bluuebunny/crossref_metadata_2025 huggingface dataset:
Shift Work and Metabolic Syndrome Updates: A Systematic Review
Authors: Schettini Maria Alice Souza , Passos Rafael Feitosa do Nascimento , Koike Bruna Del Vechio
Published: July 2023

Shift work can cause circadian cycles disturbances and misaligns the endogenous rhythms. The physiological variables are driven by the circadian system and, its misalignment, can impair the metabolic functions. Thus, the main objective of this study was to evaluate the metabolic alterations as a result of shift work and night work reported in articles published in the last 5 years, using the eligibility criteria both gender and indexed articles in English language. In order to execute this work, we perform a systematic review according to PRISMA guidelines and searched about Chronobiology Disorders and Night Work, both related to metabolism, in Medline, Lilacs, ScienceDirect and Cochrane. Cross-sectional, cohort and experimental studies with low risk of bias were included. We found a total of 132 articles, and, after the selection process, 16 articles remained to be analyzed. It was observed that shift work can cause circadian misalignment and, consequently, some metabolic parameters alterations such as an impaired glycemic control and insulin functioning, cortisol phase release, cholesterol fractions imbalance, changes in morphological indexes and melatonin secretion. There are some limitations, such as heterogenicity in used databases and the 5 years restriction period, because the effects of sleep disturbance may have been reported earlier. In conclusion, we suggest that shift work interferes with the sleep-wake cycle and eating patterns, which cause crucial physiological alterations that, together, can lead to metabolic syndrome.
Would the Actigraph Always be Sufficient for Sleep Analysis in Exercise-Based Studies? A Case Report of Negative Response of Sleep to Exercise
Authors: Atef Hady , Gaber Marwa
Published: July 2023

Introduction Sleep deprivation is common after coronary artery bypass grafting (CABG). It is mostly managed well by exercise. The number of reported post-CABG cases that respond negatively to exercise is scanty. The etiology is usually associated with the underlying sleep pathology, and how it responds to exercise. Cases with undiagnosed central sleep apnea post CABG have not been reported before.

Case description A medically stable male patient, 63 years old, hypertensive, but not diabetic, had entered coronary artery bypass grafting (CABG) 8 weeks before attending the outpatient cardiac rehabilitation unit and was referred for a cardiac rehabilitation program at this time. He entered a study in the cardiac rehabilitation center utilizing either aerobic or combined aerobic and resistance training for 10 weeks to improve sleep architecture and functional capacity post-CABG. After randomization, he entered the group doing combined aerobic and resistance exercises. All of the patients in this group improved except him, his sleep quality worsened, but his functional capacity improved. After a complete analysis of sleep on polysomnography, it was revealed that the patient had central sleep apnea that was mostly worsened by resistance training. The patient was withdrawn from the study by the 8th week, and his sleep condition improved gradually. After then, he was asked to attend the cardiac rehabilitation center again to share in aerobic exercise, having evidence that central sleep apnea does not respond negatively to this form of training. After 12 months of follow-up, the patient still shows no signs of sleep deprivation.

Conclusion Sleep deprivation is prevalent in post-CABG patients, but with different presentations and it can generally improve by exercise. Identification of the underlying cause of the sleeping difficulty is a cornerstone of targeted treatment.
Risk management in pig farming: a reality or conjecture? A systematic review
Authors: Gregolin Fabiano , Miranda Késia Oliveira da Silva
Published: July 2023

Context The complexity in swine production demands equally complex management actions. In this sense, risk management is an area that has been little explored and that may offer significant contributions to pork producers in their decision-making processes. Aims This study aimed to collect the available information on risks in pig farming and identify how the topic has been approached in recent studies. Methods A systematic review was conducted on the basis of searches in the Web of Science, Scopus and Science Direct databases, in the period ranging from 2015 to 2021. The searches resulted in 2178 documents on the theme risks in pig farming, which were then classified into 13 categories to represent the general objective of each study and into 177 subcategories representing the specific objective of each work. The data, separated into categories and subcategories, was not classified by any exclusionary criteria. On the contrary, they represent all the information found in the studied documents. Key results The results show that, although the number of studies on risks in pig farming is growing, the studies are contained in specific fields only. It was also possible to observe that although the studies focused on problems that may affect pig raising, they were not approached in a holistic manner using risk management methodologies that would allow identifying, measuring and managing risks in a consistent and systematic way. Thus, the studies cannot be characterised as having a risk management approach. Conclusion The studies on risks in pig farming focus on specific areas instead of using an integrated approach. It was found that risks in pig farming are a growing concern, but a holistic approach to the subject is still unexplored and could be quite fruitful, as it would make it possible to identify, measure and manage risks in a more consistent and systematic way. Implications Producers, veterinarians, managers and researchers can use the results of this study (1) to develop identification systems, and (2) in quantitative and qualitative analyses, planning, implementation of responses and monitoring of risks in pig farming.
What makes the blocking effect happen?
Authors: Li Nini
Published: July 2023

