bluuebunny/crossref_metadata_2025 huggingface dataset:
IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHC CII complexes
Authors: Qiu Zhijun , Khalife Jihane , Lin An-Ping , Ethiraj Purushoth , Jaafar Carine , Chiou Lilly , Huelgas-Morales Gabriela , Aslam Sadia , Arya Shailee , Gupta Yogesh K. , Dahia Patricia L. M. , Aguiar Ricardo C.T.
Published: October 2023

In diffuse large B-cell lymphoma (DLBCL), the transcription factor IRF8 is the target of a series of potentially oncogenic events, including, chromosomal translocation, focal amplification, and super-enhancer perturbations. IRF8 is also frequently mutant in DLBCL, but how these variants contribute to lymphomagenesis is unknown. We modeled IRF8 mutations in DLBCL and found that they did not meaningfully impact cell fitness. Instead, IRF8 mutants, mapping either to the DNA-binding domain (DBD) or c-terminal tail, displayed diminished transcription activity towards CIITA, a direct IRF8 target. In primary DLBCL, IRF8 mutations were mutually exclusive with mutations in genes involved in antigen presentation. Concordantly, expression of IRF8 mutants in murine B cell lymphomas uniformly suppressed CD4, but not CD8, activation elicited by antigen presentation. Unexpectedly, IRF8 mutation did not modify MHC CII expression on the cell surface, rather it downmodulated CD74 and HLA- DM, intracellular regulators of antigen peptide processing/loading in the MHC CII complex. These changes were functionally relevant as, in comparison to IRF8 WT, mice harboring IRF8 mutant lymphomas displayed a significantly higher tumor burden, in association with a substantial remodeling of the tumor microenvironment (TME), typified by depletion of CD4, CD8, Th1 and NK cells, and increase in T-regs and Tfh cells. Importantly, the clinical and immune phenotypes of IRF8-mutant lymphomas were rescued in vivo by ectopic expression of CD74. Deconvolution of bulk RNAseq data from primary human DLBCL recapitulated part of the immune remodeling detected in mice and pointed to depletion of dendritic cells as another feature of IRF8 mutant TME. We concluded that IRF8 mutations contribute to DLBCL biology by facilitating immune escape.
Information theory of chemotactic agents using both spatial and temporal gradient-sensing
Authors: Rode Julian , Novak Maja , Friedrich Benjamin M.
Published: October 2023

Biological cells and small organisms navigate in concentration fields of signaling molecules using two fundamental gradient-sensing strategies: spatial comparison of concentrations measured at different positions on their surface, or temporal comparison of concentrations measured at different locations visited along their motion path. It is believed that size and speed dictate which gradient-sensing strategy cells choose, yet this has never been formally proven. Using information theory, we investigate the optimal gradient-sensing mechanism for an ideal chemotactic agent that combines spatial and temporal comparison. We account for physical limits of chemo-sensation: molecule counting noise at physiological concentrations, and motility noise inevitable at the micro-scale. Our simulation data collapses onto an empirical power-law that predicts an optimal weighting of information as function of motility and sensing noise, demonstrating how spatial comparison becomes more beneficial for agents that are large, slow and less persistent. This refines and quantifies the previous heuristic notion. Our idealized model assuming unlimited information processing capabilities serves as a benchmark for the chemotaxis of biological cells.
Phospholipid Scramblase-1 is required for efficient neurotransmission and synaptic vesicle retrieval at cerebellar synapses
Authors: Caputo Margherita , Ivanova Daniela , Chasserot-Golaz Sylvette , Doussau Frédéric , Haeberlé Anne-Marie , Ozkan Sebahat , Ecard Jason , Bader Marie-France , Vitale Nicolas , Cousin Michael A. , Tóth Petra , Gasman Stéphane , Ory Stéphane
Published: October 2023

Structural phospholipids are asymmetrically distributed at the plasma membrane, with phosphatidylethanolamine and phosphatidylserine (PS) virtually absent from the outer leaflet. This asymmetric lipid distribution is transiently altered during specific biological processes including calcium-regulated exocytosis. However, the impact of this transient remodeling of membrane asymmetry on presynaptic function remains unknown.

PhosphoLipid SCRamblase 1 (PLSCR1), a protein that randomizes phospholipid distribution between the two leaflets of the plasma membrane in response to calcium activation is an ideal candidate to alter this asymmetry. We therefore set out to determine the role of PLSCR1 in both neurotransmitter release and synaptic vesicle recycling by combining electron microscopy, optical live cell imaging of pHluorin probes and electrophysiology in cerebellar granule cells (GrC) fromPlscr1knock-out mice (Plscr1-/-). We report that PLSCR1 is expressed in GrCs and that PLSCR1-dependent PS egress occurred at synapses in response to neuron stimulation. Furthermore, synaptic transmission is impaired at GrCPlscr1-/-synapses and both PS egress and synaptic vesicle endocytosis are inhibited inPlscr1-/-cultured neurons, demonstrating that PLSCR1 controls phospholipid asymmetry remodeling and synaptic vesicle retrieval following neurotransmitter release. Altogether, our data reveal a key role for PLSCR1 in synaptic vesicle recycling and provide the first evidence that phospholipid scrambling at the plasma membrane is a prerequisite for optimal presynaptic performance.
Deletion of SMC renders FtsK essential inCorynebacterium glutamicum
Authors: Peng Feng , Giacomelli Giacomo , Meyer Fabian , Linder Marten , Haak Markus , Rückert-Reed Christian , Weiß Manuela , Kalinowski Jörn , Bramkamp Marc
Published: October 2023

