bluuebunny/crossref_metadata_2025 huggingface dataset:
The control and training of single motor units in isometric tasks are constrained by a common synaptic input signal
Authors: Bräcklein Mario , Ibáñez Jaime , Barsakcioglu Deren Y , Eden Jonathan , Burdet Etienne , Mehring Carsten , Farina Dario
Published: August 2021

Recent developments in neural interfaces enable the real-time and non-invasive tracking of motor neuron spiking activity. Such novel interfaces provide a promising basis for human motor augmentation by extracting potential high-dimensional control signals directly from the human nervous system. However, it is unclear how flexibly humans can control the activity of individual motor neurones to effectively increase the number of degrees-of-freedom available to coordinate multiple effectors simultaneously. Here, we provided human subjects (N=7) with real-time feedback on the discharge patterns of pairs of motor units (MUs) innervating a single muscle (tibialis anterior) and encouraged them to independently control the MUs by tracking targets in a 2D space. Subjects learned control strategies to achieve the target-tracking task for various combinations of MUs. These strategies rarely corresponded to a volitional control of independent input signals to individual MUs. Conversely, MU activation was consistent with a common input to the MU pair, while individual activation of the MUs in the pair was predominantly achieved by alterations in de-recruitment order that could be explained with history-dependent changes in motor neuron excitability. These results suggest that flexible MU control based on independent synaptic inputs to single MUs is not a simple to learn control strategy.
A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics
Authors: Choi Sam B. , Muñoz-LLancao Pablo , Chiara Manzini M. , Nemes Peter
Published: August 2021

Measurement of broad types of proteins from a small number of cells to single cells would help to better understand the nervous system but requires significant leaps in high-resolution mass spectrometry (HRMS) sensitivity. Microanalytical capillary electrophoresis electrospray ionization (μCE-ESI) offers a path to ultrasensitive proteomics by integrating scalability with sensitivity. We report here a data acquisition strategy that expands the detectable and quantifiable proteome in trace amounts of digests using μCE-ESI-HRMS. Data-dependent acquisition (DDA) was programmed to progressively exclude high-intensity peptide signals during repeated measurements. These nested experiments formed rungs of our “DDA ladder.” The method was tested for replicates analyzing ~500 pg of protein digest from cultured hippocampal (primary) neurons (mouse), which estimates to the total amount of protein from a single neuron. Analysis of net amounts approximating to ~10 neurons identified 428 nonredundant proteins (415 quantified), an ~35% increase over traditional DDA. The identified proteins were enriched in neuronal marker genes and molecular pathways of neurobiological importance. The DDA ladder deepens the detectable proteome from trace amounts of proteins, expanding the analytical toolbox of neuroscience.
Bi-modal Variational Autoencoders for Metabolite Identification Using Tandem Mass Spectrometry
Authors: Kutuzova Svetlana , Igel Christian , Nielsen Mads , McCloskey Douglas
Published: August 2021

A grand challenge of analytical chemistry is the identification of unknown molecules based on tandem mass spectrometry (MS/MS) spectra. Current metabolite annotation approaches are often manual or partially automated, and commonly rely on a spectral database to search from or train machine learning classifiers on. Unfortunately, spectral databases are often instrument specific and incomplete due to the limited availability of compound standards or a molecular database, which limits the ability of methods utilizing them to predict novel molecule structures. We describe a generative modeling approach that can leverage the vast amount of unpaired and/or unlabeled molecule structures and MS/MS spectra to learn general rules for synthesizing molecule structures and MS/MS spectra. The approach is based on recent work using semi-supervised deep variational autoencoders to learn joint latent representations of multiple and complex modalities. We show that adding molecule structures with no spectra to the training set improves the prediction quality on spectra from a structure disjoint dataset of new molecules, which is not possible using bi-modal supervised approaches. The described methodology provides a demonstration and framework for how recent advances in semi-supervised machine learning can be applied to overcome bottlenecks in missing annotations and noisy data to tackle unaddressed problems in the life sciences where large volumes of data are available.
Cytoplasmic labile iron accumulates in aging stem cells perturbing a key rheostat for identity control
Authors: Kao Yun-Ruei , Chen Jiahao , Kumari Rajni , Tatiparthy Madhuri , Ma Yuhong , Aivalioti Maria M. , Zintiridou Aliona , Thiruthuvanathan Victor , Reisz Julie A. , Stranski Stephanie , Sidoli Simone , Steidl Ulrich , D’Alessandro Angelo , Will Britta
Published: August 2021