This study illustrates that for the Chinese bare form reflexive ziji ‘self’, feature conflicts can cause both the local binding blocking effect and the long-distance binding blocking effect. To make long-distance binding possible, a feature-matching requirement between the long-distance antecedent and the reindexed local reflexive must be met, as proposed by Tang (1989). In addition to this, a feature-matching requirement between the verb and its subject and object must also be satisfied, with the latter likely having a suppressive effect on the former. Further research is needed to understand the interaction of these two feature-matching requirements and what constraints exist. Furthermore, the blocking effect can be triggered by a variety of factors, including syntax, feature agreement, pragmatics, discourse prominence, animacy and thematic conditions and other combined effects. Ziji’s odd performance might be the result of their joint efforts. We need to further clarify how these factors work together.
Traduire les webtoons, le renouveau d’une filière qui
cartonne
Authors: Jeanmaire Guillaume , Kim Jeong-yeon
Published: July 2023

Depuis 2003, conçus d’emblée dans une optique d’adaptations
transmédia, les webtoons (web cartoons) sud-coréens concurrencent les mangas en
noir et blanc, renouvelant le modèle nippon par un format numérique en couleur,
adapté au smartphone. Divisés en courts épisodes hebdomadaires, ils diffèrent
des BD papier par leur format, au défilement vertical qui offre de nouvelles
possibilités graphiques et narratives : linéarisation de la lecture, continuum
graphique, accroissement de la tension narrative. Ils se distinguent également
par le recours à un registre langagier jeune sans filtre, ainsi que par la
possibilité pour les auteurs et lecteurs d’interagir et pour les éditeurs de
juger de la réception des traductions. Dès 2014, le webtoon lance d’abord ses
premières versions en anglais et couvre aujourd’hui plus de dix langues, dont le
français. Au-delà d’une simple analyse de corpus, l’article est illustré des
résultats d’enquêtes soumises à des éditeurs, traducteurs et relecteurs, pour
interpréter les choix narratifs et graphiques observés. Contraintes par les
consignes des éditeurs, les stratégies traductives oscillent entre la
localisation, le maintien et la diffusion d’éléments socioculturels coréens
portés par la Soft Power coréenne.
Covid-19 WhatsApp sticker memes as public signs in Oman
Authors: Zidjaly Najma Al , Barhi Zumurrod Al
Published: July 2023

In this article, we identify a new form of public discourse that takes the shape of WhatsApp sticker memes personally created and nationally shared on WhatsApp by citizens in Oman during the Covid-19 pandemic to concomitantly act as carriers of information and as promoters of relational work. The data consist of 67 public sign stickers culled from a larger set amassed as part of an ethnographic project on Arabs and Covid-19. Drawing upon interpersonal pragmatics and visual semiotics, we examine the interplay of textual and visual modes in featured stickers, demonstrating how Omanis translated official Covid-19 instructions into three types of terse memes to facilitate communal distribution. We suggest that to encourage public cooperation, the stickers struck a culturally-imperative balance between keeping traditional norms intact while committing socially offensive acts. The article contributes to research on digital discourse by exploring sticker use as public signs in the understudied Arabic context.
Fear appeals in Chinese public signs of COVID-19 prevention in local communities
Authors: Jia Mian , Zhao Yi
Published: July 2023

