bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell analysis of hepatoblastoma identifies distinct tumor cell signatures that predict susceptibility to chemotherapy using patient-specific tumor spheroids
Authors: Song Hanbing , Bucher Simon , Rosenberg Katherine , Tsui Margaret , Burhan Deviana , Cho Soo-Jin , Rangaswami Arun , Huang Franklin W. , Nijagal Amar , Wang Bruce
Published: October 2021

Pediatric hepatoblastoma (HB) is the most common primary liver cancer in infants and children. Studies of HB that focus exclusively on tumor cells demonstrate sparse somatic mutations and a common cell of origin, the hepatoblast, across patients. In contrast to the homogeneity these studies would suggest, HB tumors have a high degree of heterogeneity that can portend poor prognosis. In this study, we used single-cell genomic techniques to analyze resected human pediatric HB specimens. This study establishes that tumor heterogeneity can be defined by the relative proportions of five distinct subtypes of tumor cells. Notably, patient-derived HB spheroid cultures predict differential responses to treatment based on the transcriptomic signature of each tumor, suggesting a path forward for precision oncology for these tumors. Collectively, these results define HB tumor heterogeneity with single-cell resolution and demonstrate that patient-derived spheroids can be used to evaluate responses to chemotherapy.
Parkinsonian gait effects with DBS are associated with pallido-peduncular axis activation
Authors: Goftari Mojgan , Lu Chiahao , Schmidt Megan , Patriat Remi , Palnitkar Tara , Kim Jiwon , Harel Noam , Johnson Matthew D. , Cooper Scott E.
Published: October 2021

Background

Deep brain stimulation (DBS) targeting the subthalamic nucleus (STN) often shows variable outcomes on treating gait dysfunction in Parkinson’s disease (PD). Such variability may stem from which specific neuronal pathways are modulated by DBS and the extent to which those pathways are modulated relative to one another.

Objective

Leveraging ultra-high-field (7T) imaging data and subject-specific computational models, this study investigated how activation of seven distinct pathways in and around STN, including the pallidopeduncular and pedunculopallidal pathways, affect step length at clinically-optimized STN-DBS settings.

Methods

Personalized computational models were developed for 10 subjects with a clinical diagnosis of PD and with bilateral STN-DBS implants.

Results

The subject-specific pathway activation models showed a significant positive association between activation of the pedunculopallidal pathway and increased step length, and negative association on step length with pallidopeduncular pathway and hyperdirect pathway activation.

Conclusions

The STN region includes multiple pathways, including fibers of passage to and from the mesencephalic locomotor area. Future clinical optimization of STN-DBS should consider these fibers of passage in the context of treating parkinsonian gait.
PRMT5 in T cells drives Th17 responses, mixed granulocytic inflammation and severe allergic airway inflammation
Authors: Lewis Brandon W. , Amici Stephanie A. , Kim Hye-Young , Shalosky Emily , Khan Aiman , Walum Joshua , Gowdy Kymberly M. , Englert Joshua A. , Porter Ned A. , Grayson Mitchell H. , Britt Rodney D. , Guerau-de-Arellano Mireia
Published: October 2021

Severe asthma is characterized by steroid insensitivity and poor symptom control, and is responsible for the majority of asthma-related hospital costs. Therapeutic options remain limited, in part due to limited understanding in mechanisms driving severe asthma. Increased arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is increased in asthmatic lungs. Here, we show that PRMT5 drives allergic airway inflammation in a mouse model reproducing multiple aspects of human severe asthma. We find that PRMT5 is required in CD4+ T cells for chronic steroid-insensitive severe lung inflammation, with selective T cell deletion of PRMT5 robustly suppressing eosinophilic and neutrophilic lung inflammation, pathology, airway remodeling and hyperresponsiveness. Mechanistically, we observed high pulmonary sterol metabolic activity, ROR-γt and Th17 responses, with PRMT5-dependent increases in ROR-γt’s agonist desmosterol. Our work demonstrates that T cell PRMT5 drives severe allergic lung inflammation and has potential implications for the pathogenesis and therapeutic targeting of severe asthma.
Reservoir-based Tracking (TRAKR) For One-shot Classification Of Neural Time-series Patterns
Authors: Afzal Muhammad Furqan , Márton Christian David , Rich Erin L. , Mayberg Helen , Rajan Kanaka
Published: October 2021

