bluuebunny/crossref_metadata_2025 huggingface dataset:
Empirical evidence of transmission over a school-household network for SARS-CoV-2; exploration of transmission pairs stratified by primary and secondary school
Authors: van Iersel Senna C.J.L. , Backer Jantien A. , van Gaalen Rolina D. , Andeweg Stijn P. , Munday James D. , Wallinga Jacco , van Hoek Albert Jan
Published: February 2022

Background

Children play a key role in the transmission of many infectious diseases. They have many of their close social encounters at home or at school. We hypothesized that most of the transmission of respiratory infections among children occur in these two settings and that transmission patterns can be predicted by a bipartite network of schools and households.

Aim and methods

To confirm transmission over a school-household network, SARS-CoV-2 transmission pairs in children aged 4-17 years were analyzed by study year and primary/secondary school. Cases with symptom onset between the 1st of March 2021 and the 4th of April 2021 identified by source and contact-tracing in the Netherlands were included. In this period, primary schools were open and secondary school students attended class at least once per week. Within pairs, spatial distance between the postcodes was calculated as the Euclidean distance.

Results

A total of 4,059 transmission pairs were identified; 51.9% between primary schoolers; 19.6% between primary and secondary schoolers; 28.5% between secondary schoolers. Most (68.5%) of the transmission for children in the same study year occurred at school. In contrast, most of the transmission of children from different study years (64.3%) and most primary-secondary transmission (81.7%) occurred at home. The average spatial distance between infections was 1.2km (median 0.4) for primary school pairs, 1.6km (median 0) for primary-secondary school pairs and 4.1km (median 1.2) for secondary school pairs.

Conclusion

The results provide evidence of transmission on a bipartite school-household network. Schools play an important role in transmission within study years, and households play an important role in transmission between study years and between primary and secondary schools. Spatial distance between infections in a transmission pair reflects the smaller school catchment area of primary schools versus secondary schools. Many of these observed patterns likely hold for other respiratory pathogens.
A simple self-decoding model for neural coding
Authors: Bui Thach V.
Published: February 2022

Neural coding is an important tool to discover the inner workings of mind. In this work, we propose and consider a simple but novel self-decoding model for neural coding based on the principle that the neuron body represents ongoing stimulus while dendrites are used to store that stimulus as a memory. In particular, suppose t spiking presynaptic neurons transmit any stimulus directly to a population of n postsynaptic neurons, a postsynaptic neuron spikes if it does not connect to an inhibitory presynaptic neuron, and every stimulus is represented by up to d spiking postsynaptic neurons.

Our hypothesis is that the brain is organized to functionally satisfy the following six criteria: (i) decoding objective, i.e., there are up to r−1 ≥ 0 additional spiking postsynaptic neurons in response to a stimulus along with the spiking postsynaptic neurons representing the stimulus, (ii) smoothness, i.e., similar stimuli are encoded similarly by the presynaptic neurons, (iii) optimal information transmission, i.e., t is minimized, (iv) optimal energetic cost, i.e., only the t presynaptic neurons and the postsynaptic neurons representing a stimulus spike, (v) low-dimensional representation, i.e., d = o(n), and (vi) sparse coding, i.e., t = o(n).

Our finding is that some criteria cause or correlate with others. Let the characteristic set of a postsynaptic neuron be the set of the presynaptic neurons it connects with. We prove that (i) holds if and only if the union of the r characteristic sets of any r postsynaptic neurons is not included in the union of the d characteristic sets of d other postsynaptic neurons. Consequently, (ii) is attained. More importantly, we suggest that the decoding objective (i) and optimal information transmission (iii) play a fundamental role in neural computation, while (v) and (vi) correlate to each other and correlate with (iii) and (iv). We examine our hypothesis by statistically testing functional connectivity network and the presynaptic-postsynaptic connectivity in layer 2 of the medial entorhinal cortex of a rat.
Targeting OLIG2 increases therapeutic responses in SHH medulloblastoma mouse models and patient-derived medulloblastoma organoids
Authors: Li Yuchen , Dismuke Taylor , Lim Chaemin , Bruce Zara C. , Offenhäuser Carolin , Baumgartner Ulrich , Maybury Mellissa , D’Souza Rochelle C. J. , Hassall Timothy , Wainwright Brandon , Stein Gregory , Piper Michael , Johns Terrance G. , Sokolsky-Papkov Marina , Gershon Timothy R. , Day Bryan W.
Published: February 2022

