bluuebunny/crossref_metadata_2025 huggingface dataset:
Pīr Ratannāth in Devī Pātan: Nāthyogīs, Monastic Networks and Historical Memories Along the Anglo-Gorkha Border
Authors: Kasturi Malavika
Published: August 2021

Through my case study of Devī Pātan, a Śāktīpītha Nāthyogī maṭh and temple on the India–Nepal border subordinate to the Gorakhnāth maṭh, my article demonstrates that Nāthyogī monastic networks are produced through spatial practices. Specifically, it focuses on shrines connected with Pīr Ratannāth, also known as Hājjīrattan, a legendary yogī of the Nāth sampradāy, widely worshipped across religious boundaries, who is said to have built Devī Pātan. Through the elusive figure of Ratannāth, I analyse how robust monastic networks focused on pilgrimage, trade and power, ‘made’ space and borders in the colonial and postcolonial period. Devī Pātan’s relationship with the Caughera maṭh in the Gorkha kingdom of Nepal and the Gorakhnāth maṭh in British India and after 1947 illustrates how competitive Nāthyogī monastic networks were historically produced and transformed through struggles between monastic institutions over space, resources and power across fraught borders. Ratannāth’s hagiographies, which emphasise his mobility, elasticity and importance in the world of saint veneration, reflect this world in which competing Nāthyogī nodes of circulation reworked relationships with each other. Simultaneously, they challenged ‘fixed’ cartographic boundaries between British India and the Gorkha kingdom of Nepal before 1947, and thereafter of new nation states. My essay also illustrates that histories of monasticism, space and place which have been memorialised by these shrines in representations of Ratannāth and Devī Pātan in recent times question the hegemonic narratives relating to Ratannāth authorised by the Gorakhnāth maṭh, known today for its close alignment with the Sangh Parivār, and its exclusionary vision of Hindutvā. Thus, the figure of Ratannāth transcends efforts to subordinate such border-crossing yogis to problematic majoritarian cartographic and political projects.
Reasoning between Rules and Discretion: A Comparative Study of the Normative Platform for Best Interest Decision-Making on Adoption in England and Norway
Authors: Helland Hege Stein
Published: August 2021

This article examines discretionary reasoning in child’s best interest (CBI) assessments in two jurisdictions, England and Norway, in decision concerning adoption from care. The two countries’ systems differ in child protection orientations and levels of discretionary autonomy but share the legal and moral yardstick of the CBI. Judgments from the Family Court in England (n = 29) and the County Social Welfare Board in Norway (n = 29) are analysed through a qualitative content analysis, following the logics of practical reasoning. The analysis provided a rich and detailed testimony of how the CBI decisions were justified and reveal that a similar normative platform was guiding decisions across the countries. There were, however, differences within and between the countries in terms of application and justifications of norms, some of which are likely to be connected to different interpretations of the CBI and others to systemic constructions and discretionary structures. Moreover, having more legislative guidance may have contributed to more explicit and deliberative reasoning in England although it does not appear to ensure consistent or predictable reasoning as inconsistencies and variation were found in both contexts. However, while Norwegian judges’ deliberation was found to be less ‘balanced’, justifications were applied in a similar manner across judgements. Although this contributes to consistency and predictability, the use of non-democratically constituted ‘rules’ in decision-making poses a challenge for legitimate decision-making.
Unraveling the functions of uncharacterized transcription factors inEscherichia coliusing ChIP-exo
Authors: Gao Ye , Lim Hyun Gyu , Verkler Hans , Szubin Richard , Quach Daniel , Rodionova Irina , Chen Ke , Yurkovich James T , Cho Byung-Kwan , Palsson Bernhard O
Published: August 2021

Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, no TRN is fully characterized since the identity and activity of all the transcriptional regulators comprising a TRN are not known. Here, we experimentally evaluate 40 uncharacterized proteins in Escherichia coli K-12 MG1655, which were computationally predicted to be transcription factors (TFs). First, we used a multiplexed chromatin immunoprecipitation method combined with lambda exonuclease digestion (multiplexed ChIP-exo) assay to characterize binding sites for these candidate TFs; 34 of them were found to be DNA-binding proteins. We then compared the relative location between binding sites and RNA polymerase (RNAP). We found 48% (283/588) overlap between the TFs and RNAP. Finally, we used these data to infer potential functions for 10 of the 34 TFs with validated DNA binding sites and consensus binding motifs. Taken together, this study: (i) significantly expands the number of confirmed TFs to 276, close to the estimated total of about 280 TFs; (ii) provides putative functions for the newly discovered TFs and (iii) confirms the functions of four representative TFs through mutant phenotypes.
Management of venous thromboembolism in high-grade glioma: Does low molecular weight heparin increase intracranial bleeding risk?
Authors: Jo Jasmin , Donahue Joseph , Sarai Guneet , Petroni Gina , Schiff David
Published: August 2021

Background

Venous thromboembolism (VTE) occurs in up to 30% of patients with high-grade glioma (HGG). Concern for increased risk of intracranial hemorrhage (ICH) with therapeutic anticoagulation (AC) complicates VTE treatment. Some retrospective studies have reported an increased risk of ICH associated with therapeutic AC; however, effective alternatives to AC are lacking. The aim of our study is to assess the risk of ICH in HGG patients with VTE on low molecular weight heparin (LMWH).