Distinguishing between complex nonlinear neural time-series patterns is a challenging problem in neuroscience. Accurately classifying different patterns could be useful for a wide variety of applications, e.g. detecting seizures in epilepsy and optimizing control spaces for brain-machine interfaces. It remains challenging to correctly distinguish nonlinear time-series patterns because of the high intrinsic dimensionality of such data, making accurate inference of state changes (for intervention or control) difficult. On the one hand, simple distance metrics, which can be computed quickly, often do not yield accurate classifications; on the other hand, ensembles or deep supervised approaches offer high accuracy but are training data intensive. We introduce a reservoir-based tool, state tracker (TRAKR), which provides the high accuracy of ensembles or deep supervised methods while preserving the benefits of simple distance metrics in being applicable to single examples of training data (one-shot classification). We show that TRAKR instantaneously detects deviations in dynamics as they occur through time, and can distinguish between up to 40 patterns from different chaotic data recurrent neural networks (RNNs) with above-chance accuracy. We apply TRAKR to a benchmark time-series dataset – permuted sequential MNIST – and show that it achieves high accuracy, performing on par with deep supervised networks and outperforming other distance-metric based approaches. We also apply TRAKR to electrocorticography (ECoG) data from the macaque orbitofrontal cortex (OFC) and, similarly, find that TRAKR performs on par with deep supervised networks, and more accurately than commonly used approaches such as Dynamic Time Warping (DTW). Altogether, TRAKR allows for high accuracy classification of time-series patterns from a range of different biological and non-biological datasets based on single training examples. These results demonstrate that TRAKR could be a viable alternative in the analysis of time-series data, offering the potential to generate new insights into the information encoded in neural circuits from single-trial data.
A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses
Authors: Wang Pengfei , Casner Ryan G. , Nair Manoj S. , Yu Jian , Guo Yicheng , Wang Maple , Chan Jasper F.-W. , Cerutti Gabriele , Iketani Sho , Liu Lihong , Sheng Zizhang , Chen Zhiwei , Yuen Kwok-Yung , Kwong Peter D. , Huang Yaoxing , Shapiro Lawrence , Ho David D.
Published: October 2021

The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
Motor Learning Drives Dynamic Patterns of Intermittent Myelination on Learning-activated Axons
Authors: Bacmeister Clara M. , Huang Rongchen , Osso Lindsay A. , Thornton Michael A. , Conant Lauren , Chavez Anthony , Poleg-Polsky Alon , Hughes Ethan G.
Published: October 2021

Myelin plasticity occurs when newly-formed and pre-existing oligodendrocytes remodel existing patterns of myelination. Recent studies show these processes occur in response to changes in neuronal activity and are required for learning and memory. However, the link between behaviorally-relevant neuronal activity and circuit-specific changes in myelination remains unknown. Using longitudinal, in vivo two-photon imaging and targeted labeling of learning-activated neurons, we explore how the pattern of intermittent myelination is altered on individual cortical axons during learning of a dexterous reach task. We show that behavior-induced plasticity is targeted to learning-activated axons and occurs in a staged response across cortical layers in primary motor cortex. During learning, myelin sheaths retract, lengthening nodes of Ranvier. Following learning, addition of new sheaths increases the number of continuous stretches of myelination. Computational modeling suggests these changes initially slow and subsequently increase conduction speed. Finally, we show that both the magnitude and timing of nodal and myelin dynamics correlate with behavioral improvement during learning. Thus, learning-activated, circuit-specific changes to myelination may fundamentally alter how information is transferred in neural circuits during learning.
Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.)
Authors: Carlson Craig H , Choi Yongwook , Chan Agnes P , Town Christopher D , Smart Lawrence B
Published: October 2021

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid S. purpurea, diploid S. viminalis, and tetraploid S. miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.
Structural rearrangement of the intracellular gate of the serotonin transporter induced by Thr276 phosphorylation
Authors: Chan Matthew C. , Procko Erik , Shukla Diwakar
Published: October 2021

The reuptake of the neurotransmitter serotonin from the synaptic cleft by the serotonin transporter, SERT, is essential for proper neurological signaling. Biochemical studies have shown Thr276 of transmembrane helix 5 is a site of PKG-mediated SERT phosphorylation, which has been proposed to shifts the SERT conformational equlibira to promote inward-facing states, thus enhancing 5HT transport. Recent structural and simulation studies have provided insights into the conformation transitions during substrate transport but have not shed light on SERT regulation via post-translational modifications. Using molecular dynamics simulations and Markov state models, we investigate how Thr276 phosphorylation impacts the SERT mechanism and its role in enhancing transporter stability and function. Our simulations show that Thr276 phosphorylation alters the hydrogen-bonding network involving residues on transmembrane helix 5. This in turn decreases the free energy barriers for SERT to transition to the inward-facing state, thus facilitating 5HT transport. The results provide atomistic insights into in vivo SERT regulation and can be extended to other pharmacologically important transporters in the solute carrier superfamily.
Debunking the “junk”: Unraveling the role of lncRNA–miRNA–mRNA networks in fetal hemoglobin regulation
Authors: Rahaman Motiur , Bhowmick Chiranjib , Komanapalli Jaikrishna , Mukherjee Mandrita , Byram Prasanna Kumar , Shukla Praphulla Chandra , Dolai Tuphan Kanti , Chakravorty Nishant
Published: October 2021