Bone marrow resident and rarely dividing haematopoietic stem cells (HSC) harbour an extensive self-renewal capacity to sustain life-long blood formation;1–5 albeit their function declines during ageing.6, 7 Various molecular mechanisms confer stem cell identity, ensure long-term maintenance and are known to be deregulated in aged stem cells.8, 9 How these programs are coordinated, particularly during cell division, and what triggers their ageing-associated dysfunction has been unknown. Here, we demonstrate that HSC, containing the lowest amount of cytoplasmic chelatable iron (labile iron pool)10 among hematopoietic cells, activate a limited iron response during mitosis. Engagement of this iron homeostasis pathway elicits mobilization and β-oxidation of arachidonic acid and enhances stem cell-defining transcriptional programs governed by histone acetyl transferase Tip60/KAT5. We further find an age-associated expansion of the labile iron pool, along with loss of Tip60/KAT5-dependent gene regulation to contribute to the functional decline of ageing HSC, which can be mitigated by iron chelation. Together, our work reveals cytoplasmic redox active iron as a novel rheostat in adult stem cells; it demonstrates a role for the intracellular labile iron pool in coordinating a cascade of molecular events which reinforces HSC identity during cell division and to drive stem cell ageing when perturbed. As loss of iron homeostasis is commonly observed in the elderly, we anticipate these findings to trigger further studies into understanding and therapeutic mitigation of labile iron pool-dependent stem cell dysfunction in a wide range of degenerative and malignant pathologies.
Stop Bickering! Reconciling Signaling Pathway Databases with Network Topologies
Authors: Rubel Tobias , Singh Pramesh , Ritz Anna
Published: August 2021

A major goal of molecular systems biology is to understand the coordinated function of genes or proteins in response to cellular signals and to understand these dynamics in the context of disease. Signaling pathway databases such as KEGG, NetPath, NCI-PID, and Panther describe the molecular interactions involved in different cellular responses. While the same pathway may be present in different databases, prior work has shown that the particular proteins and interactions differ across database annotations. However, to our knowledge no one has attempted to quantify their structural differences. It is important to characterize artifacts or other biases within pathway databases, which can provide a more informed interpretation for downstream analyses. In this work, we consider signaling pathways as graphs and we use topological measures to study their structure. We find that topological characterization using graphlets (small, connected subgraphs) distinguishes signaling pathways from appropriate null models of interaction networks. Next, we quantify topological similarity across pathway databases. Our analysis reveals that the pathways harbor database-specific characteristics implying that even though these databases describe the same pathways, they tend to be systematically different from one another. We show that pathway-specific topology can be uncovered after accounting for database-specific structure. This work present the first step towards elucidating common pathway structure beyond their specific database annotations.
Principles of sensor-effector organization in six-transmembrane ion channels
Authors: Dou Alex , Kang Po Wei , Hou Panpan , Zaydman Mark A. , Zheng Jie , Jegla Timothy , Cui Jianmin
Published: August 2021

Receptor proteins sense stimuli and generate downstream signals via sensor and effector domains. Presently, the structural constraints on sensor-effector organization across receptor protein superfamilies are not clear. Here, we perform statistical coupling analysis (SCA) on the transient receptor potential (TRP) and voltage-gated potassium (Kv) ion channel superfamilies to characterize the networks of coevolving residues, or protein sectors, that mediate their receptor functions. Comparisons to structural and functional studies reveal a conserved “core” sector that extends from the pore and mediates effector functions, including pore gating and sensor-pore coupling, while sensors correspond to family-specific “accessory” sectors and localize according to three principles: Sensors (1) may emerge in any region with access to the core, (2) must maintain contact with the core, and (3) must preserve the integrity of the core. This sensor-core architecture may represent a conserved and generalizable paradigm for the structure-function relationships underlying the evolution of receptor proteins.
A generic hidden Markov model for multi-parent populations
Authors: Broman Karl W.
Published: August 2021

A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a probability model for the pattern of founder alleles along chromosomes, including the relative frequency of founder alleles and the probability of exchanges among them, which depend on a model for meiotic recombination and on the mating design for the population. While the precise experimental design used to generate the population may be used to derive a precise characterization of the model for exchanges among founder alleles, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly-available data on Diversity Outbred and Collaborative Cross mice
Influence of internal seiche dynamics on vertical movement of fish
Authors: Jarić Ivan , Říha Milan , Souza Allan T. , Rabaneda-Bueno Rubén , Děd Vilem , Gjelland Karl Ø. , Baktoft Henrik , Čech Martin , Blabolil Petr , Holubová Michaela , Jůza Tomáš , Muška Milan , Sajdlová Zuzana , Šmejkal Marek , Vejřík Lukáš , Vejříková Ivana , Peterka Jiří
Published: August 2021

Internal seiches are common in stratified lakes, with significant effects on stratification patterns, hydrodynamics and vertical nutrient transport. In particular, seiche can change the vertical distribution of the thermocline and the cold hypolimnetic and warm epilimnetic water masses by several meters on a timescale of a few hours. The results are rapid and strong changes in temperature profiles and oxygen availability that can have profound effects on vagrant and sessile organisms. Internal seiche dynamics could therefore affect fish communities directly through physiological stress and elevated mortality, and indirectly through prey distribution.

The aim of this study was to analyze the effects of internal seiche dynamics on lacustrine fish behaviour, and to characterize fish reaction patterns, with the main focus on vertical movement of fish in the vicinity of a shifting thermocline, and avoidance of cold hypolimnetic water.