Recurrence after therapy is the primary life-threatening complication of medulloblastoma. In Sonic Hedgehog (SHH)-subgroup medulloblastoma, OLIG2-expressing tumour stem cells are crucial to recurrence. We investigated the potential of the small-molecule OLIG2 inhibitor CT-179 to decrease recurrence in patient-derived organoids, mice genetically-engineered to develop SHH-driven MB, and mice with MB patient-derived xenograft (PDX) tumours. We found that OLIG2 mRNA significantly correlated with poor survival in patients with SHH-MB, but not other subgroups. CT-179 rapidly downregulated OLIG2 protein in vitro and displayed nanomolar IC50 values. CT-179 arrested MB cells at G2/M, with degradation of cyclin B1 and phospho-CDK1 inducing apoptosis. In vivo CT-179 induced similar cell cycle changes in MBs in Smo-mutant mice and significantly increased mouse survival. In both MB organoids and mouse models, CT-179 combined with radiotherapy showed greater efficacy than either treatment alone. These data highlight the potential for OLIG2-targeted therapy to improve MB outcomes by targeting recurrent disease.
The development of receptive field tuning properties in mouse binocular primary visual cortex
Authors: Tan Liming , Ringach Dario L. , Trachtenberg Joshua T.
Published: February 2022

The mouse primary visual cortex is a model system for understanding the relationship between cortical structure, function, and behavior (Seabrook et al., 2017; Chaplin and Margrie, 2020; Hooks and Chen, 2020; Saleem, 2020; Flossmann and Rochefort, 2021). Binocular neurons in V1 are the cellular basis of binocular vision, which is required for predation (Scholl et al., 2013; Hoy et al., 2016; La Chioma et al., 2020; Berson, 2021; Johnson et al., 2021). The normal development of binocular responses, however, has not been systematically measured. Here, we measure tuning properties of neurons to either eye in awake mice of either sex from eye-opening to the closure of the critical period. At eye-opening, we find an adult-like fraction of neurons responding to the contralateral-eye stimulation, which are selective for orientation and spatial frequency; few neurons respond to ipsilateral eye and their tuning is immature. Fraction of ipsilateral-eye responses increases rapidly in the first few days after eye opening and more slowly thereafter, reaching adult levels by critical period closure. Tuning of these responses improves with a similar time course. The development and tuning of binocular responses parallels that of ipsilateral-eye responses. Four days after eye-opening, monocular neurons respond to a full range of orientations but become more biased to cardinal orientations. Binocular responses, by contrast, lose their cardinal bias with age. Together, these data provide an in-depth accounting of the development of monocular and binocular responses in the binocular region of mouse V1 using a consistent set of visual stimuli and measurements.

Significance statement

In this manuscript, we present a full accounting of the emergence and refinement of monocular and binocular receptive field tuning properties of thousands of pyramidal neurons in mouse primary visual cortex. Our data reveal new features of monocular and binocular development that revise current models on the emergence of cortical binocularity. Given the recent interest in visually guided behaviors in mice that require binocular vision, e.g. predation, our measures will provide the basis for studies on the emergence of the neural circuitry guiding these behaviors.
SciViewer- An interactive browser for visualizing single cell datasets
Authors: Jain Dhawal , Hayat Sikander , Li Xinkai , Charkaborty Joydeep , Srinivasa Pooja , Cho Michael H. , Silverman Edwin K. , Moore Hobert , Kramann Rafael , Laux-Biehlmann Alexis
Published: February 2022

Single-cell sequencing improves our ability to understand biological systems at single-cell resolution and can be used to identify novel drug targets and optimal cell-types for target validation. However, tools that can interactively visualize and provide target-centric views of these large datasets are limited. We present SciViewer (Single-cellInteractiveViewer), a novel tool to interactively visualize, annotate and share single-cell datasets. SciViewer allows visualization of cluster, gene and pathway level information such as clustering annotation, differential expression, pathway enrichment, cell-type specificity, cellular composition, normalized gene expression and comparison across datasets. Further, we provide APIs for SciViewer to interact with publicly available pharmacogenomics databases for systematic evaluation of potential novel drug targets. We provide a module for non-programmatic upload of single-cell datasets. SciViewer will be a useful tool for data exploration and target discovery from single-cell datasets. It is available on GitHub (https://github.com/Dhawal-Jain/SciViewer).
A model of functionally buffered deleterious mutations can lead to signatures of positive selection
Authors: Shen Runxi , Wenzel Miwa , Messer Philipp W , Aquadro Charles F.
Published: February 2022

Abstract

Selective pressures on DNA sequences often result in departures from neutral evolution that can be captured by the McDonald-Kreitman (MK) test. However, the nature of such selective forces often remains unknown to experimentalists. Amino acid fixations driven by natural selection in protein coding genes are commonly associated with a genetic arms race or changing biological purposes, leading to proteins with new functionality. Here, we evaluate the expectations of a buffering mechanism driving selective amino acids to fixation, which is motivated by an observed phenotypic rescue of otherwise deleterious nonsynonymous substitutions atbag of marbles(bam) andSex lethal(Sxl). These two important genes inDrosophila melanogasterwere shown to experience strong episodic bursts of natural selection potentially due to infections of the endosymbiotic bacteriaWolbachiaobserved among multipleDrosophilaspecies. Using simulations to implement and evaluate the evolutionary dynamics of aWolbachiabuffering model, we demonstrate that selectively fixed amino acid replacements will occur, but that proportion of adaptive amino acid fixations and the statistical power of the MK test to detect the departure from an equilibrium neutral model are both significantly lower than seen for an arms race/change-in-function model that favors proteins with diversified amino acids.
Utilising TMS-EEG to assess the response to cerebellar-brain inhibition
Authors: Sasaki R , Hand B , Liao WY , Rogasch NC , Fernandez L , Semmler JG , Opie GM
Published: February 2022