Fetal hemoglobin (HbF) induction is considered to be a promising therapeutic strategy to ameliorate the clinical severity of β-hemoglobin disorders, and has gained a significant amount of attention in recent times. Despite the enormous efforts towards the pharmacological intervention of HbF reactivation, progress has been stymied due to limited understanding of γ-globin gene regulation. In this study, we intended to investigate the implications of lncRNA-associated competing endogenous RNA (ceRNA) interactions in HbF regulation. Probe repurposing strategies for extraction of lncRNA signatures and subsequent in silico analysis on publicly available datasets (GSE13284, GSE71935 and GSE7874) enabled us to identify 46 differentially expressed lncRNAs (DElncRNAs). Further, an optimum set of 11 lncRNAs that could distinguish between high HbF and normal conditions were predicted from these DElncRNAs using supervised machine learning and a stepwise selection model. The candidate lncRNAs were then linked with differentially expressed miRNAs and mRNAs to identify lncRNA-miRNA-mRNA ceRNA networks. The network revealed that 2 lncRNAs (UCA1 and ZEB1-AS1) and 4 miRNAs (hsa-miR-19b-3p,hsa-miR-3646,hsa-miR-937 and hsa-miR-548j) sequentially mediate cross-talk among different signaling pathways which provide novel insights into the lncRNA-mediated regulatory mechanisms, and thus lay the foundation of future studies to identify lncRNA-mediated therapeutic targets for HbF reactivation.
A high content microscopy-based platform for detecting antibodies to the nucleocapsid, spike and membrane proteins of SARS-CoV-2
Authors: Williams Daniel M. , Hornsby Hailey , Shehata Ola M. , Brown Rebecca , Zafred Domen , Shun-Shion Amber S.M. , Hodder Anthony J. , Bliss Deepa , Metcalfe Andrew , Edgar James R. , Gordon David E. , Sayers Jon R. , Nicklin Martin J. , Collini Paul J. , Brown Steve , de Silva Thushan I. , Peden Andrew A.
Published: October 2021

The strong humoral immune response produced against the SARS-CoV-2 nucleocapsid (N) and spike (S) proteins has underpinned serological testing but the prevalence of antibody responses to other SARS-CoV-2 proteins, which may be of use as further serological markers, is still unclear. Cell-based serological screening platforms can fulfil a crucial niche in the identification of antibodies which recognise more complex folded epitopes or those incorporating post-translation modifications which may be undetectable by other methods used to investigate the antigenicity of the SARS-CoV-2 proteome. Here, we employed automated high content immunofluorescence microscopy (AHCIM) to assess the viability of such an approach as a method capable of assaying humoral immune responses against full length SARS-CoV-2 proteins in their native cellular state. We first demonstrate that AHCIM provides high sensitivity and specificity in the detection of SARS-CoV-2 N and S IgG. Assessing the prevalence of antibody responses to the SARS-CoV-2 structural membrane protein (M), we further find that 85% of COVID-19 patients within our sample set developed detectable M IgG responses (M sensitivity 85%, N sensitivity 93%, combined N + M sensitivity 95%). The identification of M as a serological marker of high prevalence may be of value in detecting additional COVID-19 cases during the era of mass SARS-CoV-2 vaccinations, where serological screening for SARS CoV-2 infections in vaccinated individuals is dependent on detection of antibodies against N. These findings highlight the advantages of using cell-based systems as serological screening platforms and raise the possibility of using M as a widespread serological marker alongside N and S.
Vaccine effectiveness against SARS-CoV-2 transmission to household contacts during dominance of Delta variant (B.1.617.2), August-September 2021, the Netherlands
Authors: de Gier Brechje , Andeweg Stijn , Backer Jantien A. ,   RIVM COVID-19 surveillance and epidemiology team, Hahné Susan J.M. , van den Hof Susan , de Melker Hester E. , Knol Mirjam J.
Published: October 2021

We estimated vaccine effectiveness against onward transmission by comparing secondary attack rates among household members between vaccinated and unvaccinated index cases, based on source and contact tracing data collected when Delta variant was dominant. Effectiveness of full vaccination of the index against transmission to fully vaccinated household contacts was 40% (95% confidence interval (CI) 20-54%), which is in addition to the direct protection of vaccination of contacts against infection. Effectiveness of full vaccination of the index against transmission to unvaccinated household contacts was 63% (95%CI 46-75%). We previously reported effectiveness of 73% (95%CI 65-79%) against transmission to unvaccinated household contacts for the Alpha variant.
The SARS-CoV-2 infection among students in the University of Porto: a cross-sectional study
Authors: Meireles Paula , Costa Joana Pinto , João Novais Maria , Miranda Daniela , Lopes Mariana Mendes , Severo Milton , Barros Henrique
Published: October 2021

Introduction

Incidence based on notified cases of SARS-CoV-2 infection underestimates the real extension of the infection. We aimed to quantify SARS-CoV-2 specific antibodies’ seroprevalence among University students in Porto.

