bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab-AMR: A Comprehensive Repository of Acinetobacter baumannii to Understand the Molecular Landscape of Antimicrobial Resistance
Authors: Sharma Tina , Kumar Rakesh , Bhardwaj Anshu 
Published: July 2022

AbstractAb-AMR is a comprehensive repository of drug resistance mechanisms in Acinetobacter baumannii. The current version of Ab-AMR provides a drug resistance profile of 788 genomes. In order to ensure that the datasets in Ab-AMR have relevance both to the research and clinical community, standards of defining MIC breakpoints, whole genome sequence quality metrics as defined by EUCAST/CLSI and classification of isolates into susceptible, MDR, XDR and PDR as defined by CDC/ECDC are implemented. As of now, 364 DR determinants associated with antibiotic inactivation (β-lactamases, aminoglycoside modification, chloramphenicol acetyltransferase), efflux, protein modulating permeability and alteration of target site are comprehensively annotated. In addition, data from pangenome analysis across 788 genomes is also provided for identification of core and accessory DR determinants. AB ATCC 17978 (Accession-CP000521.1), the reference strain, was annotated on January 1, 2014 but subsequently the same strain was re-annotated on March 21, 2017 (NZ_CP018664.1) due to incorrect assembly. Therefore, the genome comparison of both, 2014 and 2017 versions were performed for maintaining the correct annotations as most of the literature data referred to the earlier version of the reference genome. In Ab-AMR, the reference coordinates of the revised reference genome are used to represent manually curated and comprehensively annotated data on 614 essential genes, 1334 genes mapped to pathways, 221 PDB structures, 81 reported drug targets, 364 genes with reported resistance mechanism, 118 transcription factors, 4 sigma factors and 14 two component systems. Ab-AMR is made using the standard php-mysql framework and offers various search tools including a query builder that facilitates query on over 60 different features for addressing complex questions like core genes which are also essential and have a role to play in drug resistance with no known human homolog, etc. Ab-AMR offers a centralized data resource for systematic mapping of DR determinants, both plasmid and chromosomal mediated, along with deep annotation of clinical isolates.Database URL: https://datascience.imtech.res.in/anshu/ab-amr/
Is the interaction of technology useful in laboratory haematology diagnostics?
Authors: Falda Alessandra , Falda Marco , Pacioni Aurelio , Borgo Giada , Russelli Rosolino , Antico Antonio 
Published: July 2022

AbstractBackgroundMonoclonal B lymphocytosis (MBL) increases with age and individuals with high count MBL progress to chronic lymphocytic leukaemia requiring therapy at a rate of ∼1%-5% per year. These cases usually have atypical lymphocytes at the microscope, abnormal representation in the scattergram, and positivity of flags. Using XN9000 (Sysmex), we noticed cases of MBL without this correlation. We studied customized gates for discovering MBL cases of our interest.MethodsWe considered 212 peripheral blood samples with known phenotypes: 76.7% negative and 23.3% positive for B, T, or NK lymphocytes clones. We created gates studying the XN9000 FCS files in Diva software to identify new areas for better delimiting subpopulations of our interest and calculating sensitivity and specificity.ResultsWe found significant differences between negative and positive groups for Q-flag “Blasts/Abn Lympho?” (B/AL) and LY-X (p <0.05) with lymphocyte counts below 5×109/L.A new gate P1 normalized by P2 (P1n) differentiated between phenotypes much better than Q-flag B/AL with lymphocyte counts ≤ 5 ×109/L. Moreover, cases with MBL CD5 positive had higher medians (p <0.05).ConclusionWe propose a gate P1n as a new Q-flag for lymphocytes count ≤ 5 ×109/L, in order to hypothesize the presence of MBL CD5 positives.
Protein as evolvable functionally-constrained amorphous matter
Authors: Tripathy Madhusmita , Srivastava Anand , Sastry Srikanth , Rao Madan 
Published: July 2022