Guided by the Extended Parallel Process Model (EPPM), this paper explicates the messaging strategies in Chinese
public signs of COVID-19 prevention in local communities. 162 signs were collected from Internet posts. Our results show that the
EPPM is a viable fear appeal framework to explain the communication of public health risks. Most signs communicated the threat of
the virus to the public, whereas fewer signs emphasized the efficacy to effectively control the threat. In addition to
communicating individual threat and efficacy, quite a few signs also highlighted collective threat and efficacy. Moreover, the
language used in these signs is tailored to local cultural and social conventions. These findings not only contribute to the
growing body of research on the interpersonal function of public signage from a Chinese perspective, but also demonstrate the
utility of combining pragmatic research with messaging strategies in health communication research.
“Money can buy health”
Authors: Tse Vincent Wai Sum , Wu Jasper Zhao Zhen , Theng Andre Joseph
Published: July 2023

Drawing on the notion of affect, this paper offers a multimodal critical discourse analysis of health-related
product advertising in Hong Kong during the early months of the COVID-19 pandemic. Advertisements were collected in the city’s
space of commute. We examine the construal of risk and protection in the advertisements and via their emplacement in three
spatial-temporal dimensions observed in the data: the market society, the concrete public space, and the intimate familial space.
Our analysis demonstrates that while risk and protection are linguistically and visually depicted to varying degrees across these
dimensions, the emplacement of advertisements prompts the viewers to regard their immediate space as full of risks. As individuals
encounter the advertisements, they become interpellated to see the purchase of the advertised products as necessary. Illuminating
health communication during the pandemic, this study contributes to health commercialisation and responsibilisation research and
provides insights into the ideological, interpersonal nature of affect.
Diploid and tetraploid cytotypes of the flagship Cape species Dicerothamnus rhinocerotis (Asteraceae): variation in distribution, ecological niche, morphology and genetics
Authors: Chumová Zuzana , Monier Zafar , Šemberová Kristýna , Havlíčková Eliška , Euston-Brown Douglas , Muasya A Muthama , Bergh Nicola G , Trávníček Pavel
Published: July 2023

Background and Aims

The Greater Cape Floristic Region is one of the world’s biodiversity hotspots and is considered poor in polyploids. To test this assumption, ploidy variation was investigated in a widespread Cape shrub, Dicerothamnus rhinocerotis (renosterbos, Asteraceae). The aim was to elucidate the cytotype distribution and population composition across the species range, and to assess differences in morphology, environmental niches and genetics.

Methods

Ploidy level and genome size were determined via flow cytometry and cytotype assignment was confirmed by chromosome counting. Restriction site-associated DNA sequencing (RADseq) analyses were used to infer genetic relationships. Cytotype climatic and environmental niches were compared using a range of environmental layers and a soil model, while morphological differences were examined using multivariate methods.

Key Results

The survey of 171 populations and 2370 individuals showed that the species comprises diploid and tetraploid cytotypes, no intermediates and only 16.8 % of mixed populations. Mean 2C values were 1.80–2.06 pg for diploids and 3.48–3.80 pg for tetraploids, with very similar monoploid genome sizes. Intra-cytotype variation showed a significant positive correlation with altitude and longitude in both cytotypes and with latitude in diploids. Although niches of both cytotypes were highly equivalent and similar, their optima and breadth were shifted due to differences mainly in isothermality and available water capacity. Morphometric analyses showed significant differences in the leaves and corolla traits, the number of florets per capitulum, and cypsela dimensions between the two cytotypes. Genetic analyses revealed four groups, three of them including both cytotypes.

Conclusions

Dicerothamnus rhinocerotis includes two distinct cytotypes that are genetically similar. While tetraploids arise several times independently within different genetic groups, morphological and ecological differences are evident between cytotypes. Our results open up new avenues for questions regarding the importance of ploidy in the megadiverse Cape flora, and exemplify the need for population-based studies focused on ploidy variation.
Seaweed forests are carbon sinks that may help mitigate CO2 emissions: a comment on Gallagher et al. (2022)
Authors: Filbee-Dexter Karen , Pessarrodona Albert , Duarte Carlos M , Krause-Jensen Dorte , Hancke Kasper , Smale Daniel , Wernberg Thomas
Published: July 2023