Methods

A rapid point of care testing for SARS-CoV-2 specific immunoglobulin (Ig) M and IgG antibodies was performed, and a questionnaire was applied to the 6512 voluntary students from September to December 2020. We computed the apparent IgM, IgG and IgM or IgG prevalence, and the true prevalence and 95% credible intervals (95% CI) using Bayesian inference.

Results

We found an apparent prevalence (IgM or IgG) of 9.7%, the true prevalence being 7.9% (95% CI 4.9-11.1). Prevalence was significantly higher among males (10.9% vs 9.2%), international students (18.1% vs 10.4% local vs 8.8% nationally displaced) and increased with age. Those with a known risk contact, that experienced quarantine, had symptoms, or a previous negative molecular test had a higher seroprevalence. Of the 91 (1.4%) students who reported a molecular diagnosis, 86.7% were reactive for IgM or IgG.

Conclusion

Based on immunological evidence infection was 5.6 times more frequent than if based on a molecular diagnosis. The higher seroprevalence among male, older, and international students emphasizes the importance of identifying particular groups.
Modelling airborne transmission of SARS-CoV-2 using CARA: Risk assessment for enclosed spaces
Authors: Henriques Andre , Mounet Nicolas , Aleixo Luis , Elson Philip , Devine James , Azzopardi Gabriella , Andreini Marco , Rognlien Markus , Tarocco Nicola , Tang Julian
Published: October 2021

The global crisis triggered by the COVID-19 pandemic has highlighted the need for a proper risk assessment of respiratory pathogens in indoor settings. This paper documents the COVID Airborne Risk Assessment (CARA) methodology, to assess the potential exposure of airborne SARS-CoV-2 viruses, with an emphasis on the effect of certain virological and immunological factors in the quantification of the risk. The proposed model is the result of a multidisciplinary approach linking physical, mechanical and biological domains, benchmarked with clinical and experimental data, enabling decision makers or facility managers to perform risk assessments against airborne transmission. The model was tested against two benchmark outbreaks, showing good agreement. The tool was also applied to several everyday-life settings, in particular for the cases of a shared office, classroom and ski cabin. We found that 20% of infected hosts can emit approximately 2 orders of magnitude more viral-containing particles, suggesting the importance of super-emitters in airborne transmission. The use of surgical-type masks provides a 5-fold reduction in viral emissions. Natural ventilation through the opening of windows at all times are effective strategies to decrease the concentration of virions and slightly opening a window in the winter has approximately the same effect as a full window opening during the summer. Although vaccination is an effective protection measure, non-pharmaceutical interventions, which significantly reduce the viral density in the air (ventilation, masks), should be actively supported and included early in the risk assessment process. We propose a critical threshold value approach which could be used to define an acceptable risk level in a given indoor setting.
Social and mental health risks faced by undocumented migrants during the COVID-19 pandemic: Evidence from three surveys in France
Authors: Gosselin Anne , Longchamps Cecile , Oulahal Rachid , Derluyn Ilse , Ducarroz Simon , Skovdal Morten , Verelst An , Sturm Gesine , Desgrees du Lou Annabel , Melchior Maria
Published: October 2021

Background
The often-precarious life circumstances of undocumented migrants are likely to heighten the detrimental impact of the COVID-19 pandemic on their lives. Given the paucity of research exploring how undocumented migrants are affected by the COVID-19 pandemic, we set out to explore the association between being an undocumented migrant and a range of social and mental health measures.
Methods
Our study draws on three complementary surveys conducted among migrants in France between April 1st and June 7th 2020 (APART TOGETHER, MAKASI, ECHO; n = 716). We tested associations between eight outcome measures, covering health literacy, prevention behaviours, perceptions of government responses, livelihoods and mental health (PHQ-9 score), and the participants' legal status as either undocumented or documented. We modelled the probability of food insecurity increase, job loss, depression, and responses to SARS-COV-2 symptoms with logistic regression models, adjusted for age, gender and legal status.
Results
Undocumented migrants had a higher probability of experiencing food insecurity increase (aORs=10.40 [3.59, 30.16], and 2.19 [1.39, 3.50] in APART TOGETHER and ECHO), a higher probability of depression (aOR=2.65 [1.01, 6.97] in MAKASI). In all three surveys, undocumented migrants were more likely to lose their job (aORs=6.51 [1.18, 36.00], 8.36 [1.08, 64.70] and 3.96 [1.79, 9.16] in APART TOGETHER, MAKASI and ECHO respectively).
Conclusion
Our results suggest that the lives of undocumented migrants have been dramatically worsened by the COVID-19 pandemic, exposing and amplifying the inequalities facing this group. There is an urgent need for action to address these inequalities.
COVID-19 testing in schools: Perspectives of school administrators, teachers, parents, and students in Southern California
Authors: Unger Jennifer B. , Soto Daniel W. , Lee Ryan , Deva Sohini , Shanker Kush , Sood Neeraj , Hu Howard
Published: October 2021