Background

Cerebellar-brain inhibition (CBI) is a transcranial magnetic stimulation (TMS) paradigm indexing excitability of cerebellar projections to motor cortex (M1). Stimulation involved with CBI is often considered to be uncomfortable, and alternative ways to index connectivity between cerebellum and the cortex would be valuable. Utilising electroencephalography in conjunction with TMS (combined TMS-EEG) to record the response to CBI has the potential to achieve this, but has not been attempted previously.

Objective

To investigate the utility of TMS-EEG for characterising cerebellar-cortical interactions recruited by CBI.

Methods

A total of 33 volunteers (25.7 ± 4.9 years, 20 females) participated across three experiments. These investigated EEG responses to CBI induced with a figure-of-eight (F8; experiment 1) or double cone (DC; experiment 2) conditioning coil over cerebellum, in addition to multisensory sham stimulation (experiment 3).

Results

Both F8 and DC coils suppressed early TMS-evoked EEG potentials (TEPs) produced by TMS to M1 (P < 0.05). Furthermore, the TEP produced by CBI stimulation was related to the motor inhibitory response to CBI recorded in a hand muscle (P < 0.05), but only when using the DC coil. Multisensory sham stimulation failed to modify the M1 TEP.

Conclusions

Cerebellar conditioning produced changes in the M1 TEP that were not apparent following sham stimulation, and that were related to the motor inhibitory effects of CBI. Our findings therefore suggest it is possible to index the response to CBI using TMS-EEG. In addition, while both F8 and DC coils appear to recruit cerebellar projections, the nature of these may be different.
Targeted transcutaneous cervical spinal cord stimulation promotes upper limb recovery in spinal cord and peripheral nerve injury
Authors: Chandrasekaran Santosh , Bhagat Nikunj A , Ramdeo Richard , Ebrahimi Sadegh , Sharma Pawan D , Stein Adam , Griffin Doug G , Harkema Susan J , Bouton Chad E
Published: February 2022

Long-term recovery of limb function is a significant unmet need in people with paralysis. Targeted neuromodulation through epidural stimulation of the spinal cord, when paired with intense physical therapy, has shown promising results towards restoring volitional control of the upper limb in people with tetraplegia. Non-invasive neuromodulation of the cervical spinal cord using transcutaneous spinal cord stimulation (tSCS) has shown similar improvements in upper-limb motor control rehabilitation. However, the potential rehabilitative effects of activating specific cervical spinal segments in a targeted fashion using tSCS has largely remained unexplored. We show in two individuals with SCI that tSCS of the cervical spinal cord resulted in up to 1136% increase in exerted force, with minimal physical therapy. We also show, for the first time, the effectiveness of targeted tSCS in restoring strength (407% increase) and dexterity to the digits in an individual with paralysis of the hand due to a peripheral nerve injury. Furthermore, we believe this is the first study to document a 3-point improvement in sensation in people with SCI or peripheral injury after receiving tSCS. Lastly, participant gains persisted after a one-month period void of stimulation, suggesting tSCS may lead to lasting benefits. Non-invasive targeted spinal cord stimulation shows tremendous promise as a safe and effective therapeutic approach with broad applications.
Risk of Ocular Adverse Events with Taxane Based Chemotherapy
Authors: Sodhi Mohit , Yeung Sonia N. , Maberley David , Mikelberg Frederick , Etminan Mahyar
Published: February 2022

OBJECTIVE

Taxane based chemotherapy agents such as docetaxel and paclitaxel are used for a wide range of cancers. Although much has been published on adverse events related to taxanes, data on ocular outcomes with these very important drugs is scant. We sought to quantify the risk of three ocular adverse events: 1) epiphora, 2) cystoid macular edema (CME) and 3) optic neuropathy with taxane based chemotherapy agents by undertaking a large pharmacoepidemiologic study.

DESIGN

New users, retrospective cohort study design

SUBJECTS, PARTICIPANTS, CONTROLS

We created a cohort of new users of women matched by age (within one year) on docetaxel or paclitaxel and new users of tamoxifen as controls. Study members were followed to the first incidence of the three outcomes.

METHODS

Descriptive statistics were used to examine demographics of the exposed and unexposed groups. A Cox model was constructed to compute crude and adjusted hazard ratios. Potential confounders for each outcome were adjusted for.

MAIN OUTCOME MEASURES

First diagnosis of 1) epiphora, 2) cystoid macular edema (CME) or 3) optic neuropathy ascertained using international classification for diseases 9th or 10th division codes.