AbstractWe explore current ideas around the representation of a protein as an amorphous material, in turn represented by an abstract graph 𝒢 with edges weighted by elastic stiffnesses. By embedding this graph in physical space, we can map every graph to a spectrum of conformational fluctuations and responses (as a result of say, ligand-binding). This sets up a “genotype-phenotype” map, which we use to evolve the amorphous material to select for fitness. Using this, we study the emergence of allosteric interaction, hinge joint, crack formation and a slide bolt in functional proteins such as Adenylate kinase, HSP90, Calmodulin and GPCR proteins. We find that these emergent features are associated with specific geometries and mode spectra of floppy or liquid-like regions. Our analysis provides insight into understanding the architectural demands on a protein that enable a prescribed function and its stability to mutations.
Three-dimensional humanized gingival tissue model to study oral microbiome
Authors: Adelfio Miryam , Martin-Moldes Zaira , Erndt-Marino Joshua , Tozzi Lorenzo , Duncan Margaret J. , Hasturk Hatice , Kaplan David L. , Ghezzi Chiara E. 
Published: July 2022

AbstractThe oral cavity contains different microenvironments, as the non-shedding surface of the teeth and the epithelial mucosa, where oral barriers and microbial communities coexist. The interactions and balances between these two communities are responsible for oral tissue homeostasis or dysbiosis, that ultimately dictate health or disease. Disruption of this equilibrium is the first necessary step towards chronic inflammation and permanent tissue damage in the case of chronic periodontitis. There are currently no experimental models able to mimic the structural, physical, and metabolic conditions present in the oral gingival tissue to support the long-term investigation of host-pathogens unbalances. Herein, we report a 3D anatomical gingival in vitro model based on human primary culture that recapitulates the native tissue organization, and a native oxygen gradient within the gingival pocket to support human microbiome persistence with a physiologically relevant level of microbial diversity as well as native spatial organization. The modulation of inflammatory markers in the presence of oral microbiome suggested the humanized functional response of this model. The model will be used in future studies to investigate host-pathogen unbalances in gingivitis and periodontal disease.
Hippocampal and Medial Prefrontal Cortical Maps Represent Episodes and Rules in a Common Task Space
Authors: Srinivasan Aditya , Riceberg Justin S. , Goodman Michael R. , Srinivasan Arvind , Guise Kevin G. , Shapiro Matthew L. 
Published: July 2022

AbstractMemory helps us adapt to changing circumstances but needs guidance to retrieve relevant episodes. Episodic memory requires the hippocampus, the prefrontal cortex (PFC) guides memory retrieval, but how their representations interact is unclear. Using state-space analysis of neuronal spiking, we found CA1 and PFC activity within and between rats formed similar, low-dimensional, region-specific “shapes” representing different tasks tested in the same maze. Task shapes were organized by behaviorally salient variables including time and maze start and goal locations. PFC predicted CA1 representations when both regions were needed to solve a spatial memory task, but not in a cue approach task that required neither region. Task demands imposed common dimensions on CA1 and PFC maps whose topologies distinguished episodic and rule-related computations.
Osteocytes regulate organismal senescence of bone and bone marrow
Authors: Ding Peng , Gao Chuan , Gao Youshui , Liu Delin , Li Hao , Xu Jun , Chen Xiaoyi , Huang Yigang , Zhang Changqing , Zheng Minghao , Gao Junjie 
Published: July 2022

AbstractThe skeletal system contains a series of sophisticated cellular lineages arisen from the mesenchymal stem cells (MSC) and hematopoietic stem cells (HSC), that determine the homeostasis of bone and bone marrow. Here we reasoned that osteocyte may exert a function in regulation of these lineage cell specifications and tissue homeostasis. Using a mouse model of conditional deletion of osteocytes by the expression of diphtheria toxin subunitα(DTA) in dentin matrix protein 1 (DMP-1) positive osteocytes, we demonstrated that partial ablation of DMP-1positive osteocytes caused severe sarcopenia, osteoporosis and degenerative kyphosis, leading to shorter lifespan in these animals. Osteocyte reduction altered mesenchymal lineage commitment resulting in impairment of osteogenesis and induction of osteoclastogensis. Single cell RNA sequencing further revealed that hematopoietic lineage was mobilized towards myeloid lineage differentiation with expanded myeloid progenitors, neutrophils and monocytes, while the lymphopoiesis was impaired with reduced B cells in the osteocyte ablation mice. The acquisition of a senescence-associated secretory phenotype (SASP) in both osteoprogenic and myeloid lineage cells was the underlying cause. Together, we showed that osteocytes play critical roles in regulating of lineage cell specifications in bone and bone marrow through mediation of organismal senescence.
Scaling up submerged fermentation process of Aspergillus fumigatus mga for an efficient metabolite production (xylanase)
Authors: Gares Maroua , Hiligsmann Serge , Kacem Chaouche Noreddine 
Published: July 2022

