOLOGY OF SELECTION
Authors: Brandis Michal , Rabby Yossi , Epstein Lior , Datz Hanan , Tsvitman Eyal , Amit Gal , Hershkovich David , Krasner Esther 
Published: November 2022

Abstract
This paper presents the rationale and development of a methodology of selection of a radiation detector that can be used by first responders arriving to a terror event scene, not knowing if the event involves any radioactive materials. This detector can be used to detect and quantify the presence of gamma radiation. The role of this detector in a radiological terror event is reviewed via the operational concept for handling radiological terror in Israel. The development of the methodology of selection included a literature survey of relevant radiation detector categories, followed by a user-side survey of requirements based on the first responders’ experience along with the Israeli Ministry of Defense perspective on the management of radiological events, supplemented by the input from experts in aspects of radiation detection, radiation protection and dosimetry from the Israel Atomic Energy Commission’s Soreq Nuclear Research Center. The general qualitative characterisation of requirements was then quantified using a scoring method, enabling the methodological evaluation and numerical ranking of available detectors. Plans to evaluate candidate detector models according to the developed methodology are outlined. The detectors evaluation will be conducted as part of the procurement procedure of future detectors for first responders.
Ts66Yah, an upgraded Ts65Dn mouse model for Down syndrome, for only the region homologous to Human chromosome 21
Authors: Duchon Arnaud , Muñiz Moreno Maria del Mar , Chevalier Claire , Nalesso Valérie , Andre Philippe , Fructuoso-Castellar Marta , Mondino Mary , Po Chrystelle , Noblet Vincent , Birling Marie-Christine , Potier Marie-Claude , Herault Yann 
Published: November 2022

ABSTRACTDown syndrome is caused by trisomy of human chromosome 21 (Hsa21). The understanding of phenotype-genotype relationships, the identification of driver genes and various proof-of-concepts for therapeutics have benefited from mouse models. The premier model, named Ts(1716)65Dn/J (Ts65Dn), displayed phenotypes related to the human DS features. It carries an additional minichromosome with theMir155 toZbtb21region of mouse chromosome 16 (Mmu16), homologous to Hsa21, encompassing around 90 genes, fused to the centromeric part of mouse chromosome 17 (Mmu17) fromPisd-ps2/Scaf8toPde10a, containing 46 genes, not related to Hsa21. Here, we report the investigation of a new model, Ts66Yah, generated by CrispR/Cas9 without the genomic region unrelated to Hsa21 on the minichromosome. As expected, Ts66Yah replicated DS cognitive features. However, certain phenotypes related to increased activity, spatial learning and molecular signatures, were changed suggesting genetic interactions between theMir155-Zbtb21and theScaf8-Pde10ainterval. Thus, Ts66Yah mice have a stronger construct and face validity for mimicking consequences of DS genetic overdosage. Furthermore, this report is the first to demonstrate genetic interactions between triplicated regions homologous to Hsa21 and others unrelated to Hsa21.
Screening COVID-19 by Swaasa AI Platform using cough sounds: A cross-sectional study
Authors: Padmalatha P , Rudraraju Gowrisree , Sripada Narayana Rao , Mamidgi Baswaraj , Gottipulla Charishma , Jalukuru Charan , Palreddy ShubhaDeepti , Reddy Bhoge Nikhil kumar , Firmal Priyanka , Yechuri Venkat , Sudhakar PV , Devimadhavi B , Srinivas S , Prasad K K L , Joshi Niranjan 
Published: November 2022

AbstractThe Advent of Artificial Intelligence (AI) has led to the use of auditory data for detecting various diseases, including COVID-19. SARS-CoV-2 infection has claimed more than 6 million lives till date and hence, needs a robust screening technique to control the disease spread. In the present study we developed and validated the Swaasa AI platform for screening and prioritizing COVID-19 patients based on the signature cough sound and the symptoms presented by the subjects. The cough data records collected from 234 COVID-19 suspects were subjected to validate the convolutional neural network (CNN) architecture and tabular features-based algorithm. The likelihood of the disease was predicted by combining the final output obtained from both the models. In the clinical validation phase, Swaasa was found to be 75.54% accurate in detecting the likely presence of COVID-19 with 95.45% sensitivity and 73.46% specificity. The pilot testing of Swaasa was carried out on 183 presumptive COVID subjects, out of which 82 subjects were found to be positive for the disease by Swaasa. Among them, 58 subjects were truly COVID-19 positive, which corresponds to a Positive Predictive Value of 70.73%. The currently available rapid screening methods are very costly and require technical expertise, therefore a cost effective, remote monitoring tool would be very beneficial for preliminary screening of the potential COVID-19 subject.
Rapid onset of chronic urticaria after Moderna COVID-19 booster vaccine
Authors: Duperrex Olivier , Tommasini Francesco , Muller Yannick D. 
Published: November 2022