Structural maintenance of chromosomes (SMC) are ubiquitously distributed proteins involved in chromosome organization. Deletion ofsmccauses severe growth phenotypes in many organisms. Surprisingly,smccan be deleted inCorynebacterium glutamicum, a member of the Actinomycetota phylum, without any apparent growth phenotype. Earlier work has shown that SMC inC. glutamicumis loaded in a ParB-dependent fashion to the chromosome and functions in replichore cohesion. The unexpected absence of a growth phenotype in thesmcmutant prompted us to screen for unknown synthetic interactions withinC. glutamicum. Therefore, we generated a high-density Tn-5 library based on wild-type andsmc-deletedC. glutamicumstrains. The transposon sequencing (Tn-seq) data revealed that the DNA-translocase FtsK is essential in asmcdeletion strain. FtsK localized to the septa and cell poles in wild type cells, however deletion ofsmcresulted in a decreased polar FtsK localization. Single-particle tracking analysis further suggests that prolonged FtsK complex activity is both required and sufficient to make up for the absence of SMC, thus achieving efficient chromosome segregation inC. glutamicum. Further, single molecule dynamics of FtsK is influenced, albeit indirectly, by DNA-loaded SMC. Deletion of ParB results in an increased of both SMC and FtsK mobility. While the first change agrees with previous data that show how ParB is essential for SMC loading on DNA, the latter suggests that FtsK mobility is affected in cells with defects in chromosome organization. Based on our data we propose a simple, yet efficient mechanism for efficient DNA segregation inC. glutamicum, even in absence of SMC proteins.

Importance

Faithful DNA segregation is of fundamental importance for life. Bacteria have efficient systems to coordinate chromosome compaction, DNA segregation and cell division. A key factor in DNA compaction is the SMC-complex that is found to be essential in many bacteria. In members of the Actinomycetotasmcis dispensable, but the reason for this was unclear. We show here that the divisome associated DNA-pump FtsK can compensate SMC loss and the subsequent loss in correct chromosome organization. In cells with distorted chromosomes, FtsK functions for an extended period of time at the septum, until chromosomes are segregated.
Non-responsive Celiac disease symptoms associated with microbiome network structure and function
Authors: Marcos-Zambrano Laura Judith , Lacruz-Plegezuelos Blanca , Valdés Alberto , Aguilar-Aguilar Elena , Loria-Kohen Viviana , Cifuentes Alejandro , Ramírez de Molina Ana , Carrillo de Santa Pau Enrique
Published: October 2023

Non-responsive celiac disease (NRCD) poses a challenge for clinicians due to the persistence of symptoms despite maintaining a gluten-free diet (GFD). This study investigated the gut microbiome, mucosal integrity, and metabolomic profiles of 39 NRCD patients to gain insights into the underlying mechanisms contributing to symptom persistence. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption.

Cluster 1, labelled “Low-grade symptoms,” displayed milder symptoms and lower inflammatory markers. In contrast, Cluster 2, named “High-grade symptoms,” exhibited more severe gastrointestinal and extraintestinal symptoms, along with elevated inflammatory markers and increased intestinal permeability.

Despite similar mucosal damage in both clusters, network analysis of the gut microbiome revealed specific microbial taxa with potential functional implications. Cluster 1 displayed a microbiome associated with immune homeostasis and gut barrier integrity, potentially lowering inflammation and symptom severity. In contrast, Cluster 2 had a distinct microbiome linked to lactate production, Th17 activation, possibly contributing to heightened inflammation and gastrointestinal symptoms.

Metabolomic analysis revealed differential metabolites between clusters, particularly in amino acid metabolism pathways. Metabolites associated with specific symptoms were identified, implicating their potential role in symptom manifestation. Notably, vitamin D deficiency was observed in both clusters, suggesting its relevance in the context of NRCD.