RESULTS

For the epiphora analysis there were 1,824 taxane users (PTX or DTX) and 16,395 tamoxifen users. The crude HR for this association was 7.32 (95%CI: 4.25-16.61) and adjusted HR was 5.15 (95% CI:2.79-9.54). For the CME analysis there were 1,909 taxane user and 16,524 tamoxifen users. The crude HR for CME comparing taxane users to tamoxifen users was 1.37 (95% CI: 0.72-2.60) and adjusted HR was 1.33 (95% CI: 0.70-2.53). For optic neuropathy there were 1,913 taxane users and 16,566 tamoxifen users. The crude HR was 4.43 (95% CI:1.10-17.82) and the adjusted HR was 4.44 (95% CI:1.04-18.87). When we restricted our analysis to only cases of toxic optic neuropathy the aged-matched HR remained elevated (HR=7.24, 95% CI: 1.13-46.36).

CONCLUSION

In a cohort of women who were using taxane chemotherapy agents, there was an elevated risk for epiphora, optic neuropathy and a less precise increase in risk for cystoid macular edema. Ophthalmologists and oncologists should be aware of these adverse events in women with breast cancer who use these drugs.
Relative Virulence of SARS-CoV-2 Among Vaccinated and Unvaccinated Individuals Hospitalized with SARS-CoV-2
Authors: Grima Alicia A. , Murison Kiera R. , Simmons Alison E. , Tuite Ashleigh R. , Fisman David N.
Published: February 2022

Background

The rapid development of safe and effective vaccines against the SARS-CoV-2 virus has been a singular scientific achievement. Confounding due to health seeking behaviours and differential testing by vaccination status may bias analyses towards an apparent increase in infection severity following vaccination. We sought to determine whether risks of intensive care unit (ICU) admission and death were diminished significantly by vaccination, even in individuals for whom vaccination failed to prevent hospitalization.

Methods

We used data from Ontario, Canada’s Case and Contact Management database, merged to a provincial vaccination dataset (COVaxON) to create a time-matched cohort of individuals who were hospitalized with SARS-CoV-2 infection. Each vaccinated individual was matched to up to five unvaccinated individuals based on test date of positive SARS-CoV-2 infection. Risk of ICU admission and death were evaluated using multivariable conditional logistic regression. Unmatched exploratory analyses were performed to identify sources of heterogeneity in vaccine effects.

Results

In 20,064 individuals (3,353 vaccinated and 16,711 unvaccinated) hospitalized with infection due to SARS-CoV-2 between January 1st, 2021 and January 5th, 2022, vaccination with 1, 2, or 3 doses significantly reduced the risk of ICU admission and death. An inverse dose-response relationship was observed between vaccine doses received and both outcomes (adjusted odds ratio (aOR) for ICU admission per additional dose: 0.66, 95% CI 0.62 to 0.71; aOR for death per additional dose: 0.78, 95% CI 0.72 to 0.84). The reduction in risk was greater for ICU admission than for death (P for heterogeneity <0.05), but no significant differences in risk were seen based on infecting variant of concern (VOC).

Interpretation

We identified a decrease in the risk of ICU admission and death in vaccinated individuals compared to unvaccinated, time-matched controls, even when vaccines failed to prevent infection sufficiently severe to cause hospitalization. Even with diminished efficacy of vaccines against infection with novel VOCs, vaccines remain an important tool for reduction of ICU admission and mortality.
Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
Authors: Zhang Cheng , Shi Mengnan , Kim Woonghee , Arif Muhammad , Klevstig Martina , Li Xiangyu , Yang Hong , Bayram Cemil , Bolat Ismail , Tozlu Özlem Özdemir , Hacımuftuoglu Ahmet , Yıldırım Serkan , Wei Yongjun , Shi Xiaojing , Nielsen Jens , Turkez Hasan , Uhlen Mathias , Boren Jan , Mardinoglu Adil
Published: February 2022

Background & Aims

Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, not medical treatment has been approved for the treatment of the disease. In our previous study, we found PKLR could be a potential target for treatment of NALFD. Here, the aim is to investigate the effect of PKLR in in vivo model and perform drug repositioning to identify a drug candidate for treatment of NAFLD.

Methods

Biopsies from liver, muscle, white adipose tissue and heart were obtained from control and PKLR knockout mice fed with chow and high sucrose diets. Lipidomics as well as transcriptmics analyses were conducted using these tissue samples. In addition, a computational drug repositioning analysis was performed and drug candidates were identified. The drug candidates were finally tested in both in vitro and in vivo models to evaluated their toxicity and efficacy.

Results

The Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in liver as well as other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drugs were identified as potential inhibitor of PKLR by the drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and it was demonstrated that these drugs attenuated hepatic steatosis without side effect on other tissues.