AbstractA substantial number of patients with newly onset of chronic urticaria was observed rapidly after the booster vaccine against COVID-19. This observation was unprecedented compared to the primary series of vaccination. To address this concern, we initiated an online observational study with the help of local allergists. We found a striking association between the booster dose, the Moderna vaccine, and the new onset of chronic urticaria within the following 10 days. These data were confirmed when reviewing all cases of CSU related to COVID-19 vaccination reported to Swissmedic, the Swiss regulatory agency. These data should not discourage patients from being vaccinated, as this vaccination campaign has been instrumental in reducing COVID-19 burden and preventing millions of deaths. Yet, there is an urgent need to establish appropriate guidelines and monitor this adverse event more closely, considering that a fourth dose is currently being administered.
Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci
Authors: Butler Madeleine EB , Jansen van Rensburg Melissa J , Karani Angela , Mvera Benedict , Akech Donald , Akter Asma , Forrest Calum , van Tonder Andries J , Quirk Sigríður J , Haraldsson Gunnsteinn , Bentley Stephen D , Erlendsdóttir Helga , Haraldsson Ásgeir , Kristinsson Karl G , Scott J Anthony G , Brueggemann Angela B 
Published: November 2022

AbstractBacteriocins are antimicrobial peptides produced by bacteria to inhibit other bacteria in the surrounding environment.Streptococcus pneumoniaeis a leading cause of disease worldwide and colonises the healthy human nasopharynx, where it competes for space and nutrients. Pneumococcal conjugate vaccines have reduced the incidence of disease, but they also restructure the bacterial population, and this restructuring likely alters the nasopharyngeal competition dynamics. Here, the distribution of bacteriocins was examined in over 5000 carriage and disease-causing pneumococci from Iceland and Kenya, recovered before and after the introduction of pneumococcal vaccination. Overall, up to eleven different bacteriocin gene clusters were identified per pneumococcus. Significant differences in the prevalence of bacteriocins were observed before and after vaccine introduction, and among carriage and disease-causing pneumococci, which were largely explained by the bacterial population structure. Genetically similar pneumococci generally harboured the same bacteriocins although sometimes different repertoires of bacteriocins were observed, which suggested that horizontal transfer of bacteriocin clusters had occurred. These findings demonstrated that vaccine-mediated changes in the pneumococcal population altered the prevalence and distribution of bacteriocins. The consequences of this for pneumococcal colonisation and disease remain to be determined.
Critical dynamics arise during structured information presentation: analysis of embodiedin vitroneuronal networks
Authors: Habibollahi Forough , Kagan Brett J. , Duc Daniela , Burkitt Anthony N. , French Chris 
Published: November 2022

AbstractAmongst the characteristics about information processing in the brain, observations of dynamic near-critical states have generated significant interest. However, theoretical and experimental limitations have precluded a definite answer about when and why neural criticality arises. To explore this topic, we used anin vitroneural network of cortical neurons that was trained to play a simplified game of ‘Pong’. We demonstrate that critical dynamics emerge when neural networks receive task-related structured sensory input, reorganizing the system to a near-critical state. Additionally, better task performance correlated with proximity to critical dynamics. However, criticality alone is insufficient for a neuronal network to demonstrate learning in the absence of additional information regarding the consequences of previous actions. These findings have compelling implications for the role of neural criticality.
Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis
Authors: van Keulen Siri C. , Bonvin Alexandre M.J.J. 
Published: November 2022