The study highlights the importance of the gut microbiome, mucosal integrity, and metabolic pathways in symptom persistence among NRCD patients. The associations between microbial-derived metabolites and symptom severity provide valuable insights into potential therapeutic targets. Further research is needed to validate these findings and develop targeted interventions for improving clinical outcomes in NRCD patients.
The genetic basis of novel trait gain in walking fish
Authors: Herbert Amy L , Allard Corey AH , McCoy Matthew J , Wucherpfennig Julia I , Krueger Stephanie P , Chen Heidi I , Gourlay Allex N , Jackson Kohle D , Abbo Lisa A , Bennett Scott H , Sears Joshua D , Rhyne Andrew L , Bellono Nicholas W , Kingsley David M
Published: October 2023

A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb genetbx3ain the evolution of chemosensory legs in walking fish.
Selective Smurf1 E3 ligase inhibitors that prevent transthiolation
Authors: Chuong Patrick , Statsyuk Alexander
Published: October 2023

Smurf1 is a HECT E3 ligase that is genetically micro-duplicated in human patients and is associated with osteoporosis. Smurf1-/-mice on the other hand show an increase in bone density as they age, while being viable and fertile. Therefore, Smurf1 is a promising drug target to treat osteoporosis. This paper reports the discovery, synthesis, and biochemical characterization of highly selective Smurf1 inhibitors. We show that these compounds inhibit the catalytic HECT domain of Smurf1 with 500 nM IC50, but they do not inhibit closely related Smurf2 ligase, which is 80% identical to Smurf1. We show that Smurf1 inhibitors act by preventing the trans-thiolation reaction between Smurf1 and E2∼Ub thioesters. Our preliminary studies show that the C-lobe of Smurf1 alone does not contribute to the observed high selectivity of Smurf1 inhibitors.
Temporal restriction of RNAi reveals breakdown of the segmentation clock is reversible after knock down of primary pair rule genes but not Wnt-signaling in the red flour beetle
Authors: Kaufholz Felix , Ulrich Julia , Hakeemi Muhammad Salim , Bucher Gregor
Published: October 2023

Animals from all major clades have evolved a segmented trunk, reflected for instance in the repetitive organization of the human spine or the insect segments. These units emerge during embryonic segmentation from a posterior segment addition zone, where repetitive gene activity is regulated in a spatiotemporal dynamic described by the clock and wavefront/speed gradient model. This model has been tested in the red flour beetleTribolium castaneumand other insects by studying the effect of the RNAi knockdown of segmentation genes. For upstream components such as primary pair rule genes, caudal or Wnt pathway components, this treatment often led to the breakdown of segmentation. However, it has remained untested, how the system would react to a temporally limited interruption of gene function. In order to ask such questions, we established a novel experimental system inT. castaneum, which allows blocking an ongoing RNAi effect with temporal control by expressing a viral inhibitor of RNAi. We show that theT. castaneumsegmentation machinery re-established after we blocked an ongoing RNAi response targeting the primary pair rule genesTc-eve, Tc-oddandTc-runt. However, we observed no rescue after blocking RNAi responses targeting Wnt pathway components. We conclude that the insect segmentation system contains both, robust feedback-loops that can re-establish and labile feedback loops that can breakdown irreversibly. This combination may reconcile two partially conflicting needs of the embryonic regulation of segmentation: A tightly controlled initiation and maintenance of the SAZ by labile feedback-loops ensures that only one segment addition zone is formed. Conversely, robust feedback-loops confer developmental robustness required for proper segmentation, which may be challenged by internal or external disturbances. Our results ponder the insect segmentation machinery from a different angle and introduce a new experimental tool for temporal control on RNAi.

Significance statement

The generation of repetitive body parts during embryonic segmentation has been of key interest to developmental biologists, who usually used permanent knock-down of gene function for their studies. Using a new tool to temporally stop a gene knock-down effect, we find both robust and labile feedback-loops within the segmentation machinery. Thereby, the embryo may ensure that only one trunk is formed but that trunk formation is robust against external disturbance.
Sex-specific gut bacteria manipulation impacts offspring production in the honeybee parasite small hive beetle,Aethina tumidaMurray
Authors: Biswas Md Jamil , Khan Md Kawsar , Bashiribod Sahareh , Ponton Fleur
Published: October 2023

Symbiotic bacteria play crucial roles in growth, development, behaviour, immunity, and metabolism of insects. Most of the research until now has explored the role of gut bacteria in insect model systems. The extent to which gut bacteria affect mating behaviour and reproduction of insect pest species still needs, however, to be fully comprehended. In this study, we aimed to investigate the effects of gut bacteria manipulation on mating behaviour and fecundity of a major beehive pest, the small hive beetleAethina tumida(Murray). We manipulated gut bacteria of both sexes and determined the effects on mating behaviour and reproductive output. Our results provided evidence that manipulation of the gut bacteria influences reproduction in both sexes, negatively affecting mating latency, mating number, mating duration and offspring number (larvae). These results highlight the role of gut bacteria on the reproduction of insect pests, which might help in designing new pest control methods.
Beyond six feet: The collective behavior of social distancing
Authors: Wu Zhijun
Published: October 2023