The analysis was based on acoustic telemetry data from Lake Milada, a post-mining lake in the Czech Republic, with a total of 55 tracked individuals of four species: northern pike (Esox lucius), wels catfish (Silurus glanis), tench (Tinca tinca) and rudd (Scardinius erythropthalmus).

The effects of seiche dynamics on the four species studied were weak but significant during the day, but only on rudd during the night. Upward seiche produced stronger reactions in fish than downward seiche, and the effects were manifested only during the strongest seiche events.

Thermocline shifting during seiche events may induce a transient reduction in habitat for seiche-reacting species, thus potentially affecting predation and other inter- and intra-specific interactions, and probably affecting fish community dynamics.

Graphical abstract
IL-13 promotes recovery fromC. difficileinfection
Authors: Donlan A.N. , Leslie J.L. , Simpson M.E. , Petri W.A. , Allen J.E. , Petri W.A.
Published: August 2021

Clostridioides difficileinfection (CDI) is the leading hospital-acquired infection in North America. We have previously discovered that antibiotic disruption of the gut microbiota decreases intestinal IL-33 and IL-25 and increases susceptibility to CDI. We further found that IL-33 promotes protection through type 2 Innate Lymphoid Cells (ILC2s), which produce IL-13. However, the contribution of IL-13 to disease has never been explored. We found that administration of IL-13 protected, and anti-IL-13 exacerbated CDI as measured by weight loss and clinical score, particularly during disease resolution. Additionally, concordant with IL-13 being important for M2 macrophage polarization, we saw a decrease in M2 macrophages (CD11B+CD64+CD206+) cells following neutralization of IL-13. We also observed monocyte accumulation as early as day three post-infection following IL-13 neutralization, suggesting IL-13 may be directly or indirectly important for their recruitment or transition into macrophages. Neutralization of the decoy receptor IL-13Rα2 resulted in protection from disease, likely through increased available endogenous IL-13. Our data highlight the protective role of IL-13 in promoting recovery from CDI and the association of poor responses with a dysregulated monocytemacrophage compartment. These results increase our understanding of type 2 immunity in CDI and may have implications for treating disease in patients.
Endothelial Semaphorin 3fb regulates Vegf pathway-mediated angiogenic sprouting
Authors: Watterston Charlene , Halabi Rami , McFarlane Sarah , Childs Sarah J
Published: August 2021

Vessel growth integrates diverse extrinsic signals with intrinsic signaling cascades to coordinate cell migration and sprouting morphogenesis. The pro-angiogenic effects of Vascular Endothelial Growth Factor (VEGF) are carefully controlled during sprouting to generate an efficiently patterned vascular network. We identify crosstalk between VEGF signaling and that of the secreted ligand Semaphorin 3fb (Sema3fb), one of two zebrafish paralogs of mammalian Sema3F. Thesema3fbgene is expressed by endothelial cells in actively sprouting vessels. Loss ofsema3fbresults in abnormally wide and stunted intersegmental vessel artery sprouts. Although the sprouts initiate at the correct developmental time, they have a reduced migration speed. These sprouts have persistent filopodia and abnormally spaced nuclei suggesting dysregulated control of actin assembly. sema3fbmutants show simultaneously higher expression of pro-angiogenic (VEGF receptor 2(vegfr2)anddelta-like 4(dll4))and anti-angiogenic (solubleVEGF receptor 1 (svegfr1)/soluble Fms Related Receptor Tyrosine Kinase 1 (sflt1))pathway components. We show increased phospho-ERK staining in migrating angioblasts, consistent with enhanced Vegf activity. Reducing Vegfr2 kinase activity insema3fbmutants rescues angiogenic sprouting. Our data suggest that Sema3fb plays a critical role in promoting endothelial sprouting through modulating the VEGF signaling pathway, acting as an autocrine cue that modulates intrinsic growth factor signaling.

Author summary

To supply tissues with essential oxygen and nutrients, blood vessel development is carefully orchestrated by positive ‘go’ and negative ‘stop’ growth signals as well as directional cues to shape patterning. Semaphorin proteins are named after the ‘Semaphore’ railway signaling system that directed trains along the appropriate tracks. Our work highlights the role of the Semaphorin 3fb protein in providing a pro-growth signal to developing vessels. Semaphorin 3fb is both produced by, and acts on the precursors of blood vessels as they migrate, a process known as autocrine control. We find that losing Semaphorin 3fb leads to stalled blood vessel growth, indicating it normally acts as a positive signal. It acts via modulating the VEGF growth factor signaling pathway that in turn, controls the migration process. We propose that Semaphorin3b fine-tunes vessel growth, thus ensuring a properly patterned network develops.
De novoevolution of macroscopic multicellularity
Authors: Bozdag G. Ozan , Zamani-Dahaj Seyed Alireza , Day Thomas C. , Kahn Penelope C. , Burnetti Anthony J. , Lac Dung T. , Tong Kai , Conlin Peter L. , Balwani Aishwarya H. , Dyer Eva L. , Yunker Peter J. , Ratcliff William C.
Published: August 2021