Background

School-based COVID-19 testing is a potential strategy to facilitate the safe reopening of schools that have been closed due to the pandemic. This qualitative study assessed attitudes toward this strategy among four groups of stakeholders: school administrators, teachers, parents, and high school students.

Methods

Focus groups and interviews were conducted in Los Angeles from December 2020 to January 2021 when schools were closed due to the high level of COVID transmission in the community.

Results

Findings indicated similarities and differences in attitudes toward in-school COVID-19 testing. All groups agreed that frequent in-school COVID-19 testing could increase the actual safety and perceived safety of the school environment. School administrators and teachers expressed pessimism about the financial cost and logistics of implementing a testing program. Parents supported frequent testing but expressed concerns about physical discomfort and stigma for students who test positive. Teachers and parents noted that testing would prevent parents from sending sick children to school. Students were in favor of testing because it would allow them to return to in-person school after a difficult year of online learning.

Conclusion

In-school COVID-19 testing could be a useful component of school reopening plans and will be accepted by stakeholders if logistical and financial barriers can be surmounted and stigma from positive results can be minimized.
Emergence of networks of shared restriction-modification systems in phage-bacteria ecosystems
Authors: Eriksen Rasmus Skytte , Malhotra Nitish , Narain Seshasayee Aswin Sai , Sneppen Kim , Krishna Sandeep
Published: October 2021

1

Restriction-modification (RM) systems are the most ubiquitous bacterial defense system against bacteriophages and an important part of controlling phage predation. Using genomic sequence data, we show that RM systems are often shared among bacterial strains in a structured way. Examining the network of interconnections between bacterial strains within each genus, we find that in many genera strains share more RM systems than expected from a random network. We also find that many genera have a larger than expected number of bacterial strains with unique RM systems. We use population dynamics models of closed and open phage-bacteria ecosystems to qualitatively understand the selection pressures that could lead to these non-random network structures with enhanced overlap or uniqueness. In our models we find that the phages impose a pressure that favours bacteria with more RM systems, and more overlap of RM systems with other strains, but in bacteria dominated states this is opposed by the increased cost to the growth rate of these bacteria. Similar to what we observe in the genome data, we find that two distinct bacterial strategies emerge – strains either have a larger overlap than expected, or they have more unique RM systems than one expects from a null model. The former strategy appears to dominate when the repertoire of available RM systems is smaller but the average number of RM systems per strain is larger.
Actin dynamics regulation by TTC7A/PI4KIIIα axis limits DNA damage and cell death during leukocyte migration
Authors: Gajardo Tania , Lô Marie , Bernard Mathilde , Leveau Claire , El-Daher Marie-Thérèse , Kurowska Mathieu , Lay Gregoire Le , Moshous Despina , Neven Bénédicte , Fischer Alain , Ménasché Gaël , de Saint Basile Geneviève , Vargas Pablo , Sepulveda Fernando E.
Published: October 2021

The actin cytoskeleton has a crucial role in the maintenance of the immune homeostasis by controlling various cell processes, including cell migration. Mutations in the TTC7A gene have been described as the cause of a primary immunodeficiency associated to different degrees of gut involvement and alterations in the actin cytoskeleton dynamics. Although several cellular functions have been associated with TTC7A, the role of the protein in the maintenance of the immune homeostasis is still poorly understood. Here we leverage microfabricated devices to investigate the impact of TTC7A deficiency in leukocytes migration at the single cell level. We show that TTC7A-deficient leukocytes exhibit an altered cell migration and reduced capacity to deform through narrow gaps. Mechanistically, TTC7A-deficient phenotype resulted from impaired phosphoinositides signaling, leading to the downregulation of the PI3K/AKT/RHOA regulatory axis and imbalanced actin cytoskeleton dynamic. This resulted in impaired cell motility, accumulation of DNA damage and increased cell death during chemotaxis in dense 3D gels. Our results highlight a novel role of TTC7A as a critical regulator of leukocyte migration. Impairment of this cellular function is likely to contribute to pathophysiology underlying progressive immunodeficiency in patients.
LKB1 signalling in dendritic cells controls whole-body metabolic homeostasis by limiting T helper 17 priming
Authors: van der Zande Hendrik J.P. , Brombacher Eline C. , Lambooij Joost M. , Pelgrom Leonard R. , Zawistowska-Deniziak Anna , Patente Thiago A. , Heieis Graham A. , Otto Frank , Ozir-Fazalalikhan Arifa , Yazdanbakhsh Maria , Everts Bart , Guigas Bruno
Published: October 2021