In a severe epidemic such as the COVID-19 pandemic, social distancing can be a vital tool to stop the spread of the disease and save lives. However, social distancing may induce profound negative social/economic impacts as well. How to optimize social distancing is a serious social, political, as well as public health issue yet to be resolved. This work investigates social distancing with a focus on how every individual reacts to an epidemic, what role he/she plays in social distancing, and how every individual’s decision contributes to the action of the population and vice versa. Social distancing is thus modeled as a population game, where every individual makes decision on how to participate in a set of social activities, some with higher frequencies while others lower or completely avoided, to minimize his/her social contacts with least possible social/economic costs. An optimal distancing strategy is then obtained when the game reaches an equilibrium. The game is simulated with various realistic restraints including (i) when the population is distributed over a social network, and the decision of each individual is made through the interactions with his/her social neighbors; (ii) when the individuals in different social groups such as children vs. adults or the vaccinated vs. unprotected have different distancing preferences; (iii) when leadership plays a role in decision making, with a few leaders making decisions while the rest of the population just follow. The simulation results show how the distancing game is played out in each of these scenarios, reveal the conflicting yet cooperative nature of social distancing, and shed lights on a self-organizing, bottom-up perspective of distancing practices.
Transcriptome-wide analysis of the function of Ded1 in translation preinitiation complex assembly in a reconstituted in vitro system
Authors: Zhou Fujun , Bocetti Julie M. , Hou Meizhen , Qin Daoming , Hinnebusch Alan G. , Lorsch Jon R.
Published: October 2023

We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S pre-initiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early steps in translation initiation in the absence of all other cellular components and processes. Using this approach we show that the DEAD-box ATPase Ded1 promotes 48S PIC formation on the start codons of >1000 native mRNAs, most of which have long, structured 5’-untranslated regions (5’UTRs). Remarkably, initiation measured in Rec-Seq was enhanced by Ded1 for most mRNAs previously shown to be highly Ded1-dependent by ribosome profiling ofded1mutants in vivo, demonstrating that the core translation functions of the factor are recapitulated in the purified system. Our data do not support a model in which Ded1acts by reducing initiation at alternative start codons in 5’UTRs and instead indicate it functions by directly promoting mRNA recruitment to the 43S PIC and scanning to locate the main start codon. We also provide evidence that eIF4A, another essential DEAD-box initiation factor, is required for efficient PIC assembly on almost all mRNAs, regardless of their structural complexity, in contrast to the preferential stimulation by Ded1 of initiation on mRNAs with long, structured 5’UTRs.
ListiWiki: a database for the foodborne pathogenListeria monocytogenes
Authors: Elfmann Christoph , Zhu Bingyao , Stülke Jörg , Halbedel Sven
Published: October 2023

Listeria monocytogenesis a Gram positive foodborne pathogen that regularly causes outbreaks of systemic infectious diseases. The bacterium maintains a facultative intracellular lifestyle; it thrives under a variety of environmental conditions and is able to infect human host cells.L. monocytogenesis genetically tractable and therefore has become an attractive model system to study the mechanisms employed by facultative intracellular bacteria to invade eukaryotic host cells and to replicate in their cytoplasm. Besides its importance for basic research,L. monocytogenesalso serves as a paradigmatic pathogen in genomic epidemiology, where the relative stability of its genome facilitates successful outbreak detection and elucidation of transmission chains in genomic pathogen surveillance systems. In both terms, it is necessary to keep the annotation of theL. monocytogenesgenome up to date. Therefore, we have created the databaseListiWiki (http://listiwiki.uni-goettingen.de/) which stores comprehensive information on the widely usedL. monocytogenesreference strain EDG-e.ListiWiki is designed to collect information on genes, proteins and RNAs and their relevant functional characteristics, but also further information such as mutant phenotypes, available biological material, and publications. In its present form,ListiWiki combines the most recent annotation of the EDG-e genome with published data on gene essentiality, gene expression and subcellular protein localization.ListiWiki also predicts protein-protein interactions networks based on protein homology toBacillus subtilisproteins, for which detailed interaction maps have been compiled in the sibling databaseSubtiWiki. Furthermore, crystallographic information of proteins is made accessible through integration of Protein Structure Database codes and AlphaFold structure predictions.ListiWiki is an easy-to-use web interface that has been developed with a focus on an intuitive access to all information. Use ofListiWiki is free of charge and its content can be edited by all members of the scientific community after registration. In our labs,ListiWiki has already become an important and easy to use tool to quickly access genome annotation details that we can keep updated with advancing knowledge. It also might be useful to promote the comprehensive understanding of the physiology and virulence of an important human pathogen.
Microbial communities from lean or obese are differently shaped after apple fibres supplementation
Authors: Dell’Olio Andrea , Scott William T. , Taroncher-Ferrer Silvia , San Onofre Nadia , Soriano Jose , Rubert Josep
Published: October 2023

Background

Obese microbial communities differ from lean ones. Previous studies have shown how dietary fiber interventions target the gut microbiome and effectively attenuate obesity-related conditions. Nevertheless, the mechanisms by which dietary fibres shape the gut microbiota are not elucidated yet. Thisin-vitrostudy investigated the differences between lean and obese microbiota and how they responded to dietary interventions using a multi-omics approach.

Results

By employingin vitrodigestion followed by microcolonic fermentations, we exposed obese and lean microbial communities to apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fibe. Metagenomics and metabolomics data indicated that obese and lean individuals had distinct starting microbial communities and functions. After 24 hours of exposure to different feeding conditions, the diet-responsive bacteria modulated the composition and functionality of lean and obese microbial communities. In the obese, the results suggested different mechanisms among gut commensals with an opportunistic lifestyle, allowing them to maximize their energy production from substrates breakdown and produce a specific profile of gut microbial metabolites (GMMs).