While early multicellular lineages necessarily started out as relatively simple groups of cells, little is known about how they became Darwinian entities capable of open-ended multicellular adaptation1,2. To explore this, we initiated the Multicellularity Long Term Evolution Experiment (MuLTEE), selecting for larger group size in the snowflake yeast (Saccharomyces cerevisiae) model system. Given the historical importance of oxygen limitation3, our ongoing experiment consists of three metabolic treatments4: anaerobic, obligately aerobic, and mixotrophic yeast. After 600 rounds of selection, snowflake yeast in the anaerobic treatment evolved to be macroscopic, becoming ~2·104times larger (~mm scale) and ~104-fold more biophysically tough, while retaining a clonal multicellular life cycle. They accomplished this through sustained biophysical adaptation, evolving increasingly elongate cells that initially reduced the strain of cellular packing, then facilitated branch entanglements that enabled groups of cells to stay together even after many cellular bonds fracture. In contrast, snowflake yeast competing for low oxygen remained microscopic, evolving to be just ~6-fold larger, underscoring the critical role of oxygen levels in the evolution of multicellular size. Taken together, this work provides unique insight into an ongoing evolutionary transition in individuality, showing how simple groups of cells overcome fundamental biophysical limitations via gradual, yet sustained, multicellular adaptation.
Loss of BCL-3 sensitises colorectal cancer cells to DNA damage, revealing a role for BCL-3 in double strand break repair by homologous recombination
Authors: Parker Christopher , Chambers Adam C , Flanagan Dustin , Collard Tracey J , Ngo Greg , Baird Duncan M , Timms Penny , Morgan Rhys G , Sansom Owen , Williams Ann C
Published: August 2021

Objective

The proto-oncogene BCL-3 is upregulated in a subset of colorectal cancers (CRC) and increased expression of the gene correlates with poor patient prognosis. The aim is to investigate whether inhibiting BCL-3 can increase the response to DNA damage in CRC.

Design

The function of BCL-3 in DNA damage response was studied in vitro using siRNA and CRISPR-Cas9 genome editing and in vivo using Bcl3-/- mice. DNA damage induced by γ-irradiation and/or cisplatin was quantified using H2AX and RAD51 foci, repair pathways investigated using HR/NHEJ assays and treatment with the PARP inhibitor olaparib.

Result

Suppression of BCL-3 increases double strand break number and decreases homologous recombination in CRC cells, supported by reduced RAD51 foci number and increased sensitivity to PARP inhibition. Importantly, a similar phenotype is seen in Bcl3-/- mice, where the intestinal crypts of these mice exhibit sensitivity to DNA damage and a greater number of double strand breaks compared to wild type mice. Furthermore Apc.Krasmutant x Bcl3-/- mice exhibit increased DNA damage and reduced RAD51+ cells compared to their wild type counterparts when treated with cisplatin.

Conclusion

This work identifies BCL-3 as a regulator of the cellular response to DNA damage and suggests that elevated BCL-3 expression could increase resistance of tumour cells to DNA damaging agents including radiotherapy. These findings offer a rationale for targeting BCL-3 in CRC as an adjuvant to conventional therapies and suggest that BCL-3 expression in tumours could be a useful biomarker in stratification of rectal cancer patients for neo-adjuvant chemoradiotherapy.
Single particle cryo-EM structure of the outer hair cell motor protein prestin
Authors: Butan Carmen , Song Qiang , Bai Jun-Ping , Tan Winston J. T. , Navaratnam Dhasakumar , Santos-Sacchi Joseph
Published: August 2021

The mammalian outer hair cell (OHC) protein prestin (Slc26a5), a member of the solute carrier 26 (Slc26) family of membrane proteins, differs from other members of the family owing to its unique piezoelectric-like property that drives OHC electromotility. OHCs require prestin for cochlear amplification, a process that enhances mammalian hearing. Despite substantial biophysical characterization, the mechanistic basis for the prestin’s electro-mechanical behavior is not fully understood. To gain insight into such behavior, we have used cryo-electron microscopy at subnanometer resolution (overall resolution of 4.0 Å) to investigate the three-dimensional structure of prestin from gerbil (Meriones unguiculatus). Our studies show that prestin dimerizes with a 3D architecture strikingly similar to the dimeric conformation observed in the Slc26a9 anion transporter in an inside open/intermediate state, which we infer, based on patch-clamp recordings, to reflect the contracted state of prestin. The structure shows two well-separated transmembrane (TM) subunits and two cytoplasmic sulfate transporter and anti-sigma factor antagonist (STAS) domains forming a swapped dimer. The dimerization interface is defined by interactions between the domain-swapped STAS dimer and the transmembrane domains of the opposing half unit, further strengthened by an antiparallel beta-strand at its N terminus. The structure also shows that each one of its two transmembrane subunits consists of 14 transmembrane segments organized in two inverted 7-segment repeats with a topology that was first observed in the structure of bacterial symporter UraA (Lu F, et al., Nature 472, 2011). Finally, the solved anion binding site structural features of prestin are quite similar to that of SLC26a9 and other family members. Despite this similarity, we find that SLC26a9 lacks the characteristic displacement currents (or NonLinear Capacitance(NLC)) found with prestin, and we show that mutation of prestin’s Cl- binding site removes salicylate competition with anions in the face of normal NLC, thus refuting the yet accepted extrinsic voltage sensor hypothesis and any associated transport-like requirements for voltage-driven electromotility.
The CD8+ T cell landscape of human brain metastases
Authors: Sudmeier Lisa J. , Hoang Kimberly B. , Nduom Edjah K. , Wieland Andreas , Neill Stewart G. , Schniederjan Matthew J. , Ramalingam Suresh S. , Olson Jeffrey J. , Ahmed Rafi , Hudson William H.
Published: August 2021