ABSTRACTThe steep rise in available protein sequences and structures has paved the way for bioinformatics approaches to predict residue-residue interactions in protein complexes. Multiple sequence alignments are commonly used in intermolecular contact predictions to identify co-evolving residues. These contacts, however, often include false positives (FPs), which may impair their use to predict three dimensional structures of biomolecular complexes and affect the accuracy of the generated models.Previously, we have developed DisVis to identify false positive data in mass spectrometry cross-linking data. DisVis allows to assess the accessible interaction space between two proteins consistent with a set of distance restraints. Here, we investigate if a similar approach could be applied to co-evolution predicted contacts in order to improve their precision prior to using them for modelling complexes.In this work we analyze co-evolution contact predictions with DisVis in order to identify putative FPs for a set of 26 protein-protein complexes. Next, the DisVis-reranked and the original co-evolution contacts are used to model the complexes with our integrative docking software HADDOCK using different filtering scenarios. Our results show that HADDOCK is robust with respect to the precision of the predicted contacts due to the 50% random contact removal during docking and using DisVis filtering for low precision contact data. DisVis can thus have a beneficial effect on low quality data, but overall HADDOCK can accommodate FP restraints without negatively impacting the quality of the resulting models. Other more precision-sensitive docking protocols might, however, benefit from the increased precision of the predicted contacts after DisVis filtering.
Antigen self-anchoring onto bacteriophage T5 capsid-like particles for vaccine design
Authors: Vernhes Emeline , Chérif Linda Larbi , Ducrot Nicolas , Ouldali Malika , Zig Lena , Sidibe N’diaye , Hoos Sylviane , Ramirez-Chamorro Luis , Renouard Madalena , Rossier Ombeline , England Patrick , Schoehn Guy , Boulanger Pascale , Benihoud Karim 
Published: November 2022

AbstractThe promises of vaccines based on virus-like particles stimulate demand for universal non-infectious virus-like platforms that can be efficiently grafted with large antigens. Here we harnessed the modularity and extreme affinity of the decoration protein pb10 for the capsid of bacteriophage T5. SPR experiments demonstrated that pb10 fused to mCherry or to the model antigen ovalbumin (Ova) retained picomolar affinity for DNA-free T5 capsid-like particles (T5-CLPs), while cryo-EM studies attested to the full occupancy of the 120 capsid binding sites. Mice immunisation with CLP-bound pb10-Ova chimeras elicited strong long-lasting anti-Ova humoral responses involving a large panel of isotypes, as well as CD8+T cell responses, without any extrinsic adjuvant. Therefore, T5-CLP constitutes the first DNA-free bacteriophage capsid able to irreversibly display a regular array of large antigens through highly efficient chemical-free anchoring. Its ability to elicit robust immune responses paves the way for further development of this novel vaccination platform.
Divergent selection for feed efficiency in pigs altered the duodenum transcriptome and DNA methylation profiles, resulting in greater responses to feed intake in the most efficient line
Authors: Devailly Guillaume , Fève Katia , Saci Safia , Sarry Julien , Valière Sophie , Lluch Jérôme , Bouchez Olivier , Ravon Laure , Billon Yvon , Gilbert Hélène , Riquet Juliette , Beaumont Martin , Demars Julie 
Published: November 2022

AbstractFeed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relative low-(LRFI, more efficient) and high-(HRFI, less efficient) residual feed intake (RFI). Feeding behaviour and metabolic differences have been previously reported between the two lines. We hypothesised that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine.Here we investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n=24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake, with 2,222 differentially expressed genes before and after a meal, as compared to 61 differentially expressed genes in the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. We noted that several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. However most of the differentially expressed genes were not associated with proximal changes in DNA methylation profiles.Altogether, our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency.
Path analysis of intra-metastatic hypoxia in breast cancer
Authors: Rey-Keim Sergio , Schito Luana 
Published: November 2022