Obesity-associated metaflammation drives the development of insulin resistance and type 2 diabetes, notably through modulating innate and adaptive immune cells in metabolic organs. The nutrient sensor liver kinase B1 (LKB1) has recently been shown to control cellular metabolism and T cell priming functions of dendritic cells (DCs). Here, we report that hepatic DCs from high-fat diet (HFD)-fed obese mice display increased LKB1 phosphorylation and that LKB1 deficiency in DCs (CD11cΔLKB1) worsened HFD-driven hepatic steatosis, systemic insulin resistance and glucose intolerance. Loss of LKB1 in DCs was associated with increased cellular expression of Th17-polarizing cytokines and increased hepatic CD4+ IL-17A+ Th17 cells in HFD-fed mice. Importantly, IL-17A neutralization rescued metabolic perturbations in HFD-fed CD11cΔLKB1 mice. Mechanistically, disrupted metabolic homeostasis was independent of the canonical LKB1-AMPK axis. Instead, we provide evidence for involvement of the AMPK-related salt-inducible kinase(s) in controlling Th17-polarizing cytokine expression in LKB1-deficient DCs. Altogether, our data reveal a key role for LKB1 signalling in DCs in protection against obesity-induced metabolic dysfunctions by limiting hepatic Th17 differentiation.
Pleiotropic and Non-redundant Effects of an Auxin Importer in Setaria and Maize1
Authors: Zhu Chuanmei , Box Mathew S. , Thiruppathi Dhineshkumar , Hu Hao , Yu Yunqing , Doust Andrew N. , McSteen Paula , Kellogg Elizabeth A.
Published: October 2021

Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

One sentence summary

Mutations in a single auxin importer gene Spp1/SvAUX1 uncover broad and unexpected effects in nearly all aspects of the development of shoots, inflorescences, and flowers.
Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir
Authors: Gordon Calvin J. , Lee Hery W. , Tchesnokov Egor P. , Perry Jason K. , Feng Joy Y. , Bilello John P. , Porter Danielle P. , Götte Matthias
Published: October 2021

Remdesivir (RDV) is a direct antiviral agent that is approved in several countries for the treatment of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RDV exhibits broad-spectrum antiviral activity against positive-sense RNA viruses, e.g., SARS-CoV-2 and hepatitis C virus (HCV) and non-segmented negative-sense RNA viruses, e.g., Nipah virus (NiV), while several segmented negative-sense RNA viruses such as influenza (Flu) virus or Crimean-Congo hemorrhagic fever virus (CCHFV) are not sensitive to the drug. The reasons for this apparent pattern are unknown. Here, we expressed and purified representative RNA-dependent RNA polymerases (RdRp) and studied three biochemical parameters that have been associated with the inhibitory effects of RDV-triphosphate (TP): (i) selective incorporation of the nucleotide substrate RDV-TP, (ii) the effect of the incorporated RDV-monophosphate (MP) on primer extension, and (iii) the effect of RDV-MP in the template during incorporation of the complementary UTP. The results of this study revealed a strong correlation between antiviral effects and efficient incorporation of RDV-TP. Delayed chain-termination is heterogeneous and usually inefficient at higher NTP concentrations. In contrast, template-dependent inhibition of UTP incorporation opposite the embedded RDV-MP is seen with all polymerases. Molecular modeling suggests a steric conflict between the 1’-cyano group of RDV-MP and conserved residues of RdRp motif F. We conclude that future efforts in the development of nucleotide analogues with a broader spectrum of antiviral activities should focus on improving rates of incorporation while capitalizing on the inhibitory effects of a bulky 1’-modification.
Ionic strength modulates HU protein-induced DNA supercoiling
Authors: Zhang Alexander , Yan Yan , Leng Fenfei , Dunlap David , Finzi Laura
Published: October 2021

The histone-like protein from E. coli strain U93 (HU) is an abundant nucleoid-associated protein that contributes to the compaction of the bacterial genome as well as to the regulation of many of its transactions. Despite many years of investigations, the way and extent to which HU binding alters the DNA double helix and/or generates hierarchical structures using DNA as a scaffold is not completely understood. Here we combined single-molecule magnetic measurements with circular dichroism studies to monitor structural changes in the DNA-HU fiber as HU concentration was increased from 0 to 1000 nM under low and physiological monovalent salt conditions. We confirmed that DNA compaction correlated with HU concentration in a biphasic manner but DNA unwinding varied monotonically with HU concentration in 100 mM KCl. Instead, in more physiological 200 mM salt conditions, DNA compaction was monotonic while HU-induced DNA unwinding was negligible. Differential compaction and unwinding of DNA may be part of the response of bacteria to large variations in salt concentrations.
Modular Derivation and Unbiased Single-cell Analysis of Regional Human Hindbrain And Spinal Neurons Enables Discovery of Nuanced Transcriptomic Patterns along Developmental Axes
Authors: Iyer Nisha R. , Shin Junha , Cuskey Stephanie , Tian Yucheng , Nicol Noah R. , Doersch Tessa E. , McCalla Sunnie Grace , Roy Sushmita , Ashton Randolph S.
Published: October 2021