Despite improved outcomes with checkpoint blockade immunotherapy, patients with brain metastases have the worst prognosis among patients with metastatic cancer. Immune checkpoint blockade agents target inhibitory receptors, such as PD-1, on exhausted CD8+ T cells to restore their anti-cancer function. Many patients, however, either do not respond or progress after an initial response to immune checkpoint blockade, and distant intracranial failure is common despite excellent options for local treatment of brain metastasis. To develop more effective therapeutic strategies for the treatment of brain metastases, an understanding of the phenotype of brain metastasis-infiltrating CD8+ T cells is essential. Here we performed a detailed characterization of the CD8+ T cells contained in brain metastases. Brain metastases were densely infiltrated by CD8+ T cells; blood contamination of tumor samples was rare. Compared to patient-matched circulating cells, brain metastasis-infiltrating CD8+ T cells had a distinct phenotype characterized by more frequent expression of PD-1, with subpopulations defined by expression of additional co-inhibitory molecules and the residence marker CD69. Single cell RNA-sequencing identified four phenotypic subpopulations within brain metastasis-infiltrating PD-1+ CD8+ T cells. Two of these populations — a terminally-differentiated and a dividing population — were characterized by high expression of co-inhibitory molecules and lacked expression of progenitor markers such as TCF-1. There was significant T cell receptor (TCR) overlap between the terminally-differentiated and dividing populations, suggesting that the dividing cells give rise to the terminally-differentiated cells. There was minimal TCR overlap between these two populations and other brain metastasis-infiltrating PD-1+ CD8+ T cells. T cell clones from brain metastasis-infiltrating CD8+ T cells were rare in circulation, particularly clones from the terminally-differentiated and dividing populations. We systematically identified bystander CD8+ T cells specific for microbial antigens; these cells infiltrated brain metastases and expressed genes shared with exhausted progenitor CD8+ T cells, such as TCF7 and IL7R. We performed spatial transcriptomics on brain metastases and used a novel method to obtain TCR sequences from spatial transcriptomics data. These data revealed distinct niches within the TME defined by their gene expression patterns and cytokine profiles. Terminally-differentiated CD8+ T cells preferentially occupied niches within the tumor parenchyma. Together, our results show that antigen-specificity restricts the spatial localization, phenotypic states, and differentiation pathways available to CD8+ T cells within the brain metastasis TME.
Flexible recruitments of fundamental muscle synergies in the trunk and lower limbs for highly variable movements and postures
Authors: Saito Hiroki , Yokoyama Hikaru , Sasaki Atsushi , Kato Tatsuya , Nakazawa Kimitaka
Published: August 2021

The extent to which muscle synergies represent the neural control of human behavior remains unknown. Here, we tested whether certain sets of muscle synergies that are fundamentally necessary across behaviors exist. We measured the electromyographic activities of 26 muscles including bilateral trunk and lower limb muscles during 24 locomotion, dynamic and static stability tasks, and extracted the muscle synergies using non-negative matrix factorization. Our results showed that 13 muscle synergies that may have unique functional roles accounted for almost all 24 tasks by combinations of single and/or merging of synergies. Therefore, our results may support the notion of the low dimensionality in motor outputs, in which the central nervous system flexibly recruits fundamental muscle synergies to execute diverse human behaviors. Further studies using manipulations of the central nervous system and/or neural recording are required the neural representation with such fundamental components of muscle synergies.
The biosynthetic pathway of ubiquinone contributes to pathogenicity ofFrancisella
Authors: Kazemzadeh Katayoun , Chehade Mahmoud Hajj , Hourdoir Gautier , Brunet Camille , Caspar Yvan , Loiseau Laurent , Barras Frederic , Pierrel Fabien , Pelosi Ludovic
Published: August 2021