Methods

We performed a retrospective matched cohort study of HGG patients from January 2005 to August 2016. Blinded review of neuroimaging for ICH was performed. For analysis of the primary endpoint, estimates of cumulative incidence (CI) of ICH were calculated using competing risk analysis with death as competing risk; significance testing was performed using the Gray’s test. Median survival was estimated using the Kaplan-Meier method.

Results

Two hundred twenty patients were included, 88 (40%) with VTE treated with LMWH, 22 (10%) with VTE, not on AC, and 110 (50%) without VTE. A total of 43 measurable ICH was recorded: 19 (26%) in LMWH, 3 (14%) in VTE not on AC, and 21 (19%) in non-VTE cohort. No significant difference was observed in the 1-year CI of ICH in the LMWH cohort and non-AC with VTE group (17% vs 9%; Gray’s test, P = .36). Among patients without VTE, the 1-year CI of ICH was 13%. Median survival was similar among all 3 cohorts.

Conclusions

Our data suggest that therapeutic LMWH is not associated with substantially increased risk of ICH in HGG patients.
Carbon Starved Anther modulates sugar and ABA metabolism to protect rice seed germination and seedling fitness
Authors: Sun Linlin , Yuan Zheng , Wang Duoxiang , Li Jingbin , Shi Jin , Hu Yangyang , Yu Jing , Chen Xiaofei , Chen Sixue , Liang Wanqi , Zhang Dabing
Published: August 2021

Seed germination is critical for plant survival and agricultural production, which is affected by both internal seed factors and external environmental conditions. However, the genetic basis and underlying molecular mechanisms of early seed germination in crops remain largely unclear. Here, we report that R2R3 MYB transcription factor Carbon Starved Anther (CSA) is expressed specifically in Oryza sativa embryo and aleurone in response to seed imbibition, peaking at 3–6 h and undetectable by 24-h post-imbibition. CSA seeds germinated more quickly than wild-type rice seeds and had higher levels of amylase activity, glucose, and inactive abscisic acid-glucose ester (ABA-GE), but lower levels of ABA. Through analyzing the CSA-associated transcriptome and CSA binding to downstream target genes, we identified two glycolytic genes as direct CSA targets. CSA inhibits Amylase 3A expression to limit glucose production from starch and activates Os3BGlu6 expression to promote de-conjugation of ABA-GE to ABA; these functions serve to slow germination and improve seedling resilience to abiotic stress in the first 3 weeks of growth. Therefore, this study unveils a protection mechanism conferred by CSA during early seed germination by balancing glucose and ABA metabolism to optimize seed germination and stress response fitness.
Dam-break reflection
Authors: Hogg Andrew J , Skevington Edward W G
Published: August 2021

The unsteady reflection of dam-break flow along a horizontal channel by a remote barrier is modelled using the nonlinear shallow water equations. The interaction generates an upstream moving bore that connects the collapsing reservoir of fluid to a rapidly deepening fluid layer adjacent to the barrier. These motions are modified when the fluid is released into a channel containing a pre-wetted layer, because the oncoming flow is itself headed by a bore that alters the initial reflection. Solutions for these flows are calculated using quasi-analytical techniques that utilise the method of characteristics and the hodograph transformation of the governing equations, and the results are validated by comparison with direct numerical integration of the shallow water equations. The analytical solutions enable the precise identification of dynamical features in the flow, including the onset and development of discontinuous solutions that are manifest as bores, as well as their long term behaviour, the rate at which energy is dissipated, and for flows generated from the release of a finite reservoir, the maximum depth of the fluid layer at the barrier.
Capital Spillover, House Prices, and Consumer Spending: Quasi-Experimental Evidence from House Purchase Restrictions
Authors: Deng Yinglu , Liao Li , Yu Jiaheng , Zhang Yu
Published: August 2021

We use a unique quasi-experiment–spillovers from the imposition of purchase restrictions on local housing to nearby unregulated cities–to study the effects of out-of-town housing demand on house prices and consumer spending. While these restrictions effectively stymied the surge in local house prices, they induced capital flight and sharp abnormal increases in house prices in nearby unregulated cities. The effect of the house price increases on consumer spending is positive in the aggregate, but echoing Favilukis and Van Nieuwerburgh (2021), is redistributive, that is, negative for renters and positive for homeowners.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online
Siglec-1 expression on monocytes is associated with the interferon signature in juvenile dermatomyositis and can predict treatment response
Authors: Lerkvaleekul Butsabong , Veldkamp Saskia R , van der Wal M Marlot , Schatorjé Ellen J H , Kamphuis Sylvia S M , van den Berg J Merlijn , Hissink Muller Petra C E , Armbrust Wineke , Vastert Sebastiaan J , Wienke Judith , Jansen Marc H A , van Royen-Kerkhof Annet , van Wijk Femke
Published: August 2021

Objective

JDM is a rare chronic immune-mediated inflammatory disease with a predominant role for type I IFN responses. We aimed to determine the potential of Siglec-1 expression on monocytes as a novel IFN-inducible biomarker for disease activity monitoring and prediction of treatment response in patients with JDM.