Conclusion

In conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which has been validated in preclinical experiment.
2-Arachodonoylglycerol-mediated endocannabinoid signaling modulates mechanical hypersensitivity associated with alcohol withdrawal in mice
Authors: Morgan Amanda , Adank Danielle , Johnson Keenan , Blunt Emily , Patel Sachin
Published: February 2022

Alcohol use disorder (AUDs) commonly co-occurs in patients with chronic pain, and a major barrier to achieving abstinence and preventing relapse is the emergence of hyperalgesia during alcohol withdrawal. Elucidating novel therapeutic approaches to target hyperalgesia associated with alcohol withdrawal could have important implications for the treatment of AUD. Here we examined the role of 2-arachidonoylglycerol (2-AG)-mediated endocannabinoid (eCB) signaling in the regulation of hyperalgesia associated with alcohol withdrawal in mice and tested the hypothesis that pharmacological augmentation of 2-AG signaling could reduce hyperalgesia during withdrawal. After 72 hours of withdrawal from a continuous access two-bottle choice drinking paradigm, male and female mice exhibited increased mechanical but not thermal hypersensitivity, which normalized by 7 days. This effect was reversed by pretreatment with the monoacylglycerol lipase (MAGL) inhibitor JZL184, which elevates levels of 2-AG. The effects of JZL184 were prevented by coadministration of either a CB1 or CB2 antagonist. Inhibition of the 2-AG synthetic enzyme diacylglycerol lipase (DAGL) with DO34 exacerbated mechanical hypersensitivity during alcohol withdrawal, causing an earlier onset and persistent hypersensitivity even one week into withdrawal. Our findings demonstrate the critical role of 2-AG signaling in the bidirectional regulation of mechanical sensitivity during alcohol withdrawal, with enhancement of 2-AG levels reducing sensitivity, and inhibition of 2-AG synthesis exacerbating sensitivity. These data suggest 2-AG augmentation could represent a novel approach to the treatment of alcohol withdrawal-associated hyperalgesia and AUD in patients with comorbid pain disorders.
Pathogen profiling of Australian rabbits by metatranscriptomic sequencing
Authors: Jenckel Maria , Hall Robyn , Strive Tanja
Published: February 2022

Australia is known for its long history of using biocontrol agents, like myxoma virus and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia we subjected a subset of these RHDV-negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non-infectious causes of death. We identified transcripts from severalClostridiaspecies,Pasteurella multocida, Pseudomonas, andEimeria stiedaein liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing fulminant disease. In addition, we identifiedHepatitis E virusandCyniclomycesyeast in some samples, both of which are not usually associated with severe disease. In one third of the sequenced liver samples, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of upregulated host immune responses, while immune response pathways were not upregulated whenE. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.

Importance

We have observed that approximately 40% of rabbit liver samples submitted for RHDV testing (from rabbits that had died suddenly without obvious cause) are RHDV-negative. Interestingly, a similar finding was reported in pet rabbits in the United Kingdom. This raises the intriguing question of what else is killing rabbits, both in Australia and internationally? Using a metatranscriptomic sequencing approach, we found thatClostridiaceae, Pasteurella multocida, andEimeriaare frequently detected in cases of sudden rabbit death in Australia. While we did not identify any potential new pathogens that could be explored in the context of wild rabbit management, we have validated an approach to explore future mortality events of lagomorphs that may identify candidate novel biocontrols. Furthermore, our findings reaffirm the recommendation to follow good hygiene practices when handling rabbits, since domestic rabbits harboured several pathogens of potential public health significance, includingEscherichia, Pasteurella multocida, and Hepatitis E virus.
Metabotropic purinergic receptor profiles and calcium signalling in primary mice myoblasts differ depending on their muscle origin and are altered in cells with mutated dystrophin gene (mdx mice)
Authors: Róg Justyna , Oksiejuk Aleksandra , Górecki Dariusz C. , Zabłocki Krzysztof
Published: February 2022

Mortality of Duchenne Muscular Dystrophy (DMD) is a direct consequence of progressive wasting of muscle fibres leading to skeletal muscle deterioration and cardiomyopathy. However pathophysiological effects of mutations in the dystrophin encoding gene, which result in improper muscle maturation are detectable in muscle precursor cells which do not express dystrophin gene at the protein level because of early stage of differentiation thus irrespectively of changes in dystrophin-encoding gene. Among these abnormalities elevated activity of P2X7 receptors and increased store-operated calcium entry, have been identified in mdx mouse myoblasts. Moreover the increased response of immortalized mdx myoblasts to agonists activating metabotropic purinergic receptors was characterised. Experiments on immortalized myoblasts do not allow indicating potentially specific effects of mdx mutation on cells derived from particular muscles. Moreover an immortalization of cells itself may influence their metabolism in poorly defined way. Therefore here the metabotropic response of primary myoblasts derived from various muscles of normal and mdx mice to nucleotide stimulation has been investigated. Transcript and protein level of P2Y receptors, sensitivity to antagonist, and cellular localization clearly indicate P2RY2 as the most affected in mdx myoblasts. This meets our previous conclusion drawn from experiments with immortalized cells. However a pattern of expression and activity of P2Y receptors among myoblasts derived from four muscles differ. Also cellular levels of some other proteins belonging to the “calcium signalling toolkit” differ in myoblasts from various muscle and are differently changed due to mdx mutation. Finally, these results complement and strongly support previously formulated conclusion that phenotypic effects of DMD emerge as early as in undifferentiated muscle and therefore traditional understanding of DMD pathogenesis needs re-evaluation.
Monitoring the quality of eggs depending on the hens breeding systems by Raman spectroscopy
Authors: Kopec M. , Abramczyk H.
Published: February 2022