AbstractHypoxia (low O2) signals into the nucleus of cancer cells through hypoxia-inducible factor (HIF)-1α-dependent transcription triggering proliferative, metabolic and vascular adaptations linked to therapy resistance and mortality due to overt metastasis. In contrast with the wealth of molecular data on primary intra-tumoral hypoxia, there is a dearth of statistical modelling studies addressing the mechanisms of intra-metastatic hypoxia. In this study, we used path analysis to model intra-metastatic hypoxia (Hx), HIF-1α expression and microvascular area (MVA) as functions of metastatic cross-sectional area (MCSA) in an advanced mouse breast cancer model; in this context, we tested the effect of conventional, maximum-tolerated dose (MTD) or low-dose metronomic (LDM) chemotherapy. Iterative analysis of 34 non-isomorphic paths yielded four well-fitting, configuration-invariant models [χ2(6,171)≥ 6.12;P≥ 0.328; CFI ≥ 0.998; RMSEA ≤ 0.07]. All four models contained HIF-1α as a mediating variable within the MCSA↔Hx↔MVA path, as well as significant Hx↔MVA interactions. LDM disrupted the HIF-1α↔MCSA→Hx and HIF-1α↔MVA paths; furthermore, all LDM and MTD combinations impaired Hx↔HIF-1α. These results confirmed well-established hypoxic interactions, whilst uncovering possible differential effects of chemotherapeutic modalities upon metastatic size, hypoxia, HIF-1α and vascularisation. Our data indicate that MVA can act as a downstream readout, rather than an adaptive angiogenic mechanism alleviating intra-metastatic hypoxia. Moreover, well-fitting path models locate HIF-1α activity either upstream or downstream of hypoxia, thereby allowing us to posit the existence of bi-directional feedback loops driving vascularisation and growth in metastatic tumours, of relevance for targeted therapies.
Glutathione induces ArabidopsisPHT1;5gene via WRKY75 transcription factor to regulate phosphate homeostasis
Authors: Shee Ranjana , Shee Dibyendu , Sahid Salman , Paul Soumitra , Datta Riddhi 
Published: November 2022

AbstractPhosphorus is a macronutrient that regulates a wide range of physiological processes, including plant growth and development. The scarcity of bioavailable phosphate is often a constraint for plant growth in most agricultural ecosystems. Under phosphate limited conditions, plants increase phosphate acquisition or alter its distribution within tissues by activating different phosphate transporters and phosphate starvation-induced genes. Glutathione (GSH), on the other hand, is known to play a critical role in regulating iron and zinc homeostasis in Arabidopsis. However, how it regulates phosphate homeostasis under phosphate limited conditions remains unexplored. We found that the two GSH-deficient mutants,cad2-1, andpad2-1, were hypersensitive to phosphate starvation. Under phosphate-sufficient condition, the root phosphate content was lower in the mutants but significantly higher in the shoot over the Col-0 plants. The pattern was reversed under phosphate-deficient condition. Interestingly, among the different phosphate transporters analyzed, theAtPHT1;5was significantly down-regulated in the two GSH-deficient mutants. Treatment with exogenous GSH could alter phosphate accumulation in Col-0 and thepht1;5complementation lines but not in thepht1;5mutant. This observation confirmed the role of GSH in phosphate reallocation during phosphate starvation via theAtPHT1;5 transporter. Further, promoter analysis demonstrated that GSH regulates the transcription of theAtPHT1;5gene. The phosphate-responsive transcription factor (TF),AtWRKY75 was identified to interact with theAtPHT1;5promoter, and phosphate deficiency or GSH treatment enhanced its binding affinity. Together our investigation delineates that GSH regulates theAtPHT1;5 transporter via theAtWRKY75 TF to modulate phosphate distribution under altered phosphate conditions.Summary statementGlutathione regulates phosphate translocation in Arabidopsis under altered phosphate condition via transcriptional activation ofAtPHT1;5gene byAtWRKY75 transcription factor.
IL-17A promotes epithelial cell IL-33 production during nematode lung migration
Authors: Ajendra Jesuthas , Pearson Stella , Parkinson James E. , Chan Brian H.K. , McSorley Henry J. , Sutherland Tara E. , Allen Judith E. 
Published: November 2022

AbstractThe early migratory phase of pulmonary helminth infections is characterized by tissue injury leading to the release of the alarmin IL-33 and subsequent induction of type 2 immune responses. We recently described a role for IL-17A, through regulation of IFNγ, as an important inducer of type 2 responses during infection with the lung-migrating rodent nematodeNippostrongylus brasiliensis. Here, we aimed to investigate the interaction between IL-17A and IL-33 during the early lung migratory stages ofN. brasiliensisinfection. In this brief report, we demonstrate that deficiency of IL-17A leads to impaired IL-33 expression and secretion early in infection, independent of IL-17A suppression of IFNγ. Impaired IL-33 production was evident in lung epithelial cells, but not innate immune cells. Therefore, our results demonstrate that IL-17A can drive IL-33 during helminth infection, highlighting an additional mechanism through which IL-17A can regulate pulmonary type 2 immunity.