Francisella tularensisis the causative agent of tularemia. Because of its extreme infectivity and high mortality rate, this pathogen was classified as a biothreat agent.Francisellaspp are strict aerobe and ubiquinone (UQ) has been previously identified in these bacteria. While the UQ biosynthetic pathways were extensively studied inEscherichia coliallowing the identification of fifteen Ubi-proteins to date, little is known aboutFrancisellaspp. In this study, and usingFrancisella novicidaas a surrogate organism, we first identified UQ8as the major quinone found in the membranes of this bacterium. Then, we characterized the UQ biosynthetic pathway inF. novicidausing a combination of bioinformatics, genetics and biochemical approaches. Our analysis disclosed the presence inFrancisellaof ten putative Ubi-proteins and we confirmed eight of them by heterologous complementation inE. coli. The UQ biosynthetic pathways fromF. novicidaandE. colishare a similar pattern. However, differences were highlighted: the decarboxylase remains unidentified inFrancisellaspp and homologs of the Ubi-proteins involved in the O2-independent UQ pathway are not present. This is in agreement with the strictly aerobic niche of this bacterium. Then,viatwo approaches, i.e. the use of an inhibitor (3-amino-4-hydroxybenzoic acid) and a transposon mutant, which both strongly impair the synthesis of UQ, we demonstrated that UQ is essential for the growth ofF. novicidain a respiratory medium and contributes to its pathogenicity inGalleria mellonellaused as an alternative animal model.

Importance

Francisella tularensisis the causative bacterium of tularemia and is classified as a biothreat agent. Using multidisciplinary approaches, we investigated the ubiquinone (UQ) biosynthetic pathway that operates inF. novicidaused as a surrogate. We showed that UQ8is the major quinone identified in the membranes ofFrancisella novicida. We identified a new competitive inhibitor, which strongly decreased the biosynthesis of UQ. Our demonstration of the crucial role of UQ for the respiratory metabolism ofF. novicidaand for the involving in its pathogenicity in theGalleria mellonellamodel should stimulate the search for selective inhibitors of bacterial UQ biosynthesis.
DEVELOPMENT AND VALIDATION OF A MODEL FOR THE PREDICTION OF MORTALITY IN CHILDREN UNDER FIVE YEARS WITH CLINICAL PNEUMONIA IN RURAL GAMBIA
Authors: Jarde Alexander , Jeffries David J. , Mackenzie Grant A.
Published: August 2021

Background

Pneumonia is the leading cause of death in children aged 1-59 months. Prediction models for child pneumonia mortality have been developed using regression methods but their performance is insufficient for clinical use.

Methods

We used a variety of machine learning methods to develop a predictive model for mortality in children with clinical pneumonia enrolled in population-based surveillance in the Basse Health and Demographic Surveillance System in rural Gambia (n=11,012). Four machine learning algorithms (support vector machine, random forest, artifical neural network, and regularized logistic regression) were implemented, fitting all possible combinations of two or more of 16 selected features. Models were shortlisted based on their training set performance, the number of included features, and the reliability of feature measurement. The final model was selected considering its clinical interpretability.

Results

When we applied the final model to the test set (55 deaths), the area under the Receiver Operating Characteristic Curve was 0.88 (95% confidence interval: 0.84, 0.91), sensitivity was 0.78 and specificity was 0.77.

Conclusions

Our evaluation of multiple machine learning methods combined with minimal and pragmatic feature selection led to a predictive model with very good performance. We plan further validation of our model in different populations.
Association between anticholinergic burden and dementia in UK Biobank
Authors: Mur J. , Russ T.C. , Cox S. R. , Marioni R. E. , Muniz-Terrera G.
Published: August 2021

Previous studies on the association between the long-term use of anticholinergic drugs and dementia report heterogenous results. This variability could be due to, among other factors, different anticholinergic scales used, and differential effects of distinct classes of anticholinergic drugs. Here, we use 171,775 participants of UK Biobank with linked GP prescription records to calculate the cumulative annual anticholinergic burden (ACB) and ascertain dementia diagnoses through GP- and inpatient records. We then compare 13 anticholinergic scales and anticholinergic burden (ACB) due to different classes of drugs in their association with dementia. We find dementia to be more strongly predicted by ACB than by polypharmacy across most anticholinergic scales (standardised ORs range: 1.027-1.125). Furthermore, not only the baseline ACB, but the slope of the longitudinal trajectory of ACB (HR=1.094; 95% CI: 1.068-1.119) is predictive of dementia. However, the association between ACB and dementia holds only for some classes of drugs – especially antidepressants, antiepileptics, and high-ceiling antidiuretics. Moreover, we do not find a clear relationship between reported anticholinergic potency and dementia risk. The heterogeneity in findings on the association between ACB and dementia may in part be due to different effects for different classes of drugs. Future studies should establish such differences in more detail and further examine the practicality of using a general measure of anticholinergic potency as it relates to the risk of dementia.
Learning about COVID-19 across borders: Public health information and adherence among international travellers to the UK
Authors: Cai Shenghan , Zhang Tingting , Robin Charlotte , Sawyer Clare , Rice Wendy , Smith Louise E. , Amlôt Richard , Rubin G. James , Yardley Lucy , Hickman Matthew , Oliver Isabel , Lambert Helen
Published: August 2021

Objective

Public health control measures at borders have long been central to national strategies for the prevention and containment of infectious diseases. Travel was inevitably associated with the rapid global transmission of COVID-19. In the UK, public health authorities took action to reduce risks of travel-associated spread by providing public health information at ports of entry. This study aims to understand individual risk assessment processes, decision making, and adherence to official advice among international travellers; to provide evidence to inform future policy on the presentation of public health information to facilitate safer international travel.