The aim of this study is show that Raman spectroscopy is a sensitive tool, which can be used for analyses eggs obtained in various hens housing system. This study provided a new and simple method for hens’ eggs breeding systems testing. Raman methods have potential to be applied by commercial inspections in food industry for verification indications placed on eggs. The development of functional technological methods to study the quality of eggs could be an interesting way to gain profitability for the food industry, in addition to improving the general conditions of public health. A label-free Raman method for detecting spectral changes in eggs from cage systems, barn systems, free range systems and ecological systems is presented. The most important advantage of Raman spectroscopy is the ability to identify biomarkers that help estimate the quality of eggs from various hens housing systems based on spectra typical for lipids, proteins and carotenoids. We have proved that ratios 1656/1004, 1656/1444, 1444/1520 and 1656/1156 can be used as universal biomarkers to distinguish eggs from various hens housing systems. Chemometric methods have shown that eggs from ecological systems and barn systems can be distinguished based on their vibrational properties.

Graphical Abstract
Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history
Authors: Barnett Samuel E. , Youngblut Nicholas D. , Buckley Daniel H.
Published: February 2022

Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of 13C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are predictable from soil DNA content. Soil DNA yield is easy to measure and it predicts microbial community dynamics linked to soil carbon cycling.

Originality-Significance Statement

Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Microbial communities vary with respect to land-use, but we still have an incomplete understanding of how variation in community structure links to variation in community function. DNA stable isotope probing (DNA-SIP) is a high-resolution method that can identify specific microbial taxa that assimilate carbon in situ. We conducted a large-scale multi-substrate DNA-SIP experiment to explore differences in bacterial activity across land-use regimes. We show that microbial community dynamics vary with land-use, that these dynamics are linked to soil carbon cycling, and that they are predicted from easily measured soil properties.
Purely enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR
Authors: Feyrer Hannes , Gurdap Cenk Onur , Marušič Maja , Schlagnitweit Judith , Petzold Katja
Published: February 2022

Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods pose as an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.
Immune cell regulation in stem cell niche contacting glioblastomas
Authors: Bartkowiak Todd , Lima Sierra M. , Hayes Madeline J. , Mistry Akshitkumar M. , Sinnaeve Justine , Leelatian Nalin , Roe Caroline E. , Mobley Bret C. , Weaver Kyle D. , Thompson Reid C. , Chambless Lola B. , Ihrie Rebecca A. , Irish Jonathan M.
Published: February 2022

Glioblastomas (GBM) are tumors for which immune-targeted therapies have failed to show clinical benefit and for which few biomarkers provide context for meaningful therapeutic stratification. Radiographic contact of GBM tumors with the lateral ventricle stem cell niche correlates with worse patient prognosis; however, the extent to which proximity to the ventricle impacts antitumor immunity remains unknown. We demonstrate that T cell checkpoint receptor expression is elevated in ventricle-contacting GBM as is the abundance of a specific, suppressive CD32+CD44+HLADhigh myeloid population suggesting a distinct immunoregulatory influence on antitumor immunity in proximity to the lateral ventricle. Phospho-specific mass cytometric profiling revealed extensively impaired immune signaling in ventricle-contacting GBM in response to inflammatory cytokine stimulation, further supporting a suppressive milieu influencing immunity at the lateral ventricle. Collectively, we identify a regulatory impact of ventricle contact on antitumor immunity in the brain, and reveal novel clinically targetable mechanisms of immunomodulation in patients with glioblastoma.

Significance Statement

We demonstrate that the immune microenvironment of glioblastoma tumors contacting the lateral ventricle differs from non-contacting tumors. This work connects immune-biology to a radiographically detectable feature, the lateral ventricle, and highlights non-invasive imaging as a means to identify targetable immune features in glioblastoma tumors.
Natural Trajectory of Recovery of COVID-19 Associated Olfactory Loss
Authors: Khan Amish M. , Lee Jake , Rammaha Thue , Gupta Shruti , Smith Harrison , Kannampallil Thomas , Farrell Nyssa , Kallogjeri Dorina , Piccirillo Jay F.
Published: February 2022

Importance

Prevalence of post-viral olfactory loss has increased dramatically due to the frequency and severity of olfactory dysfunction associated with infection by the SARS-CoV-2 virus.

Objective

To determine the trajectory of COVID-19 olfactory loss over a six-month period. A key secondary objective is to assess predictive factors associated with the recovery of olfaction.