Conclusion

At the taxonomical and functional level, our results underscore that dietary fibres shape bacterial communities differently depending on their initial microbial composition. This modulation affects the production of GMMs. Eating foods high in fiber is recognised to promotes a healthy gut microbiome. However, the same intervention can result in varying metabolic profiles depending on the microbial communities, which may affect the host differently.
Dynamic changes in subplate and cortical plate microstructure at the onset of cortical folding in vivo
Authors: Wilson Siân , Christiaens Daan , Yun Hyukjin , Uus Alena , Cordero-Grande Lucilio , Karolis Vyacheslav , Price Anthony , Deprez Maria , Tournier Jacques-Donald , Rutherford Mary , Grant Ellen , Hajnal Joseph V. , Edwards A David , Arichi Tomoki , O’Muircheartaigh Jonathan , Im Kiho
Published: October 2023

Cortical gyrification takes place predominantly during the second to third trimester, alongside other fundamental developmental processes, such as the development of white matter connections, lamination of the cortex and formation of neural circuits. The mechanistic biology that drives the formation cortical folding patterns remains an open question in neuroscience. In our previous work, we modelled the in utero diffusion signal to quantify the maturation of microstructure in transient fetal compartments, identifying patterns of change in diffusion metrics that reflect critical neurobiological transitions occurring in the second to third trimester. In this work, we apply the same modelling approach to explore whether microstructural maturation of these compartments is correlated with the process of gyrification. We quantify the relationship between sulcal depth and tissue anisotropy within the cortical plate (CP) and underlying subplate (SP), key transient fetal compartments often implicated in mechanistic hypotheses about the onset of gyrification. Using in utero high angular resolution multi-shell diffusion-weighted imaging (HARDI) from the Developing Human Connectome Project (dHCP), our analysis reveals that the anisotropic, tissue component of the diffusion signal in the SP and CP decreases immediately prior to the formation of sulcal pits in the fetal brain. By back-projecting a map of folded brain regions onto the unfolded brain, we find evidence for cytoarchitectural differences between gyral and sulcal areas in the late second trimester, suggesting that regional variation in the microstructure of transient fetal compartments precedes, and thus may have a mechanistic function, in the onset of cortical folding in the developing human brain.
Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer
Authors: Wang Hexiao , Canasto-Chibuque Claudia , Kim Jun Hyun , Hohl Marcel , Leslie Christina , Reis-Filho Jorge S , Petrini John HJ
Published: October 2023

The Mre11 complex (comprising Mre11, Rad50, Nbs1) is integral to the maintenance of genome stability. We previously showed that a hypomorphicMre11mutant mouse strain (Mre11ATLD1/ATLD1) was highly susceptible to oncogene induced breast cancer. Here we used a mammary organoid system to examine which Mre11 dependent responses are tumor suppressive. We found thatMre11ATLD1/ATLD1organoids exhibited an elevated interferon stimulated gene (ISG) signature and sustained changes in chromatin accessibility. ThisMre11ATLD1/ATLD1phenotype depended on DNA binding of a nuclear innate immune sensor, IFI205. Ablation ofIfi205inMre11ATLD1/ATLD1organoids restored baseline and oncogene-induced chromatin accessibility patterns to those observed inWT. Implantation ofMre11ATLD1/ATLD1organoids and activation of oncogene led to aggressive metastatic breast cancer. This outcome was reversed in implantedIfi205-/-Mre11ATLD1/ATLD1organoids. These data reveal a connection between innate immune signaling and tumor suppression in mammary epithelium. Given the abundance of aberrant DNA structures that arise in the context of genome instability syndromes, the data further suggest that cancer predisposition in those contexts may be partially attributable to tonic innate immune transcriptional programs.
Assessing three soil removal methods for environmental DNA analysis of mock forensic geology evidence
Authors: Tiedge Teresa M. , Meiklejohn Kelly A.
Published: October 2023

Soil is useful in criminal investigations as it is highly variable and readily transferred. Forensic geologists use several different techniques to removal soil from evidence prior to the analysis of inorganic components. There has been recent interest from the forensic science community to analyze environmental deoxyribonucleic acid (eDNA) associated with soil to augment existing forensic analyses. Notably however, limited research has been conducted to compare commonly used soil removal methods for downstream eDNA analysis. In this study, three soil removal methods were assessed: picking/scraping, sonication, and swabbing. Three mock evidence types (t‐shirts, boot soles, and trowels) were sampled in triplicate with each removal method (n = 27). Soil samples underwent DNA isolation, quantification, and amplification of four genomic barcode regions: 16S for bacteria, ITS1 for fungi, ITS2 for plants, and COI for arthropods. Amplicons were prepared into libraries for DNA sequencing on an Illumina® MiniSeq. DNA concentrations were highest in picked/scraped samples and were statistically significant compared with swabbed and sonicated samples. Amplicon sequence variants (ASVs) were identified, and removal methods had no impact on the recovery of the total number of target ASVs. Additionally, when assessing each sample in multidimensional space, picked/scraped samples tended to cluster separately from swabbed and sonicated samples. The soil core used a reference in this study also clustered with the picked/scraped samples, indicating that these samples may be more reflective of the communities collected from soil cores. Based on these data, we identified that picking/scraping is an acceptable soil removal method for eDNA analysis.
Non‐abstinent recovery in alcohol use disorder is associated with greater regional cortical volumes than heavy drinking
Authors: May A. C. , Meyerhoff D. J. , Durazzo T. C.
Published: October 2023