Study design

This study is a qualitative study evaluation.

Method

Semi-structured interviews were conducted to investigate risk assessment processes, decision making, and adherence to official Public Health England (PHE) advice among travellers.

Results

Participants regarded official advice as adequate at the time, despite observing differences between the intervention measures implemented in the countries of departure. Participants however also described adopting precautionary measures including self-isolation and the use of face coverings that went beyond official advice, and variability in the extent to which they adhered to guidance on contacting health authorities. Adherence to official guidance was informed by the perceived salience of specific transmission possibilities and containment measures assessed in relation to participants’ social and institutional environments.

Conclusion

Analysis of travellers’ reported motivations demonstrates that responses to public health advice constitute a proactive process of risk assessment and rationalised decision-making that incorporates consideration of living situation, trust in information sources, correspondence with cultural logics, and willingness to accept potential risk to self and significant others in guiding preventive action. Our findings concerning international passengers’ understanding of, and compliance with, official advice and mitigation measures provide valuable evidence to inform future policy and we provide recommendations on the presentation of public health information to facilitate safer international travel. Access to a central source of regularly updated official information would help minimise confusion between different national guidelines. Greater attention to the differentiated information needs of diverse groups in creating future public-facing guidance would help to minimise the uncertainties generated by receipt of generic information.
Association between obesity and hospitalization in mild COVID-19 young adult outpatients in Brazil: a prospective cohort study
Authors: Sartor Ivaine Tais Sauthier , de David Caroline Nespolo , Telo Gabriela Heiden , Zavaglia Gabriela Oliveira , Fernandes Ingrid Rodrigues , Kern Luciane Beatriz , Polese-Bonatto Márcia , Azevedo Thaís Raupp , Santos Amanda Paz , de Almeida Walquiria Aparecida Ferreira , Porto Victor Bertollo Gomes , Varela Fernanda Hammes , Scotta Marcelo Comerlato , Rosa Regis Goulart , Stein Renato T. ,   COVIDa study group
Published: August 2021

Background/Objectives

The aim of this study was to evaluate the association between obesity and hospitalization in mild COVID-19 adult outpatients in Brazil.

Subjects/Methods

Adults with signs and symptoms suggestive of acute SARS-CoV-2 infection who sought two hospitals (one public and one private) emergency department (ED) were prospectively enrolled. Patients with confirmed COVID-19 at inclusion were followed by phone calls at day (D) D7, D14 and D28. Multivariable logistic regression models were employed to explore the association between obesity and other potential predictors for hospitalization.

Results

A total of 1,050 participants were screened, 310 were diagnosed with COVID-19 by RT-PCR. Median age was 37.4 (IQR 29.8-45.0) years, and 186 (60.0%) were female. Duration of symptoms was 3.0 (IQR 2.0-5.0) days, and 10.0 (IQR 8.0-12.0) was the median number of symptoms at inclusion. A total of 98 (31.6%) were obese, and 243 (78.4%) had no previous medical conditions. Twenty three participants (23/310, 7.4%) required hospitalization during the period. After adjusting, obesity (BMI≥30.0 kg/m2) (OR=2.69, 95%CI 1.63-4.83, P<0.001) and older age (OR=1.05, 95%CI 1.01-1.09, P<0.001), were significantly associated with higher risks of hospitalization.

Conclusions

Obesity, followed by aging, was the main factor associated with hospital admission for COVID-19 in a young population in a low-middle income country. Our findings highlighted the need for actions to promote additional protection for obese population, such as vaccination, and to encourage lifestyle changes.
More rapid, robust and sustainable antibody responses to mRNA COVID-19 vaccine in convalescent COVID-19 individuals
Authors: Racine-Brzostek Sabrina E. , Yee Jim , Sukhu Ashley , Qiu Yuqing , Rand Sophie , Barone Paul , Hao Ying , Yang He S. , Meng Qing H , Apple Fred S , Shi Yuanyuan , Chadburn Amy , Golden Encouse , Formenti Silvia C. , Cushing Melissa M. , Zhao Zhen
Published: August 2021

Longitudinal studies are needed to evaluate the SARS-CoV-2 mRNA vaccine antibody response under “real-world” conditions. This longitudinal study investigated the quantity and quality of SARS-CoV-2 antibody response in 846 specimens from 350 subjects: comparing BNT162b2-vaccinated individuals (19 previously diagnosed with COVID-19 [RecoVax]; 49 never been diagnosed [NaïveVax]) to 122 hospitalized unvaccinated (HospNoVax) and 160 outpatient unvaccinated (OutPtNoVax) COVID-19 patients.