Methods

Siglec-1 was measured by flow cytometry on circulating monocytes of 21 newly diagnosed JDM patients before start of treatment and, for 10 of these, also during follow-up. The expression levels of five type I IFN-stimulated genes, MX1, IFI44, IFI44L, LY6E and IFIT3, were measured by RT-qPCR to determine the IFN signature and calculate an IFN score. IFN-inducible plasma proteins CXCL10 and galectin-9 were measured by multiplex immunoassay.

Results

Siglec-1 and IFN score were increased in JDM patients compared with controls and correlated with clinical disease activity. Stratification of patients by Siglec-1 expression at diagnosis identified those with high Siglec-1 expression as having a higher risk of requiring treatment intensification within the first 3 months after diagnosis (55% vs 0% of patients, P = 0.01). Siglec-1 expression strongly correlated with plasma levels of previously validated biomarkers CXCL10 (rs = 0.81, P < 0.0001) and galectin-9 (rs = 0.83, P < 0.0001), and was superior to the IFN score in predicting treatment response (area under the curve 0.87 vs 0.53, P = 0.01).

Conclusion

Siglec-1 on monocytes is a novel IFN-inducible biomarker in JDM that correlates with clinical disease activity and identifies patients at risk for a suboptimal treatment response. Further studies are required to validate these findings and their clinical potential.
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals
Authors: Naser-Khdour Suha , Quang Minh Bui , Lanfear Robert
Published: August 2021

Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular clocks. In this study, we investigate the utility of nonreversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. [Bootstrap; nonreversible models; phylogenetic inference; root estimation.]
UBO registers in the EU and the case of a company controlled by a trust
Authors: Panico Paolo
Published: August 2021

UBO registers of companies and trusts are being introduced all over the EU under the 4th and the 5th AML Directive. Very few EU Member States have expressly dealt with the case of an EU company controlled by a trust. The UBO registers of companies are fully open to the public while those of trusts are accessible only to people demonstrating a legitimate interest. This is consistent with the respect of privacy that goes back to the ‘Declaration of the Rights of Man and the Citizen’ of 1789. Some countries such as Belgium and Cyprus have issued regulations requesting that only the trust be mentioned in the UBO register of the underlying company while the details of the UBOs of that trust are filed in the corresponding, non-public register.
A Tale of Two Programs: Assessing Treatment and Control in NREGA Studies
Authors: Bahal Girish
Published: August 2021

This article revisits impact evaluation studies on the largest public workfare in the world, NREGA. In an environment where randomization is not feasible, I show why an impact evaluation exercise on NREGA should acknowledge the existence of an older program, SGRY. Using novel district-level expenditure data on SGRY, this article shows how ignoring the older program is likely to underestimate the general equilibrium impact of the employment policy on various relevant socioeconomic outcomes. In most cases, ignoring SGRY underestimates NREGA’s impact by 30–40 percent.
Brief Report: “What Is This PrEP?”—Sources and Accuracy of HIV Pre-Exposure Prophylaxis (PrEP) Awareness Among Adolescent Girls and Young Women Attending Family Planning and Maternal Child Health Clinics in Western Kenya
Authors: Dettinger Julia C. , Pintye Jillian , Dollah Annabell , Awuor Mercy , Abuna Felix , Lagat Harrison , Kohler Pamela , John-Stewart Grace , O'Malley Gabrielle , Kinuthia John , Beima-Sofie Kristin
Published: August 2021

Background:

Pre-exposure prophylaxis (PrEP) delivery to adolescent girls and young women (AGYW) is scaling up in sub-Saharan African countries. Understanding how AGYW learn about PrEP is needed to inform programs seeking to reach AGYW with HIV prevention tools.

Methods:

AGYW (ages 15–24), attending routine family planning and maternal child health clinics in Kisumu, Kenya, participated in in-depth interviews. AGYW were recruited if they either declined or accepted PrEP when offered that day in clinic or were currently or previously on PrEP. Thematic analysis was used to identify key themes related to the type and quality of knowledge sources from which AGYW first became aware of PrEP.

Results:

Overall, 140 in-depth interviews were conducted with AGYW. The median age was 21.5 years (interquartile range: 20.0–23.0), 65% of participants were married, and almost half (45.7%) were currently taking PrEP. Participants reported learning about PrEP from 3 primary sources: (1) clinic-based education; (2) friends, family, or other PrEP users; and (3) media and community outreach. Participants who reported learning about PrEP from friends or family were highly enthusiastic about PrEP. The accuracy and completeness of knowledge varied with most inaccuracies around the cost, dosing, and who benefits from PrEP. Community outreach campaigns provided fewer details, resulting in more inaccurate information and distrust of information received.