Background

Harm‐reduction (i.e., non‐abstinent recovery) approaches to substance use treatment have garnered increasing attention. Reduced levels of alcohol consumption post‐treatment have been associated with better psychosocial functioning and physical health, yet less is known regarding differences in brain structures associated with varying levels of alcohol consumption. This study investigated regional cortical volumes after alcohol use disorder (AUD) treatment among individuals who achieved complete abstinence and those who returned to lower and higher levels of consumption.

Methods

Data were collected from individuals with AUD (n = 68) approximately 8 months after the initiation of treatment. Using risk drinking levels defined by the World Health Organization, participants were classified as abstaining (AB) or relapsing with low (RL) or higher (RH) levels. Data were also obtained from 34 age‐matched light/non‐drinking controls (LN). All participants completed a 1.5 T magnetic resonance imaging session and volumes for 34 bilateral cortical regions of interest were quantitated with FreeSurfer. Generalized linear models were used to examine group differences in cortical volume. All group findings are significant at an FDR‐corrected value of 0.018.

Results

Adjusting for age and intracranial volume, significant group differences were found in 13/34 cortical regions. AB showed greater volumes than RL in 2/13 regions and RH in 6/13 regions. RH demonstrated significantly smaller volumes than LN in 12/13 ROIs, whereas RL differed from LN in 9/13 regions. RH and RL differed in only two cortical regions.

Conclusions

Individuals who consumed low‐risk levels of alcohol post‐treatment exhibited regional cortical volumes more similar to abstainers than individuals who returned to higher‐risk levels. This suggests that low‐risk levels of alcohol consumption are associated with brain integrity that is comparable to that seen with complete abstinence. Given the previously demonstrated improvement in psychosocial and physical health with reduced levels of alcohol consumption post‐treatment, harm reduction may be a beneficial and more attainable goal for some individuals with AUD who are seeking treatment.
Comparison of chemical and enzymatic maceration processes for soft tissue removal from arterial silicone casts on skull scaffolds
Authors: Granroth Janne , Laakkonen Juha
Published: October 2023

The various models used in gross anatomical studies to improve the visualization of blood vessels differ in the amount of manual labour, cost, equipment and time involved. This study aimed to compare chemical and enzymatic maceration processes for soft‐tissue removal from arterial silicone casts on skull scaffolds using ringed seal (Pusa hispida) skull specimens. Both processes produced specimens that covered all anatomical aspects required to visualize the intracranial arterial arrangement on a bone scaffold. Overall, the enzyme maceration process was better for production of such specimens, as this process is easy and safe to perform, is less harmful to the bony parts of the specimen, and the resulting specimens are visually more appealing for display and teaching. Compared with previously published models, the end result varied in the amount of dissolved bone tissue and the visual presentation of the model.
How open innovation specialists contribute to corporate sustainability and responsibility: A latent Dirichlet allocation approach
Authors: Culasso Francesca , Giacosa Elisa , Giordino Daniele , Crocco Edoardo
Published: October 2023

This study examines the job postings for open innovation (OI) specialists to determine a universal archetype of what competencies and tasks are requested from said professionals and their implications for corporate sustainability and responsibility. This research uses Bayesian statistics and latent Dirichlet allocation (LDA) topic modeling to measure multiple dimensions of the 341 sampled job postings. Our empirical findings unveil the pivotal role that OI specialists have in engaging with stakeholders and monitoring OI dynamics. Multiple dimensions are expected from OI specialists, addressing a multitude of concerns, such as the environment and technologies. Moreover, this study underlines the need for OI specialists to comprehend both internal and external stakeholders' needs. This research contributes to the literature as follows. First, it underlines the value of topic modeling analysis in job profiling research. Second, it bridges existing knowledge gaps on OI specialists' competencies and roles with empirical evidence obtained from a global dataset. Third, it outlines the current market expectations and requirements for OI specialists, which is useful to both candidates and companies.
Perspectives on technology: to use or to reuse, that is the endoscopic question—a systematic review of single‐use endoscopes
Authors: Anderson Steven , Patterson Kenneth , Skolarikos Andreas , Somani Bhaskar , Bolton Damien M. , Davis Niall F.
Published: October 2023

Objective

To compare clinical outcomes of single‐use endoscopes with those of reusable endoscopes to better define their role within urology.

Methods

A systematic search of electronic databases was performed. All studies comparing the clinical outcomes of participants undergoing urological procedures with single‐use endoscopes to those of participants treated with reusable endoscopes were included. Results are reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) 2020 statement.