NaïveVax experienced a delay in generating SARS-CoV-2 total antibody levels (TAb) and neutralizing antibodies (SNAb) after the 1st vaccine dose (D1), but a rapid increase in antibody levels was observed after the 2nddose (D2). However, these never reached the robust levels observed in RecoVax. In fact, NaïveVax TAb and SNAb levels decreased 4-weeks post-D2 (p=0.003;p<0.001). For the most part, RecoVax TAb persisted throughout this study, after reaching maximal levels 2-weeks post-D2; but SNAb decreased significantly ∼6-months post-D1 (p=0.002). Although NaïveVax avidity lagged behind that of RecoVax for most of the follow-up periods, NaïveVax did reach similar avidity by ∼6-months post-D1. These data suggest that one vaccine dose elicits maximal antibody response in RecoVax and may be sufficient. Also, despite decreasing levels in TAb and SNAb overtime, long-term avidity maybe a measure worth evaluating and possibly correlating to vaccine efficacy.
Better together – relative retention time plus spectral matching improves automated glycan characterization using PGC-nLC-IT-ESI-MS/MS
Authors: Alagesan Kathirvel , Schirmeister Falko , Möginger Uwe , Everest-Dass Arun , Altmann Friedrich , Seeberger Peter H , von Itzstein Mark , Packer Nicolle H , Kolarich Daniel
Published: August 2021

Porous Graphitized Carbon nano-liquid chromatography tandem mass spectrometry (PGC-nLC-MS/MS) is a glycomics technique with the unique capacity to differentiate isobaric glycans. The lack of suitable software tools integrating chromatography and MS-information delivered by PGC-nLC-MS/MS has been limiting fast and robust glycan identification and quantitation. We report a LC-system-independent strategy called GlycoRRT that combines relative retention time (RRT) and negative ion fragment spectra analyses for isobaric structure-specific glycomics of PGC-nLC-MS/MS data. The GlycoRRT toolset is fully customizable and easily adaptable enabling semi-automated high-throughput structural assignments. The current library contains over 200 entries and their individual meta-data (MS instrumentation, experimental conditions, retention times, fragmentation profiles and glycan structural diagnostic ion features) relevant for reliable data analyses. The GlycoRRT workflow was employed to map the N- and O-glycome in blood group matched human plasma and urine as well as decipher Immunoglobulin (IgG) glycosylation features from 13 different animal species. We have also developed visualization tools to enable a consistent, reliable, and reproducible analysis of large sets of multidimensional PGC-nLC-MS/MS glycomics data. This comprehensive glycan resource provides the glycan map of human and animal species, will serve as a reference in dissecting the role of glycans in host pathogen interaction and zoonotic disease transmission.
Are members of the Anopheles fluviatilis complex conspecific?
Authors: Singh Om P , Sindhania Ankita , Sharma Gunjan , Mishra Shobhna , Sharma Surya K , Singh Piyoosh K , Das Manoj K.
Published: August 2021

Anopheles fluviatilis sensu lato, a primary malaria vector in India, was identified to be comprised of four cryptic species, provisionally designated as species S, T, U and V. However, Kumar et al. (Mol Ecol Resour, 2013;13:354-61) considered all of the then known three members of this species complex (S, T and U) conspecific. The specific status of species S and T was refuted based on the lack of sufficient barcode gap in mitochondrial-CO1 and the perceived presence of heterozygotes in populations as detected through one of the two species-specific PCR assays employed for the cryptic species identification. The existence of species U was refuted claiming that earlier investigations have already refuted their existence. This conclusion is concerning because of the differential public health implications of members of the Fluviatilis Complex. Here we discuss problems associated with the CO1-based barcode approach for delimitation of cryptic species, the perceived heterozygosity between species S and T based on a species-specific PCR assay, and interpretation of published reports. We demonstrated that fixed differences do exist in the ITS2-rDNA sequence of species S and T with no evidence of heterozygotes in sympatric populations and, that the observed heterozygosity by Kumar et al. in the ITS2-based species diagnostic PCR is due to the high mispriming tendency of the T-specific primer with species S. We infer that mitochondrial DNA-based ‘barcoding gap’, an arbitrary threshold recommended for species delimitation, alone, is inadequate to delimit the members of An. fluviatilis complex.
Sequence dependence of transient Hoogsteen base-pairing in DNA
Authors: de Alba Ortíz Alberto Pérez , Vreede Jocelyne , Ensing Bernd
Published: August 2021

Hoogsteen (HG) base-pairing is characterized by a 180° rotation of the purine base with respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both conformations coexist in a dynamical equilibrium and that several biological functions require HG pairs. This relevance has motivated experimental and computational investigations of the base-pairing transition. However, a systematic simulation of sequence variations has remained out of reach. Here, we employ advanced path-based methods to perform unprecedented free-energy calculations. Our methodology enables us to study the different mechanisms of purine rotation, either remaining inside or after flipping outside of the double helix. We study seven different sequences, which are neighbor variations of a well-studied A·T pair in A6-DNA. We observe the known effect of A·T steps favoring HG stability, and find evidence of triple-hydrogen-bonded neighbors hindering the inside transition. More importantly, we identify a dominant factor: the direction of the A rotation, with the 6-ring pointing either towards the longer or shorter segment of the chain, respectively relating to a lower or higher barrier. This highlights the role of DNA’s relative flexibility as a modulator of the WCF/HG dynamic equilibrium. Additionally, we provide a robust methodology for future HG proclivity studies.