Conclusion:

PrEP information reaches AGYW through many sources with variable accuracy and completeness. Training providers and peer leaders to disseminate thorough and accurate PrEP information when counseling AGYW could positively impact acceptance and proper use.
Urban rat exposure to anticoagulant rodenticides and zoonotic infection risk
Authors: Murray Maureen H. , Sánchez Cecilia A.
Published: August 2021

Anticoagulant rodenticides (ARs) deployed to control rodent pest populations can increase the risk of pathogen infection for some wildlife. However, it is unknown whether ARs also increase infection risk for target rodents, which are common hosts for zoonotic (animal-to-human transmitted) pathogens. In this study, we tested whether rats exposed to ARs were more likely to be infected with zoonotic pathogens, specifically
Leptospira
spp. or
Escherichia coli
, after controlling for known predictors of infection (i.e. sex, age, body condition). We collected biological samples from 99 rats trapped in Chicago alleys and tested these for
Leptospira
infection,
E. coli
shedding and AR exposure. We found that rats that had been exposed to ARs and survived until the time of trapping, as well as older rats, were significantly more likely to be infected with
Leptospira
spp. than other rats. We found no significant association between
E. coli
shedding and any predictors. Our results show that human actions to manage rats can affect rat disease ecology and public health risks in unintended ways, and more broadly, contribute to a growing awareness of bidirectional relationships between humans and natural systems in cities.
Sparse nonlinear models of chaotic electroconvection
Authors: Guan Yifei , Brunton Steven L. , Novosselov Igor
Published: August 2021

Convection is a fundamental fluid transport phenomenon, where the large-scale motion of a fluid is driven, for example, by a thermal gradient or an electric potential. Modelling convection has given rise to the development of chaos theory and the reduced-order modelling of multiphysics systems; however, these models have been limited to relatively simple thermal convection phenomena. In this work, we develop a reduced-order model for chaotic electroconvection at high electric Rayleigh number. The chaos in this system is related to the standard Lorenz model obtained from Rayleigh–Benard convection, although our system is driven by a more complex three-way coupling between the fluid, the charge density, and the electric field. Coherent structures are extracted from temporally and spatially resolved charge density fields via proper orthogonal decomposition (POD). A nonlinear model is then developed for the chaotic time evolution of these coherent structures using the sparse identification of nonlinear dynamics (SINDy) algorithm, constrained to preserve the symmetries observed in the original system. The resulting model exhibits the dominant chaotic dynamics of the original high-dimensional system, capturing the essential nonlinear interactions with a simple reduced-order model.
Predicting the risk of rupture for vertebral aneurysm based on geometric features of blood vessels
Authors: Li Shixuan , Pan Ruiqi , Gupta Arvind , Xu Shixin , Fang Yibin , Huang Huaxiong
Published: August 2021

A significant proportion of the adult population worldwide suffers from cerebral aneurysms. If left untreated, aneurysms may rupture and lead to fatal massive internal bleeding. On the other hand, treatment of aneurysms also involve significant risks. It is desirable, therefore, to have an objective tool that can be used to predict the risk of rupture and assist in surgical decision for operating on the aneurysms. Currently, such decisions are made mostly based on medical expertise of the healthcare team. In this paper, we investigate the possibility of using machine learning algorithms to predict rupture risk of vertebral artery fusiform aneurysms based on geometric features of the blood vessels surrounding but excluding the aneurysm. For each of the aneurysm images (12 ruptured and 25 unruptured), the vessel is segmented into distal and proximal parts by cross-sectional area and 382 non-aneurysm-related geometric features extracted. The decision tree model using two of the features (standard deviation of eccentricity of proximal vessel, and diameter at the distal endpoint) achieved 83.8% classification accuracy. Additionally, with support vector machine and logistic regression, we also achieved 83.8% accuracy with another set of two features (ratio of mean curvature between distal and proximal parts, and diameter at the distal endpoint). Combining the aforementioned three features with integration of curvature of proximal vessel and also ratio of mean cross-sectional area between distal and proximal parts, these models achieve an impressive 94.6% accuracy. These results strongly suggest the usefulness of geometric features in predicting the risk of rupture.
Efficient Bayesian inference of fully stochastic epidemiological models with applications to COVID-19
Authors: Li Yuting I. , Turk Günther , Rohrbach Paul B. , Pietzonka Patrick , Kappler Julian , Singh Rajesh , Dolezal Jakub , Ekeh Timothy , Kikuchi Lukas , Peterson Joseph D. , Bolitho Austen , Kobayashi Hideki , Cates Michael E. , Adhikari R. , Jack Robert L.
Published: August 2021

Epidemiological forecasts are beset by uncertainties about the underlying epidemiological processes, and the surveillance process through which data are acquired. We present a Bayesian inference methodology that quantifies these uncertainties, for epidemics that are modelled by (possibly) non-stationary, continuous-time, Markov population processes. The efficiency of the method derives from a functional central limit theorem approximation of the likelihood, valid for large populations. We demonstrate the methodology by analysing the early stages of the COVID-19 pandemic in the UK, based on age-structured data for the number of deaths. This includes maximuma posterioriestimates, Markov chain Monte Carlo sampling of the posterior, computation of the model evidence, and the determination of parameter sensitivities via the Fisher information matrix. Our methodology is implemented in PyRoss, an open-source platform for analysis of epidemiological compartment models.
Complex evolutionary dynamics due to punishment and free space in ecological multigames
Authors: Chowdhury Sayantan Nag , Kundu Srilena , Perc Matjaž , Ghosh Dibakar
Published: August 2021