AbstractFungal metabolites production at an industrial scale requires a sufficient yield at relatively low cost. Indeed, the scaling-up process is one of the main bottlenecks in the fermentation procedure; the reproduction of the best conditions achieved in small bio-reactors when transferring them to a much larger fermentation scale is near impossible.The present study seeks to study the fermentation profile of Aspergillus fumigatus fungi, in order to spot it logarithmic phase using xylose as substrate in different volumes; 250 mL flasks, 2 L and 20 L bioreactors, before conducting further experiments for an efficient secondary metabolite production (xylanase). The agitation speed impact on the morphological changing of this fungi was also studied.
Network analysis reveals the molecular bases of statin pleiotropy that vary with genetic background
Authors: del Rio Hernandez Cintya E. , Campbell Lani J. , Atkinson Paul H. , Munkacsi Andrew B. 
Published: July 2022

AbstractMany approved drugs are pleiotropic, for example statins, whose main cholesterol lowering activity is complemented by anticancer and pro-diabetogenic mechanisms involving poorly characterized genetic interaction networks. We investigated these using theSaccharomyces cerevisiaegenetic model where most genetic interactions known are limited to the statin-sensitive S288C genetic background. We therefore broadened our approach by investigating gene interactions to include two statin-resistant UWOPS87-2421 and Y55 genetic backgrounds. Networks were functionally focused by selection ofHMG1andBTS1mevalonate pathway genes for detecting genetic interactions. Networks, multi-layered by genetic background, were analysed for modifying key genes using network centrality (degree, betweenness, closeness), pathway enrichment, functional community modules and gene ontology. Statin treatment induces the unfolded protein response and we found modifying genes related to dysregulated endocytosis and autophagic cell death. To translate results to human cells, human orthologues were searched for other drugs targets, thus identifying candidates for synergistic anticancer bioactivity.
SOCS2 regulation of growth hormone signaling requires a canonical interaction with phosphotyrosine
Authors: Li Kunlun , Meza-Guzman Lizeth , Whitehead Lachlan , Leong Evelyn , Kueh Andrew , Alexander Warren S. , Kershaw Nadia J. , Babon Jeffrey J. , Doggett Karen , Nicholson Sandra E. 
Published: July 2022

AbstractSuppressor Of Cytokine Signaling (SOCS) 2 is the critical negative regulator of growth hormone (GH) and prolactin signaling. Mice lacking SOCS2 display gigantism with increased body weight and length, and an enhanced response to GH treatment. Here we characterized mice carrying a germ-line R96C mutation within the SOCS2-SH2 domain, which disrupts the ability of SOCS2 to interact with tyrosine phosphorylated targets.Socs2R96C/R96Cmice displayed a similar increase in growth as previously observed in SOCS2 null (Socs2-/-) mice, with a proportional increase in body and organ weight, and bone length. Embryonic fibroblasts isolated fromSocs2R96C/R96CandSocs2-/-mice also showed a comparable increase in phosphorylation of STAT5 following GH stimulation, indicating the critical role of phosphotyrosine binding in SOCS2 function.
The evolution of cooperation in the unidirectional linear division of labour of finite roles
Authors: Afif Nirjhor Md Sams , Nakamaru Mayuko 
Published: July 2022