Results

Twenty‐one studies in 3943 participants were identified. Six different single‐use flexible ureteroscopes and two different single‐use flexible cystoscopes were assessed. There were no differences in mean postoperative infection rates (4.0% vs 4.4%;P = 0.87) or overall complication rates (11.5% vs 11.9%;P = 0.88) between single‐use and reusable endoscopes. For patients undergoing flexible ureteroscopy there were no differences in operating time (mean difference −0.05 min;P = 0.96), length of hospital stay (LOS; mean difference 0.06 days;P = 0.18) or stone‐free rate (SFR; 74% vs 74.3%;P = 0.54) between the single‐use and reusable flexible ureteroscope groups.

Conclusion

This study is the largest to compare the clinical outcomes of single‐use endoscopes to those of reusable endoscopes within urology, and demonstrated no difference in LOS, complication rate or SFR, with a shorter operating time associated with single‐use flexible cystoscope use. It also highlights that the cost efficiency and environmental impact of single‐use endoscopes is largely dependent on the caseload and reprocessing facilities available within a given institution. Urologists can therefore feel confident that whether they choose to ‘use’ or to ‘reuse’ based on the financial and environmental implications, they can do so without negatively impacting patient outcomes.
Cathemerality: a key temporal niche
Authors: Cox Daniel T. C. , Gaston Kevin J.
Published: October 2023

Given the marked variation in abiotic and biotic conditions between day and night, many species specialise their physical activity to being diurnal or nocturnal, and it was long thought that these strategies were commonly fairly fixed and invariant. The term ‘cathemeral’, was coined in 1987, when Tattersall noted activity in a Madagascan primate during the hours of both daylight and darkness. Initially thought to be rare, cathemerality is now known to be a quite widespread form of time partitioning amongst arthropods, fish, birds, and mammals. Herein we provide a synthesis of present understanding of cathemeral behaviour, arguing that it should routinely be included alongside diurnal and nocturnal strategies in schemes that distinguish and categorise species across taxa according to temporal niche. This synthesis is particularly timely because (i) the study of animal activity patterns is being revolutionised by new and improved technologies; (ii) it is becoming apparent that cathemerality covers a diverse range of obligate to facultative forms, each with their own common sets of functional traits, geographic ranges and evolutionary history; (iii) daytime and nighttime activity likely plays an important but currently neglected role in temporal niche partitioning and ecosystem functioning; and (iv) cathemerality may have an important role in the ability of species to adapt to human‐mediated pressures.
Tilt table testing, methodology and practical insights for the clinic
Authors: van Zanten Steven , Sutton Richard , Hamrefors Viktor , Fedorowski Artur , de Lange Frederik J.
Published: October 2023

Tilt table testing (TTT) has been used for decades to study short‐term blood pressure (BP) and heart rate regulation during orthostatic challenges. TTT provokes vasovagal reflex in many syncope patients as a background of widespread use. Despite the availability of evidence‐based practice syncope guidelines, proper application and interpretation of TTT in the day‐to‐day care of syncope patients remain challenging. In this review, we offer practical information on what is needed to perform TTT, how results should be interpreted including the Vasovagal Syncope International Study classification, why syncope induction on TTT is necessary in patients with unexplained syncope and on indications for TTT in syncope patient care. The minimum requirements to perform TTT are a tilt table with an appropriate tilt‐down time, a continuous beat‐to‐beat BP monitor with at least three electrocardiogram leads and trained staff. We emphasize that TTT remains a valuable asset that adds to history building but cannot replace it, and highlight the importance of recognition when TTT is abnormal even without syncope. Acknowledgement by the patient/eyewitness of the reproducibility of the induced attack is mandatory in concluding a diagnosis. TTT may be indicated when the initial syncope evaluation does not yield a certain, highly likely, or possible diagnosis, but raises clinical suspicion of (1) reflex syncope, (2) orthostatic hypotension (OH), (3) postural orthostatic tachycardia syndrome or (4) psychogenic pseudosyncope. A therapeutic indication for TTT in the patient with a certain, highly likely or possible diagnosis of reflex syncope, may be to educate patients on prodromes. In patients with reflex syncope with OH TTT can be therapeutic to recognize hypotensive symptoms causing near‐syncope to perform physical countermanoeuvres for syncope prevention (biofeedback). Detection of hypotensive susceptibility requiring therapy is of special value.
Diabetes duration, perceived comfort with self‐management and glycaemic control in adolescents with type 1 diabetes: A cross‐sectional study
Authors: Renaud‐Charest Olivier , Mok Elise , Frei Jennifer , Brunet Marie‐Laurence , Henderson Mélanie , Rahme Elham , Dasgupta Kaberi , Nakhla Meranda
Published: October 2023

Aims

Evidence is lacking on whether diabetes duration is associated with type 1 diabetes (T1D) self‐management during late adolescence before transfer from paediatric to adult care. We examined associations of diabetes duration with dimensions of perceived comfort with diabetes self‐management (self‐efficacy, transition readiness, diabetes distress) and glycaemic control in late adolescence.