Our inability to derive the vast neuronal diversity of the posterior central nervous system (pCNS) using human pluripotent stem cells (hPSCs) poses a major impediment to understanding human neurodevelopment and disease in the hindbrain and spinal cord. Here we establish a modular differentiation paradigm that recapitulates patterning along both the rostrocaudal (R/C) and dorsoventral (D/V) axes of the pCNS, enabling derivation of any neuronal phenotype with discrete regional specificity. First, neuromesodermal progenitors (NMPs) with discrete Hox profiles are efficiently converted to pCNS progenitors (pCNSPs). Then by tuning D/V signaling, pCNSPs are directed to ventral Shh-dependent MNs (MNs) and locomotor interneurons (INs) or dorsal TGF-β-dependent proprioceptive INs and TGF-β-independent sensory INs. We applied D/V protocols to NMPs spanning the R/C axis for expansive single-cell RNA-sequencing (scRNAseq) analysis. By implementing a novel computational pipeline comprising sparse non-negative matrix factorization, consensus clustering, and combinatorial gene expression pattern identification, we detect hundreds of transcriptional markers within region-specific neuronal phenotypes, enabling discovery of gene expression patterns along the developmental axes. These findings highlight the potential of these resources to advance a mechanistic understanding of pCNS development, expand the potential and accuracy of in vitro models, and inform novel regenerative therapeutic strategies.
Understanding the contexts and mechanisms of bluespace prescription programmes implemented in health and social care settings: a realist review
Authors: Alejandre Julius Cesar , Chastin Sebastien , Irvine Katherine N. , Georgiou Michail , Khanna Preeti , Tieges Zoë , Smith Niamh , Chong Yong-Yee , Onagan Frances Claire , Price Lesley , Pfleger Sharon , Helliwell Rachel , Singleton Judith , Curran Samuel , Helwig Karin
Published: October 2021

Background

Nature-based social prescribing programmes such as ‘bluespace prescription’ may promote public health and health improvement of individuals with long-term conditions. However, there is limited systematically synthesised evidence that investigates the contexts and mechanisms of Bluespace Prescription Programmes (BPPs) that could inform programme theories for policy and practice.

Methods

We conducted a realist review by searching six databases for articles published between January 2000 and February 2020, in English, about health and social care professionals providing referral to or prescription of blue space activities with health-related outcomes. We developed themes of contextual factors by analysing the contexts of BPPs. We used these contextual factors to develop programme theories describing the mechanisms of BPP implementation. Our study was registered with PROSPERO (CRD42020170660).

Results

Fifteen studies with adequate to strong quality were included from 6,736 records. Service users had improvements on their physical, mental, social health, and environmental knowledge after participating in BPPs referred to or prescribed by health and social care professionals. Patient-related contextual factors were referral information, free equipment and transportation, social support, blue space environments, and skills of service providers. Programme-related contextual factors were communication, multi-stakeholder collaboration, financing, and adequate service providers. Programme theories on patient enrolment, engagement, adherence, communication protocols, and long-term programme sustainability described the mechanisms of BPP implementation.

Conclusion

BPPs could support health and social care services if contextual factors and mechanisms of programme theories associated with patients and programme delivery are considered for implementation. Our findings have implications in planning, development, and implementation of similar nature-based social prescribing programmes in health and social care settings.
Brain predictors of fatigue in Rheumatoid Arthritis: a machine learning study
Authors: Goñi María , Basu Neil , Murray Alison D. , Waiter Gordon D.
Published: October 2021

Background

Fatigue is a common and burdensome symptom in Rheumatoid Arthritis (RA), yet is poorly understood. Currently, clinicians rely solely on fatigue questionnaires, which are inherently subjective measures. For the effective development of future therapies and stratification, it is of vital importance to identify biomarkers of fatigue. In this study, we identify brain differences between RA patients who improved and did not improve their levels of fatigue, and we compared the performance of different classifiers to distinguish between these samples at baseline.