Recently, Gallagher et al. (2022) suggested that seaweed ecosystems are net heterotrophic carbon sources due to CO2 released from the consumption of external subsidies. Here we outline several flaws in their argument, which we believe confuse research on the blue carbon potential of seaweed ecosystems, and unjustifiably generate doubt around initiatives to protect and restore seaweed forests. Gallagher et al.’s evidence relies on 18 studies with highly variable measures of net ecosystem production, which do not statistically support their conclusion that most seaweed ecosystems are heterotrophic. This dataset is also inappropriate as it is incomplete and misrepresents seaweed ecosystems globally, particularly seaweed forests, which contribute disproportionately to global seaweed productivity. We maintain that the climate change mitigation value of an ecosystem depends on the net difference in CO2 uptake between the original ecosystem and its replacement ecosystem. We provide evidence that most seaweed ecosystems, which drawdown the largest carbon flux of any vegetated coastal habitat, are indeed net autotrophic ecosystems. We recognize that substantial uncertainties remain concerning the magnitude of CO2 drawdown by seaweed ecosystems and recommend that carbon fluxes around seaweed ecosystems should be considered more broadly and taken into account in estimates of their CO2 mitigation potential.
School Resource Officers: More than Just Law Enforcers?
Authors: Montes Andrea N , Trinkner Rick , Scott Michael S
Published: July 2023

Research about school resource officers (SROs) has focussed on their ability to legally intervene and detain or arrest youth. On many campuses, though, their role extends beyond that of law enforcement to include mentorship, counselling, and education. The current study draws on a survey of SROs from the Phoenix, Arizona, Police Department—one of the largest police departments in the United States—to examine what roles SROs prioritize and how they implement their duties. The results show that although one of SROs’ primary roles is that of law enforcer, SROs were more likely to prioritize their role as mentors. SROs also reported that it was school personnel, rather than teachers or the SROs themselves, who most commonly initiated SRO involvement in student misbehaviour, whether in a law enforcement or mentorship capacity. The paper concludes with a discussion about implications for scholarship and practice.
The Determinants of Taxation Innovation Policy in Spain’s Common Regime Autonomous Communities (1986–2018)
Authors: Kölling Mario , Toubeau Simon , Godoy Deborah Zak
Published: July 2023

This article studies the determinants of tax innovation in Spain’s Common Regime Autonomous Communities (ACs) over the period 1986–2018, across the different types of taxes included in their “own taxes.” Our central finding is that the introduction of taxes is motivated by politics: ACs governments introduce taxes when governed by left-wing parties or by a coalition government that included a regionalist party. Second, we find that parties in government follow a strategic calculus when introducing new taxes: an approaching election and a previously introduced tax decrease the chances of tax innovation. Third, we find that AC government also respond to functional pressures and introduce new taxes to shore-up their revenues when faced with a budget deficit. Two important negative results to come out of this analysis are that taxation innovation is not sensitive to geographical diffusion or to the availability of alternative source of revenue in the system of territorial financing.
Phylogenetic revision of whisker-cheeked suckermouth catfishes (Loricariidae: Lasiancistrus) from east of the Andes: five species where once there were two
Authors: Poveda-Cuellar José Luis , Conde-Saldaña Cristhian Camilo , Villa-Navarro Francisco Antonio , Lujan Nathan K , Dergam dos Santos Jorge Abdala
Published: July 2023

We integrated large sample sizes, morphometric and molecular data, and phylogenetic and species delimitation analyses to test the 17-year-old hypothesis that only two species of whisker-cheeked suckermouth catfishes (genus Lasiancistrus) occur in river drainages west of the Andes Mountains. Our results reject this hypothesis, demonstrating that, in addition to the previously recognized Lasiancistrus guacharote from Lake Maracaibo, a Lasiancistrus clade from west of the Sierra de Perijá contains at least four allopatric, genetically differentiated and morphologically distinct lineages. One of these lineages had no previous name associated with it and is described here as the new species Lasiancistrus wiwa. Phylogenetic relationships and geographical distributions of all five trans-Andean lineages are concordant with watershed boundaries and major mountain ranges that form these boundaries, with the following five freshwater basins or regions each containing a single species: Lake Maracaibo (L. guacharote), Rancheria River basin (L. wiwa), Upper and Middle Magdalena River and lower Cauca River basins (Lasiancistrus volcanensis), Upper Cauca River basin (Lasiancistrus caucanus) and Pacific Coastal watersheds between central Colombia and central Panama (Lasiancistrus mayoloi). Evolutionary relationships among these lineages suggest that Andean uplift-mediated vicariance contributed significantly to the cladogenesis and allopatric distributions of these fishes.
A systematic assessment of the impact of rare canonical splice site variants on splicing using functional andin silicomethods
Authors: Oh Rachel Y. , AlMail Ali , Cheerie David , Guirguis George , Hou Huayun , Yuki Kyoko E. , Haque Bushra , Thiruvahindrapuram Bhooma , Marshall Christian R. , Mendoza-Londono Roberto , Shlien Adam , Kyriakopoulou Lianna G , Walker Susan , Dowling James J. , Wilson Michael D. , Costain Gregory
Published: July 2023