Methods

Using a cross‐sectional design, we conducted a secondary analysis of baseline data of adolescents (ages 16–17 years) with T1D followed at paediatric diabetes academic hospitals in Montreal and enrolled in the Group Education Trial to Improve Transition (GET‐IT‐T1D). Participants completed validated questionnaires on self‐efficacy (Self‐Efficacy for Diabetes Self‐Management Measure [SEDM], score 1 to 10), diabetes distress and transition readiness, as well as a haemoglobin (HbA1c) capillary blood test. Our primary outcome was self‐efficacy. We examined associations of diabetes duration with self‐efficacy, diabetes distress, transition readiness and HbA1c using linear and logistic regression models adjusted for sex, socioeconomic status, insulin pump use, glucose sensor use and psychiatric comorbidity.

Results

Of 203 adolescents with T1D, mean diabetes duration (SD) was 7.57 (4.44) years. Mean SEDM score was 6.83 (SD 1.62). Diabetes duration was not associated with self‐efficacy, diabetes distress or transition readiness. Each additional year of diabetes duration was associated with 0.11% (95% CI, 0.05 to 0.16) higher HbA1c.

Conclusions

Although diabetes duration is not associated with dimensions of perceived comfort with diabetes self‐management, adolescents with longer diabetes duration are at risk for higher HbA1c and may need additional support to improve glycaemic control before transition to adult care.
Good enough for outstanding growth: The experience of Bangladesh in comparative perspective
Authors: Beyer Robert C. M. , Wacker Konstantin M.
Published: October 2023

Motivation

Bangladesh's economic growth rate over the past three decades has been one of the highest in the world. This success is difficult to reconcile with a single macroeconomic explanation of development.

Purpose

Previous studies have investigated individual aspects that can explain Bangladesh's successful development. But a consistent account of how individual factors contributed to growth is currently missing. Can factors that correlate with growth in other countries explain the outstanding growth performance of Bangladesh? Or is the country's experience unique?

Methods and approach

We construct a panel data set for 149 countries since 1970 and combine growth regression techniques with a peer group comparison. Different specifications, subsamples, and estimation techniques are considered.

Findings

Factors correlating with growth in other countries can well explain the growth experience of Bangladesh. But two features are specific to the country. First, a combination of “good enough” policies led to considerable growth impulses between 1990 and 2005: the country's improvements in typical correlates of growth during this period were among the global top 5% for any 15‐year period investigated. Second, despite the absence of major reforms after 2005, Bangladesh defied the mean reversion in growth rates experienced by most fast‐growing economies and peer countries.

Policy implications

Our results support the idea that a combination of “good enough” policies can jump‐start high growth in low‐income countries. Our findings further demonstrate that a stable macroeconomic and institutional environment helps when it comes to reaping the benefits of structural improvements in the long run.
Shannon‐Cosine wavelet precision integration method for image enhancement based on fractional partial differential equations
Authors: Liu Meng , Min Zhao , Li Li , Cattani Piercarlo , Mei Shuli
Published: October 2023

Fractional order partial differential equations have a wide range of applications in image processing. The solution of partial differential equations is generally obtained using the finite difference method, which still requires improvement in terms of efficiency and effectiveness. In this work, a multi‐scale interpolative wavelet operator is constructed by means of Shannon‐Cosine wavelets with interpolation, smoothness, compact support and other excellent properties. We use the wavelet operator instead of the finite difference operator to solve fractional‐order partial differential equations. The proposed method can limit the artefacts and remove the noises appeared in the processed images effectively. In addition, for the loss of texture in the denoised image, we enhance the image by employing fractional order differential equations to improve the quality of the image. Finally, the biological sections images are taken as the examples to illustrate the effectiveness of the proposed method.
Ensemble learning model identifies adaptation classification and turning points of river microbial communities in response to heatwaves
Authors: Qu Qian , Xu Jing , Kang Weilu , Feng Ruihong , Hu Xiangang
Published: October 2023

Heatwaves are a global issue that threaten microbial populations and deteriorate ecosystems. However, how river microbial communities respond to heatwaves and whether and how high temperatures exceed microbial adaptation remain unclear. In this study, we proposed four types of pulse temperature‐induced microbial responses and predicted the possibility of microbial adaptation to high temperature in global rivers using ensemble machine learning models. Our findings suggest that microbial communities in parts of South American (e.g., Brazil and Chile) and Southeast Asian (e.g., Vietnam) countries are likely to change due to heatwave disturbance from 25 to 37°C for consecutive days. Furthermore, the microbial communities in approximately 48.4% of the global river gauge stations are prone to fast stress inadaptation, with approximately 76.9% of these stations expected to exceed microbial adaptation after heatwave disturbances. If emissions of particulate matter with sizes not more than 2.5 μm (PM2.5, an indicator of human activities) increase by twofold, the number of global rivers associated with the fast stress adaptation type will decrease by ~13.7% after heatwave disturbances. Understanding microbial responses is crucially important for effective ecosystem management, especially for fragile and sensitive rivers facing heatwave events.