Methods

Fifty-four fatigued RA patients underwent a magnetic resonance (MR) scan at baseline and 6 months later. At 6 months we identified those whose fatigue levels improved and those for whom it did not. More than 900 brain features across three data sets were assessed as potential predictors of fatigue improvement. These data sets included clinical, structural MRI (sMRI) and diffusion tensor imaging (DTI) data. A genetic algorithm was used for feature selection. Three classifiers were employed in the discrimination of improvers and non-improvers of fatigue: a Least Square Linear Discriminant (LSLD), a linear Support Vector Machine (SVM) and a SVM with Radial Basis Function kernel. Results: The highest accuracy (67.9%) was achieved with the sMRI set, followed by the DTI set (63.8%), whereas classification performance using clinical features was at the chance level. The mean curvature of the left superior temporal sulcus was most strongly selected during the feature selection step, followed by the surface are of the right frontal pole and the surface area of the left banks of the superior temporal sulcus. Conclusions: The results presented in this study evidence a superiority of brain metrics over clinical metrics in predicting fatigue changes. Further exploration of these methods may enable clinicians to triage patients towards the most appropriate fatigue alleviating therapies.
A scoping review of the research integrity architecture and how it is addressed in legal frameworks, institutional policies, and the scholarly literature: Research protocol
Authors: Pérez Juan Guillermo , Torres-Sarmiento Carolina , Castro Andrés Felipe Duarte , Gómez Luis Eduardo , Bachelet Vivienne C.
Published: October 2021

Background

Research integrity is a dynamic area within the ethical research ecosystem. Several efforts have been made to incorporate this topic in scientific governance frameworks. However, the efforts generally result in non-binding declarations and policies. Due to differences in legal systems, research cultures, and institutional approaches worldwide, there is a need to identify and map existent strategies on sound scientific practices.

Objective

This scoping review aims to systematically search, map, and evaluate the best available evidence on strategies and recommendations regarding research integrity. The goal is to identify international, national, regional, and local legal frameworks, institutional policies and guidelines, research integrity policies, interventions, strategies, and recommendations for:

The design and conduct of research projects,

The publication of research results,

The monitoring of scientific practices,

The implementation of corrective actions, and

Mentoring and education on research integrity.

Methods

The search will follow the PRISMA Extension for Scoping Reviews (PRISMA-ScR) and the methodological approach designed by Arksey and O’Malley. It will include legal frameworks, national and international governmental and non-governmental documentation, and scholarly articles published in peer-reviewed journals on research integrity. The search will be conducted in PubMed/MEDLINE, Web of Science, JSTOR, Latin American & Caribbean Health Sciences Literature (Lilacs), Scopus, OECD Library. It will be complemented with hand searching and scanning, covering other databases and grey literature sources. We will extract and synthesize the data using two macro-genres: legal documents (soft law and hard law) and non-legal documents.
A Thermostable Cas12b fromBrevibacillusLeverages One-pot Detection of SARS-CoV-2 Variants of Concern
Authors: Nguyen Long T. , Macaluso Nicolas C. , Pizzano Brianna L.M. , Cash Melanie N. , Spacek Jan , Karasek Jan , Dinglasan Rhoel R. , Salemi Marco , Jain Piyush K.
Published: October 2021

Current SARS-CoV-2 detection platforms lack the ability to differentiate among variants of concern (VOCs) in an efficient manner. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) has the potential to transform diagnostics due to its programmability. However, many of the CRISPR-based detection methods are reliant on either a multi-step process involving amplification or elaborate guide RNA designs. A complete one-pot detection reaction using alternative Cas effector endonucleases has been proposed to overcome these challenges. Yet, current approaches usingAlicyclobacillus acidiphilusCas12b (AapCas12b) are limited by its thermal instability at optimum reverse transcription loop-mediated isothermal amplification (RT-LAMP) reaction temperatures. Herein, we demonstrate that a novel Cas12b fromBrevibacillussp. SYP-B805 (referred to as BrCas12b) has robust trans-cleavage activity at ideal RT-LAMP conditions. A competitive profiling study of BrCas12b against Cas12b homologs from other bacteria genera underscores the potential of BrCas12b in the development of new diagnostics. As a proof-of-concept, we incorporated BrCas12b into an RT-LAMP-mediated one-pot reaction system, coined CRISPR-SPADE (CRISPR Single Pot Assay for Detecting Emerging VOCs) to enable rapid, differential detection of SARS-CoV-2 VOCs, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) in 205 clinical samples. Notably, a BrCas12b detection signal was observed within 1-3 minutes of amplification, achieving an overall 98.1% specificity, 91.2% accuracy, and 88.1% sensitivity within 30 minutes. Significantly, for samples with high viral load (Ctvalue ≤ 30), 100% accuracy and sensitivity were attained. To facilitate dissemination and global implementation of the assay, we combined the lyophilized one-pot reagents with a portable multiplexing device capable of interpreting fluorescence signals at a fraction of the cost of a qPCR system. With relaxed design requirements, one-pot detection, and simple instrumentation, this assay has the capability to advance future diagnostics.