The concurrence of ecological and evolutionary processes often arises as an integral part of various biological and social systems. We here study eco-evolutionary dynamics by adopting two paradigmatic metaphors of social dilemmas with contrasting outcomes. We use the Prisoner’s Dilemma and Snowdrift games as the backbone of the proposed mathematical model. Since cooperation is a costly proposition in the face of the Darwinian theory of evolution, we go beyond the traditional framework by introducing punishment as an additional strategy. Punishers bare an additional cost from their own resources to try and discourage or prohibit free-riding from selfish defectors. Our model also incorporates the ecological signature of free space, which has an altruistic-like impact because it allows others to replicate and potentially thrive. We show that the consideration of these factors has broad implications for better understanding the emergent complex evolutionary dynamics. In particular, we report the simultaneous presence of different subpopulations through the spontaneous emergence of cyclic dominance, and we determine various stationary points using traditional game-theoretic concepts and stability analysis.
Jinshanibacter allomyrinae sp. nov., isolated from larvae of Allomyrina dichotoma, proposal of Insectihabitans xujianqingii gen. nov., comb. nov. and emended descriptions of the genera Jinshanibacter, Limnobaculum and Pragia
Authors: Lee Soon Dong , Byeon Yeong-Sik , Kim Sung-Min , Yang Hong Lim , Kim In Seop
Published: August 2021

Taxonomic positions of four Gram-negative bacterial strains, which were isolated from larvae of two insects in Jeju, Republic of Korea, were determined by a polyphasic approach. Strains CWB-B4, CWB-B41 and CWB-B43 were recovered from larvae of Protaetia brevitarsis seulensis, whereas strain BWR-B9T was from larvae of Allomyrina dichotoma. All the isolates grew at 10–37 °C, at pH 5.0–9.0 and in the presence of 4 % (w/v) NaCl. The 16S rRNA gene phylogeny showed that the four isolates formed two distinct sublines within the order

Enterobacteriales

and closely associated with members of the genus

Jinshanibacter

. The first group represented by strain CWB-B4 formed a tight cluster with

Jinshanibacter xujianqingii

CF-1111T (99.3 % sequence similarity), whereas strain BWR-B9T was most closely related to

Jinshanibacter zhutongyuii

CF-458T (99.5 % sequence similarity). The 92 core gene analysis showed that the isolates belonged to the family

Budviciaceae

and supported the clustering shown in 16S rRNA gene phylogeny. The genomic DNA G+C content of the isolates was 45.2 mol%. A combination of overall genomic relatedness and phenotypic distinctness supported that three isolates from Protaetia brevitarsis seulensis are different strains of

Jinshanibacter xujianqingii

, whereas one isolate from Allomyrina dichotoma represents a new species of the genus

Jinshanibacter

. On the basis of results obtained here, Jinshanibacter allomyrinae sp. nov. (type strain BWR-B9T=KACC 22153T=NBRC 114879T) and Insectihabitans xujianqingii gen. nov., comb. nov. are proposed, with the emended descriptions of the genera

Jinshanibacter

,

Limnobaculum

and

Pragia

.
Rodentibacter haemolyticus sp. nov. isolated from laboratory rodents
Authors: Benga Laurentiu , Nicklas Werner , Lautwein Tobias , Verbarg Susanne , Gougoula Christina , Engelhardt Eva , Benten W. Peter M. , Köhrer Karl , Sager Martin , Christensen Henrik
Published: August 2021

Nine strains of a

Rodentibacter

-related bacterium were isolated over a period of 38 years from a laboratory mouse (Mus musculus), seven laboratory rats (Rattus norvegicus) and a Syrian hamster (Mesocricetus auratus) in Düsseldorf and Heidelberg, Germany. The isolates are genotypically and phenotypically distinct from all previously described

Rodentibacter

species. Sequence analysis of 16S rRNA and rpoB gene sequences placed the isolates as a novel lineage within the genus

Rodentibacter

. In addition to the single-gene analysis, the whole genome sequence of the strain 1625/19T revealed distinct genome-to-genome distance values to the other

Rodentibacter

species. The genomic DNA G+C content of strain 1625/19T was 40.8 mol% within the range of

Rodentibacter

. At least six phenotypic characteristics separate the new isolates from the other

Rodentibacter

species, with

Rodentibacter heylii

being the most closely related. In contrast to the latter, the new strains display β-haemolysis and are β-glucuronidase, d-mannitol and sorbitol positive, but fail to produce lysine decarboxylase and trehalose. The genotypic and phenotypic differences between the novel strains and the other closely related strains of the genus

Rodentibacter

indicate that they represent a novel species within the genus

Rodentibacter

, family

Pasteurellaceae

, for which the name Rodentibacter haemolyticus sp. nov. is proposed. The type strain 1625/19T, (=DSM 111151T=CCM 9081T), was isolated in 2019 from the nose of a laboratory mouse (Mus musculus) in Düsseldorf, Germany.
Mental health impacts of the COVID-19 pandemic on children and adolescents with chronic health conditions
Authors: Crowe Louise M , Clarke Cathriona , Hearps Stephen , Pugh Remy , Kilpatrick Nicky , Branson Emma , Payne Jonathan M , Haebich Kristina M , McCloughan Natalie , Kintakas Christopher , Charles Genevieve , Trajanovska Misel , Hsieh Ivy , Hartmann Penelope L , King Sebastian , Anderson Nicholas , Anderson Vicki A
Published: August 2021

Objective

To investigate the changes in mental health and activities of children with chronic health conditions (CHC) during the pandemic. Additionally, to gather information from parents about their children’s healthcare experience, family stressors and mental health during the COVID-19 pandemic.