Design

Longitudinal repeated-measures study that enrolled from May 5, 2020 to February 2, 2021, with the last date of data collection on June 15, 2021.

Setting

Barnes-Jewish HealthCare/Washington University School of Medicine facilities (Saint Louis, Missouri, USA).

Participants

Individuals who tested positive for SARS-CoV-2 by real-time polymerase chain reaction on nasopharyngeal swab and indicated olfactory loss on COVID-19 screening questionnaire. Individuals were excluded if they had previously diagnosed history of olfactory loss, neurodegenerative disorders, less than 18 years of age, admitted to hospital service, unable to read, write, and understand English, or lacked computer or internet access.

Interventions/Exposures

Watch and wait for spontaneous recovery.

Main Outcome(s) and Measure(s)

Participants completed olfactory assessments every 30 days for six months. Each assessment consisted of the University of Pennsylvania Smell Identification Test (UPSIT), an objective “scratch-and-sniff” test, and Clinical Global Impressions (CGI), a subjective Likert rating scale.

Results

The mean age was 41 years old (SD = 16). 39 (80%) were female and 42 (86%) white. At baseline assessment of objective olfaction, 18 (36%) participants had anosmia or severe hyposmia. Subjective, complete recovery at six months was 81% (95% CI 74% to 88%). Likelihood of recovery was associated with age less than 50 years (aHR = 8.1 (95% CI 1.1 to 64.1)) and mild olfactory loss at baseline (UPSIT = 30-33 for males and 31-34 for females) (aHR 6.2 (95% CI 1.2 to 33.0)).

Conclusions and Relevance

The trajectory of olfactory recovery among adults with COVID-19 olfactory loss illustrated rapid recovery within 2-3 weeks of infection, and by six months 81% had recovered based on self-report. Age less than 50 years old and mild severity of olfactory loss at baseline were associated with increased likelihood of recovery of olfaction. These findings can be used to inform shared decision-making with patients.
UK Withdrawal from the EU: Supremacy, Indirect Effect and Retained EU Law
Authors: Hameed Asif
Published: February 2022

The UK has left the EU and its withdrawal is managed by the European Union (Withdrawal) Act 2018 (EUWA). The EUWA domesticates a snapshot of EU law as ‘retained EU law’. The supremacy principle is also domesticated, and benefits retained EU law in its interaction with prior (pre‐IP completion day) domestic law. The domesticated supremacy principle's explicit confinement in this backward‐facing way is designed to maintain continuity with the previous state of affairs, during EU membership, while also allowing for future regulatory divergence. In spite of this, however, this article argues that retained EU law has important ramifications vis‐à‐vis future UK Acts of Parliament through the forward‐facing operation of the domesticated doctrine of indirect effect which the EUWA does not confine. The upshot is that the capacity to diverge in future from retained EU law is legally more constrained than might otherwise have been anticipated.
Catalyst‐free synthesis of phytosterol diacid monoesters and their competitive effect on the solubilization of cholesterol in model bile mixed micelles
Authors: Hu Yuyuan , Ma Chuanguo , Chen Xiaowei , Bai Ge , Guo Shujing
Published: February 2022

Phytosterols have received an extensive attention owing to their excellent cholesterol‐lowering activity and the role in cardiovascular diseases prevention. Phytosterol diacid monoesters, the important intermediates in the structural modification of free phytosterols, were usually obtained by chemical method with catalyst. The aim of this research was to provide an eco‐friendly approach for the preparation of phytosterol diacid monoester and explore the possible mechanism of their hypocholesteremic effect using model bile mixed micelles. Catalyst‐free synthesis of β‐sitosterol with succinic anhydride, maleic anhydride, and glutaric anhydride was investigated and optimized. The yields of three β‐sitosterol diacid monoesters all reached above 94% under optimum reaction conditions and their chemical structures were confirmed further by mass spectroscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy. Compared with β‐sitosterol, β‐sitosterol diacid monoesters possessed the increased thermal stability (up to an above 355.28°C) and improved solubility in binary mixed micelle system (exceeding 1.7 mM) and similar cholesterol‐lowering activity (7.78%–11.05%). Moreover, β‐sitosterol diacid monoesters showed the competitive effect on solubilization of cholesterol due to their enhanced micellar incorporation capacity. Overall, the competition with cholesterol in vitro gives useful information about the cholesterol‐lowering activity of phytosterol diacid monoesters, which will further expand their applications in the food industry and health.