AbstractEvolution of cooperation is a puzzle in evolutionary biology and social sciences. Previous studies assumed that players are equal and have symmetric relationships. In our society, players are in different roles, have an asymmetric relationship, and cooperate together. We focused on the linear division of labour in a unidirectional chain that has finite roles, each of which is assigned to one group with cooperators and defectors. A cooperator in an upstream group produces and modifies a product, paying a cost of cooperation, and hands it to a player in a downstream group who obtains the benefit from the product. If players in all roles cooperate, a final product can be completed. However, if a player in a group chooses defection, the division of labour stops, the final product cannot be completed, and all players in all roles suffer damage. By using the replicator equations of the asymmetric game, we investigate which sanction system promotes the evolution of cooperation in the division of labour. We find that not the benefit of the product but the cost of cooperation matters to the evolutionary dynamics and that the probability of finding a defector determines which sanction system promotes the evolution of cooperation.
Drivers and prevalence of COVID-19 vaccine uptake among homeless and precariously housed people in France: a cross-sectional population-based study
Authors: Roederer Thomas , Mollo Bastien , Vincent Charline , Leduc Ghislain , Sayyad Jessica , Mosnier Marine , Vandentorren Stéphanie 
Published: July 2022

ABSTRACTBackgroundFew global data exist regarding COVID-19 vaccine coverage in people experiencing homelessness (PEH) or precariously housed (PH) who are at high risk for COVID-19 infection, hospitalization, and death. Given the absence of documented French data, we aimed to determine COVID-19 vaccine coverage in PEH/PH in France, and its drivers.MethodsWe carried out a cross-sectional study following a two-stage cluster-sampling design in Ile-de-France and Marseille, France, in late 2021. Participants aged over 18 years were recruited where they slept the previous night, and then stratified for analysis into three housing groups (“Streets”, “Accommodated”, and “Housed”). Interviews were conducted face-to-face in the participant’s preferred language. Multilevel univariate and multivariable logistic regression models were built.Findings3,690 individuals were surveyed: 855 in the “Housed” stratum, 2,321 in the “Accommodated” stratum and 514 in the “Streets” stratum. 76·2% (95%CI 74·3-78·1) reported receiving at least one COVID-19 vaccine dose. Vaccine uptake varied by stratum, with uptake highest (85.6%; reference) in “Housed”, followed by “Accommodated” (75·4%; AOR=0·79 ; 95%CI 0·51-1·09 vs Housed) and lowest in “Streets” (42·0%; AOR=0·38 ; 95%CI 0·25-0·57 vs Housed). Use for vaccine certificate, socioeconomic drivers and vaccine hesitancy explained vaccine coverage.InterpretationIn France, PEH/PH are less likely than the general population likely to receive COVID-19 vaccines; with the most excluded being the least likely. The influence of both structural drivers and vaccine beliefs in PEH/PH reinforces the importance of targeted outreach, on-site vaccination and sensitisation activities to further vaccine uptake.FundingSanté Publique France, Agence Nationale de Recherches sur le Sida/Capnet, Agence Régionale de Santé – Ile de France, Médecins Sans Frontières, and Société de Pathologie Infectieuse de Langue Française.
A pilot surveillance report of SARS-CoV-2 rapid antigen test results among volunteers in Germany, 1st week of July 2022
Authors: Stemler Jannik , Salmanton-García Jon , Weise Ben , Többen Christina , Joisten Carolin , Fleig Julian , Cornely Oliver A. 
Published: July 2022

AbstractWe hypothesized that reported SARS-CoV-2 infection numbers are underestimated and piloted a point prevalence by rapid antigen testing in the VACCELERATE volunteer registry.Between July-1 and July-7, 2022, 7/419 (1.67%) tests were positive. Compared to reports of the German Federal Government, our results suggest a 2.39-fold higher prevalence.Our findings imply that the actual prevalence of SARS-CoV-2 may be higher than detected by current surveillance systems, so that current pandemic surveillance and testing strategies need to be adapted.
COVID-19 Vaccine Booster Dose Willingness Among Patients with Inflammatory Bowel Disease on Infliximab and Vedolizumab: A Cross-Sectional Study
Authors: Shehab Mohammad , Alrashed Fatema , Alfadhli Ahmad 
Published: July 2022