Design

A prospective longitudinal single site cohort study

Setting

Royal Children’s Hospital, Melbourne, Australia

Participants

151 parents of children aged 1.5-17 years (M = 9.8 years, 58.3% male) with a CHC (colorectal disorder, cleft palate and neurofibromatosis type 1) completed the survey.

Main outcome measures

An adapted version of the COVID-19 Wellbeing and Mental Health Survey for Children and Adolescents (Parent/Caregiver version) (CRISIS) was utilised. The CRISIS tool provides data on child’s activities and mental health and parent mental health prior to, and during, the COVID-19 pandemic. Healthcare experiences families was also examined. Parents completed the Kessler 10.

Results

Compared to pre-COVID lockdown, parents reported their children were experiencing higher rates of loneliness, irritability, worry and anxiety. Parents reported that the restrictions in face-to-face contact with family and friends had been stressful for 80.0% of children. Children’s activities changed considerably during the COVID-19 pandemic with screen time increasing by 40%. Thirty percent of parents reported significant distress of their own. Parents felt telehealth were of poorer quality than face-to-face appointments.

Conclusions

Children with CHC experienced a significant increase in mental health symptoms during lockdown for the COVID-19 pandemic. Our findings highlight the increased need for clinical monitoring for children with CHC during periods of community stress and restrictions.
Heterogeneity in COVID-19 Pandemic-Induced Lifestyle Stressors and Predicts Future Mental Health in Adults and Children in the US and UK
Authors: Nikolaidis Aki , DeRosa Jacob , Kass Mirelle , Droney Irene , Alexander Lindsay , Di Martino Adriana , Bromet Evelyn , Merikangas Kathleen , Milham Michael Peter , Paksarian Diana
Published: August 2021

Identifying predictors of mental health symptoms after the initial phase of the pandemic may inform the development of targeted interventions to reduce its negative long-term mental health consequences. In the current study, we aimed to simultaneously evaluate the prospective influence of life change stress, personal COVID-19 impact, prior mental health, worry about COVID-19, state-level indicators of pandemic threat, and socio-demographic factors on mood and anxiety symptoms in November 2020 among adults and children in the US and UK. We used a longitudinal cohort study using the Coronavirus Health Impact Survey (CRISIS) collected at 3 time points: an initial assessment in April 2020 (“April”), a reassessment 3 weeks later (“May”), and a 7-month follow-up in November 2020 (“November”). Online surveys were collected in the United States and United Kingdom by Prolific Academic, a survey recruitment service, with a final sample of 859 Adults and 780 children (collected via parent report). We found subtypes of pandemic-related life change stress in social and economic domains derived through Louvain Community Detection. We assessed recalled mood and perceived mental health prior to the pandemic; worries about COVID-19; personal and family impacts of COVID-19; and socio-demographic characteristics. Levels of mood symptoms in November 2020 measured with the circumplex model of affect. We found 3 life change stress subtypes among adults and children: Lower Social/Lower Economic (adults and children), Higher Social/Higher Economic (adults and children), Lower Social/Higher Economic (adults), and Intermediate Social/Lower Economic (children). Overall, mood symptoms decreased between April and November 2020, but shifting from lower to higher-stress subtypes between time points was associated with increasing symptoms. For both adults and children, the most informative predictors of mood symptoms in November identified by conditional random forest models were prior mood and perceived mental health, worries about COVID, and sources of life change. The relative importance of these predictors was the most prominent difference in findings between adults and children, with lifestyle changes stress regarding friendships being more predictive of mood outcomes than worries about COVID in children. In the US, objective state-level indicators of COVID-19 threat were less predictive of November mood than these other predictors. We found that in addition to the well-established influences of prior mood and worry, heterogeneous subtypes of pandemic-related stress were differentially associated with mood after the initial phase of the pandemic. Greater research on diverse patterns of pandemic experience may elucidate modifiable targets for treatment and prevention.
Phylogenetic analysis of TALE superclass homeobox genes in amphipod crustaceans
Authors: Chang Wai Hoong , Lai Alvina G.
Published: August 2021

TALE class genes are a group of developmentally conserved transcription factors found in animals. Here, we describe the identification and phylogenetic analysis of TALE class genes in amphipod crustaceans. We identified 241 putative TALE class genes from 56 amphipod crustacean species. Phylogenetic analysis of the genes revealed six subclasses. We provide a list of FASTA sequences of the genes identified. Results from this work may inform future evolutionary and comparative genomics studies on animal development.
Quantifying the antimicrobial activity of CRISPR-Cas9-accA modified ΔB. subtilismutants againstV. harveyiandE. Coli
Authors: Hillman Tatiana
Published: August 2021