Practical Application

Modified phytosterols, phytosterol diacid monoesters, were successfully synthesized in petroleum ether without catalyst. These products enhanced the thermal stability of free phytosterols and reduced the dissolution capacity of cholesterol in model bile mixed micelles due to competitive solubilization. These results indicated that phytosterol diacid monoesters represented cholesterol‐lowering potential, which might further expand the applications in the food industry and health.
Antifungal activities and mechanisms of trans‐cinnamaldehyde and thymol against food‐spoilage yeast Zygosaccharomyces rouxii
Authors: Wang Huxuan , Peng Zhonghua , Sun Hongmin
Published: February 2022

Due to hydrophobicity, plant essential oil components trans‐cinnamaldehyde and thymol exert broad‐spectrum antimicrobial activities by interfering with the structures and functions of microbial cell membranes, yet their antifungal properties against food‐spoilage yeast Zygosaccharomyces rouxii are still unclear. This work aimed to elucidate their antifungal activities and mechanisms against Z. rouxii. Minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) were measured using broth dilution method to evaluate the antifungal activities. Membrane permeability, potential and integrity, intracellular ATP content, and intracellular pH (pHin) were determined, and membrane damage was observed by scanning electron microscope (SEM) to investigate the antifungal mechanisms. The MICs of trans‐cinnamaldehyde and thymol were 0.3125 and 0.0625 mg/ml, respectively, and the MFCs were 1.25 and 0.125 mg/ml, respectively. Increased membrane permeability, membrane hyperpolarization, decreased membrane integrity, reduced intracellular ATP content, and lowered pHin were found after trans‐cinnamaldehyde or thymol treatment at the MIC and MFC levels, and thymol exhibited more severe influence on cell membrane. SEM observation further confirmed that trans‐cinnamaldehyde caused cell membrane shrinkage and invagination, while thymol resulted in perforation in cell membrane. These results suggest that trans‐cinnamaldehyde and thymol exert anti‐Z. rouxii activities by inducing cell membrane damage and subsequent intracellular homeostasis disruption. Cellular contents leakage and intracellular homeostasis disruption probably proceed more rapidly after thymol inducing perforation in the cell surface, thereby thymol exerting better anti‐Z. rouxii activity.

Practical Application

The addition of a small amount of thymol (0.125 mg/ml) is sufficient to effectively inhibit the growth of Z. rouxii in apple juice concentrate. Based on our previous work, the addition of thymol (0.125 mg/ml) in apple juice concentrate did not significantly affect the organoleptic property of the diluted apple juice (5°Brix) used for producing commercial apple juice products. Therefore, thymol is practical for application at the effective concentration (0.125 mg/ml) in apple juice concentrate.
Bentong ginger oleoresin mitigates liver injury and modulates gut microbiota in mouse with nonalcoholic fatty liver disease induced by high‐fat diet
Authors: Wang Kunli , Li Bei , Fu Rao , Jiang Zefang , Wen Xin , Ni Yuanying
Published: February 2022

The present study aimed to examine the protective effect of Bentong ginger oleoresin (BGO) on the occurrence of nonalcoholic fatty liver disease (NAFLD) and its underlying mechanism. In the present study, 14‐week BGO treatment reduced the high‐fat diet (HFD)‐induced obesity. The serum total cholesterol (TC) was reduced from 4.76 ± 0.30 to 3.542 ± 0.49 mmol/L and fatty liver score decreased to the normal level (1.6 ± 0.55). BGO had antihypercholesterolemia activity, alleviated abnormal lipid metabolism, and improved liver fat accumulation. In addition, liver inflammatory cytokine tests and Western blotting analysis indicated that BGO might play an anti‐inflammatory role by mediating the NF‐κB signaling pathway. Moreover, BGO regulated the gut microbiota in NAFLD mice and finally mediated their benefits for the host, which might be associated with reduced abundance ofLachnospiraceae_NK4A136_groupandFournierella. BGO showed effective liver protection and regulation of gut microbiota for the HFD‐induced NAFLD in obese mice. As a result, BGO may serve as an effective dietary supplement for the improvement of NAFLD‐related metabolic diseases.

Practical Application

This study provides a new way to improve the added value of Bentong ginger. It also provides certain experimental data on BGO as a kind of the functional food ingredient. The current work also provides new ideas for the improvement and treatment of NAFLD.
isotracer: An R package for the analysis of tracer addition experiments
Authors: Bruneaux Matthieu , López‐Sepulcre Andrés
Published: February 2022

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. However, performing rigorous statistical analyses to gain reliable quantitative insights from these experiments often remains challenging.

We present an approach based on Hidden Markov Models (HMMs) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. The isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments and pulse‐chase experiments. It can also take into account tracer decay when radioactive isotopes are used.

To illustrate its use, we present three case studies based on published data and spanning different levels of biological organization: a molecular‐level study of protein synthesis and degradation in Arabidopsis thaliana, an organismal‐level study of phosphorus incorporation in the eelgrass Zostera marina and an ecosystem‐level study of nitrogen dynamics in Trinidadian montane streams. With these case studies, we illustrate how isotracer can be used to estimate uptake rates, turnover rates and total flows, as well as their uncertainty. We also show how to perform model selection to compare alternative hypotheses.

The isotracer package allows researchers from a broad range of disciplines to fully take advantage of their datasets through rigorous statistical analyses. We conclude by discussing isotracer’s further applications, limitations and possible future improvements and expansions.