AbstractBackgroundVaccination has been effective in preventing COVID-19 infections and related mortality. However, waning immunity after the two-dose vaccination prompted health authorities to recommend a third dose of COVID-19 vaccine to boost immunity. The aim of our study was to assess willingness to receive a third (booster) dose among patients with IBD.MethodsA cross-sectional study was performed at a tertiary care inflammatory bowel disease center. Patients were recruited at the infusion room from January 1st, 2022, until March 31st, 2022. The primary outcome was the prevalence of BNT162b2 third (booster) dose in infliximab- or vedolizumab-treated patients with IBD. The secondary outcome evaluated whether the prevalence of BNT162b2 third (booster) dose differed based on type of COVID-19 vaccine, gender, age, type of biologic therapy and citizenship.ResultsIn total, 499 patients with IBD were included in this study. The median age was 34.5 years, and 60% had ulcerative colitis (UC). Among the study participants, 302 (60.5%) patients were vaccinated with BNT162b2, and 197 (39.5%) were vaccinated with ChAdOx1 nCoV-19. Of the total number of participants, 400 (80.2%) were receiving infliximab, and 99 (19.8%) were receiving vedolizumab. Overall, 290 (58.1%) of the included patients were willing to receive the third (booster) dose. Patients vaccinated with BNT162b2 were more likely to receive booster dose compared to patients vaccinated with ChAdOx1 nCoV-19 [201 (66.5%) vs 101 (33.5%), p = 0.014]. Infliximab-treated patients were more likely to receive booster dose compared to patients receiving vedolizumab [310 (77.5%) vs 62 (62.6%), p = 0.002]. There was no statistical difference in willingness to receive booster dose in terms of age, nationality, or gender.ConclusionThe percentage of patients with IBD willing or have received a third (booster) dose of BNT162b2 vaccine was lower compared to general population. In addition, patients who received two doses of BNT162b2 vaccines were more likely to receive a third (booster) dose compared to patients who received ChAdOx1 nCoV-19. Patients treated with infliximab were more likely to receive a third (booster) dose of COVID-19 vaccine.
Phenome-wide association network demonstrates close connection with individual disease trajectories from the HUNT study
Authors: Hall Martina , Skinderhaug Marit K. , Almaas Eivind 
Published: July 2022

AbstractBackgroundDisease networks offer a potential road map of connections between diseases. Several studies have created disease networks where diseases are connected either based on shared genes or Single Nucleotide Polymorphisms (SNP) associations. However, it is still unclear to which degree SNP-based networks map to empirical co-observed diseases within a different, general, adult study population spanning over a long time period.MethodsWe create a SNP-based disease network (PheNet) from a large population using the UK biobank phenome-wide association studies. Importantly, the SNP-associations are adjusted for linkage disequilibrium, case/control imbalances, as well as relatedness. We map the PheNet on to significantly co-occurring diseases in the Norwegian HUNT study population, and further, identify consecutively occurring diseases with significant occurrence in the PheNet.ResultsWe find that the overlap between the networks are far larger than expected, where most diseases tend to link to diseases of the same category and some categories are more linked to each other than expected by chance. Considering the ordering of consecutively occurring diseases in the HUNT data, we find that many diabetic disorders and cardiovascular disorders are subsequent the diagnostication of obesity and overweight, and cardiovascular disorders that often tend to be observed subsequent to other diseases are associated with higher mortality rates.ConclusionsThe HUNT sub-PheNet showing both genetically and co-observed diseases offers an interesting framework to study groups of diseases and examine if they, in fact, are comorbidities and pinpoint exactly which mutation(s) that constitute shared cause of the diseases. This could be of great benefit to both researchers and clinicians studying relationships between diseases.
Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics
Authors: Saarenpää Sami , Shalev Or , Ashkenazy Haim , de Oliveira-Carlos Vanessa , Lundberg Derek Severi , Weigel Detlef , Giacomello Stefania 
Published: July 2022

AbstractAll multicellular organisms are closely associated with microbes, which have a major impact on the health of their host. The interactions of microbes among themselves and with the host take place at the microscale, forming complex networks and spatial patterns that are rarely well understood due to the lack of suitable analytical methods. The importance of high-resolution spatial molecular information has become widely appreciated with the recent advent of spatially resolved transcriptomics. Here, we present Spatial metaTranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and found tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intra-kingdom spatial interactions among microbes, as well as the host response to microbial hotspots. SmT is a powerful new strategy that will be pivotal to answering fundamental questions on host-microbiome interplay.