Probiotics are increasingly popular, currently. Probiotics have been described with the ability to treat many disorders of the gastrointestinal tract (GIT) such as irritable bowel syndrome (IBS) and Crohn’s disease. Types of probiotics include bacterial strains fromLactobacillusandBifidobacterium. Probiotics can restore balance to gut microbiota by outcompeting pathogenic bacteria for nutrients and secrete antimicrobials to eliminate these bacterial pathogens. However, the viability of most advertised probiotics lose their potency due to being freeze dried into powders during storage or for consuming. Many probiotics become ineffective and produce lower CFUs while traversing through the gastric acids of the digestive system. For these reasons, this study sought to enhance the antimicrobial response of a highly potent probiotic known asBacillus subtilis. B. subtilishas been used to treat many disorders of the gut and secrete many antimicrobials lethal for pathogenic microbes.B. subtiliswas genetically modified to express CRISPR-Cas9 nuclease deletion of theaccAgene (ΔB.subtilismutants), which inhibits expression of an essentialaccAgene a part of the fatty acid synthesis (FAS) metabolic pathway. The CRISPR-Cas9-accA ΔB.subtilismutants were co-cultured withV. harveyiandE. Coli. Bacterial growth, biofilm formation, antimicrobial activity, and antibiotic resistance were quantified. It was found thatΔB.subtilismutants co-cultured withV. harveyiandE. Colilessened bacterial growth, amplified biofilm withV. harveyi, reduced biofilm formation ofE. Coli, the co-cultures with the mutants lacked antimicrobial activity, and increased the antibiotic resistance ofV. harveyiandE. Coli. It can be concluded that there is an immense potential for using genetically engineered probiotic strains to enhance the antimicrobial activity ofB. subtilis, which can amplify the reduction of pathogenic bacteria. However, the safety and frugality of usingB. subtilisas a probiotic requires further consideration.
Repair of Noise-Induced Damage to Stereocilia F-actin Cores is Facilitated by XIRP2
Authors: Wagner E.L. , Im J.S. , Nakahata M.I. , Imbery T.E. , Li S. , Chen D. , Noy Y. , Archer D.W. , Xu W. , Hashisaki G. , Avraham K.B. , Shin J.-B.
Published: August 2021

Prolonged exposure to loud noise has been shown to affect inner ear sensory hair cells in a variety of deleterious manners, including damaging the stereocilia core. The damaged sites can be visualized as “gaps” in phalloidin staining of F-actin, and the enrichment of monomeric actin at these sites, along with an actin nucleator and crosslinker, suggests that localized remodeling occurs to repair the broken filaments. Herein we show that gaps in mouse auditory hair cells are largely repaired within one week of traumatic noise exposure through the incorporation of newly synthesized actin. Additionally, we report that XIRP2 is required for the repair process and facilitates the enrichment of monomeric γ-actin at gaps through its LIM domain-containing C-terminus. Our study describes a novel process by which hair cells can recover from sub-lethal hair bundle damage and which may contribute to recovery from temporary hearing threshold shifts and the prevention of age-related hearing loss.
Multiomics reveals the genomic, proteomic and metabolic influences of the histidyl dipeptides on heart
Authors: Yan Keqing , Mei Zhanlong , Zhao Jingjing , Prodhan Md Aminul Islam , Obal Detlef , Katragadda Kartik , Doeling Ben , Hoetker David , Posa Dheeraj Kumar , He Liqing , Yin Xinmin , Shah Jasmit , Pan Jianmin , Rai Shesh , Lorkiewicz Pawel Konrad , Zhang Xiang , Li Siqi , Bhatnagar Aruni , Baba Shahid P.
Published: August 2021

Histidyl dipeptides, are synthesized in the heartviaenzyme carnosine synthase (Carns), which facilitates glycolysis and glucose oxidation by proton buffering and attenuate ischemia and reperfusion injury. However, a composite understanding of the histidyl dipeptide mediated responses in the heart are lacking. We performed multilayer omics in the cardio specificCarnsoverexpressing mice, showing higher myocardial levels of histidyl dipeptides lead to extensive changes in microRNAs that could target the expression of contractile proteins and enzymes involved inβ-fatty acid oxidation and citric acid cycle (TCA). Similarly, global proteomics showed contractile function, fatty acid degradation and TCA cycle, pathways were enriched in the CarnsTg heart. Parallel with these changes, free fatty acids, and TCA intermediate-succinic acid were lower under aerobic and significantly attenuated under anaerobic conditions in the CarnsTg heart. Integration of multiomics data showsβ-fatty acid oxidation and TCA cycle exhibit correlative changes at all three levels in CarnsTg heart, suggesting histidyl dipeptides are critical regulators of myocardial structure, function and energetics.
Tissue-based IL-10 signalling in helminth infection limits IFNγ expression and promotes the intestinal Th2 response
Authors: Webster Holly C. , Gamino Virginia , Shergold Amy L. , Andrusaite Anna T. , Heieis Graham A. , Milling Simon W.F. , Maizels Rick M. , Perona-Wright Georgia
Published: August 2021

Type 2 immunity is activated in response to both allergens and helminth infection. It can be detrimental or beneficial, and there is a pressing need to better understand its regulation. The immunosuppressive cytokine IL-10 is known as a T helper 2 (Th2) effector molecule, but it is currently unclear whether IL-10 dampens or promotes Th2 differentiation during infection. Here we show that helminth infection in mice elicits IL-10 expression in both the intestinal lamina propria and the draining mesenteric lymph node, with higher expression in the infected tissue. In vitro, exogenous IL-10 enhanced Th2 differentiation in isolated CD4+ T cells, increasing expression of GATA3 and production of IL-5 and IL-13. The ability of IL-10 to amplify the Th2 response coincided with its suppression of IFNγ expression and, in vivo, we found that, in intestinal helminth infection, IL-10 receptor expression was higher on Th1 cells in the small intestine than on Th2 cells in the same tissue, or on any Th cell in the draining lymph node. In vivo blockade of IL-10 signalling during helminth infection resulted in an expansion of IFNγ+ and Tbet+ Th1 cells in the small intestine and caused a coincident decrease in IL-13, IL-5 and GATA3 expression by intestinal T cells. Together our data indicate that IL-10 signalling promotes Th2 differentiation during helminth infection at least in part by regulating competing Th1 cells in the infected tissue.
CytokineLink: a cytokine communication map to analyse immune responses in inflammatory and infectious diseases
Authors: Olbei Marton , Thomas John P. , Hautefort Isabelle , Treveil Agatha , Bohar Balazs , Madgwick Matthew , Gul Lejla , Csabai Luca , Modos Dezso , Korcsmaros Tamas
Published: August 2021

Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines downstream. However, there are no readily available bioinformatic resources that can model cytokine - cytokine interactions. In this effort, we built a communication map between major tissues and blood cells that reveals how cytokine-mediated intercellular networks form during homeostatic conditions. We collated the most prevalent cytokines from literature, and assigned the proteins and their corresponding receptors to source tissue and blood cell types based on enriched consensus RNA-Seq data from the Human Protein Atlas database. To assign more confidence to the interactions, we integrated literature information on cell - cytokine interactions from two systems immunology databases, immuneXpresso and ImmunoGlobe. From the collated information, we defined two metanetworks: a cell-cell communication network connected by cytokines; and a cytokine-cytokine interaction network depicting the potential ways in which cytokines can affect the activity of each other. Using expression data from disease states, we then applied this resource to reveal perturbations in cytokine-mediated intercellular signalling in inflammatory and infectious diseases (ulcerative colitis and COVID-19, respectively). For ulcerative colitis, with CytokineLink we demonstrated a significant rewiring of cytokine-mediated intercellular communication between non-inflamed and inflamed colonic tissues. For COVID-19, we were able to identify inactive cell types and cytokine interactions that may be important following SARS-CoV-2 infection when comparing the cytokine response with other viruses capable of initiating a cytokine storm. Such findings have potential to inform the development of novel, cytokine-targeted therapeutic strategies. CytokineLink is freely available for the scientific community through the NDEx platform and the project github repository (https://github.com/korcsmarosgroup/CytokineLink).
Expression of remyelination-modulating genes in astrocytes are controlled by MALAT1 and Lnc-DC long non-coding RNAs
Authors: Askari Shahrzad , Khani-Habibabadi Fatemeh , Behmanesh Mehrdad
Published: August 2021

This manuscript has been withdrawn by the authors as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Internalizing and externalizing behaviors in school-aged children are related to state anxiety during magnetic resonance imaging
Authors: Eijlers Robin , Blok Elisabet , White Tonya , Utens Elisabeth M.W.J. , Tiemeier Henning , Staals Lonneke M. , Berghmans Johan M. , Wijnen Rene M.H. , Hillegers Manon H.J. , Legerstee Jeroen S. , Dierckx Bram
Published: August 2021

Magnetic resonance imaging (MRI) procedures often evoke anxiety in children. Further, anxious children may be less likely to participate in MRI research, leading to a possible selection bias, and may be more likely to move during image acquisition, resulting in lower image quality and possible information bias. Therefore, state anxiety is problematic for functional and structural MRI studies. Children with behavioral problems, such as internalizing and externalizing behaviors, may be more likely to experience state anxiety prior to and during MRI scanning. Therefore, our first aim was to investigate the relationship between internalizing/externalizing behavior and children’s MRI-related state anxiety. Our second aim was to investigate the relationship between internalizing and externalizing behavior and MRI research participation. Our final aim was to investigate the effect of internalizing and externalizing behavior as well as MRI-related anxiety on image quality in children. We included 1,241 six- to ten-year-old children who underwent a mock MRI. Afterwards, if not too anxious, these children were scanned using a 3-Tesla GE Discovery MRI system (n= 1,070). Internalizing and externalizing behaviors were assessed with the Child Behavior Checklist. State anxiety was assessed with a visual analogue scale. Internalizing behaviors were positively associated with child state anxiety, as reported by child, parent, and researcher. For state anxiety reported by the parent and researcher, this relationship was independent of externalizing behaviors. Externalizing behaviors were related to state anxiety reported by the researcher, but this difference was not independent of internalizing behaviors, pointing towards a relationship via the shared variance with internalizing behaviors. Further, children with more internalizing and externalizing behaviors were less likely to participate in the actual MRI scanning procedure. Lastly, internalizing and externalizing behaviors, as well as MRI-related state anxiety were associated with worse image quality. These results underscore the potential for biases and methodological issues caused by MRI-related state anxiety in children.