Background/Objectives

Canonical splice site variants (CSSVs) are often presumed to cause loss-of-function (LoF) and are assigned very strong evidence of pathogenicity (according to ACMG criterion PVS1). However, the exact nature and predictability of splicing effects of unselected rare CSSVs in blood-expressed genes is poorly understood.

Methods

A total of 184 rare CSSVs in unselected blood-expressed genes were identified by genome sequencing in 121 individuals, and their impact on splicing was interrogated manually in RNA sequencing (RNA-seq) data. Blind to these RNA-seq data, we attempted to predict the precise impact of CSSVs by applyingin silicotools and the ClinGen Sequence Variant Interpretation Working Group 2018 guidelines for applying PVS1 criterion.

Results

There was no evidence of a frameshift nor of reduced expression consistent with nonsense-mediated decay (NMD) for 24% of CSSVs: 17% had wildtype splicing only and normal junction depths, 3.25% resulted in cryptic splice site usage and in-frame indels, 3.25% resulted in full exon skipping (in-frame), and 0.5% resulted in full intron inclusion (in-frame). Misclassification rates for splicing outcome (frameshift/NMD vs. no frameshift/no NMD) using (i) SpliceAI, (ii) MaxEntScan, and (iii) AutoPVS1 ranged from 30-41%, with none outperforming a simple “zero rule” classifier.

Conclusion

Nearly 1 in 4 CSSVs may not cause LoF based on analysis of RNA-seq data. Predictions fromin silicomethods were often discordant with findings from RNA-seq. More caution may be warranted in applying PVS1-level evidence to CSSVs in the absence of functional data.
Phase-locked auditory pulse stimulation at home enhancing slow sleep waves: A pilot real-world study
Authors: Xi Guannan , Zheng Xin , Gao Anchen , Huang Siyang , Lei Huijie , Ding Jing , Zhang Qianqian , Jiang Jian
Published: July 2023

Background

Deep sleep, also known as slow-wave sleep (SWS), is essential for maintaining good health and is characterized by electroencephalographic (EEG) slow-wave activity (SWA). The use of phase-locked auditory stimulation (PLAS) to enhance SWA has emerged as a promising approach. However, the effectiveness of home-based PLAS has not yet been fully established.

Method

We used a newly developed wearable EEG device, called LANMAO, to record sleeping EEG signals and synchronize acoustic tones with SWA. We employed a within-subject design to investigate whether acoustic stimulation could increase SWA in a home setting using six subjects (mean age: 29±4.2 years, 3 males). Specifically, we applied acoustic stimulation (STIM) on odd-numbered slow waves and no stimulation (SHAM) on even-numbered slow waves.

Results

The PLAS significantly enhanced SWA, theta, alpha, fast spindle and slow spindle activity on STIM condition compare to SHAM condition across all subjects in home setting.

Conclusion

These results indicated that the capacity of PLAS, based on LANMAO device, could enhance the SWA in home setting. Our findings shed lights on the wide application of home-based deep sleep intervention.
Effect of Women’s View Toward Their Rights on Receiving Better Antenatal Care in Bangladesh
Authors: Morshed Ramisa
Published: July 2023

Background

In a country, many girls may forcefully be married off at an early age where they might have no hand in it. But the thought and view they carry throughout their lifetime can be resembled in their children’s lives too and can proclaim plenty of the country’s problems, especially receiving improved antenatal care (ANC). A woman or a prospective mother’s view of her husband beating her tells a lot about a country’s view, and a woman’s preferred age of marrying can also exhibit her attitude toward her rights and goals. However, limited research has focused on understanding women’s perspectives on their rights and their relation with ANC quality in Bangladesh. The findings of this study will contribute to a deeper understanding of women’s perspectives on their rights and the barriers they face in accessing quality ANC.

Objective

This study aims to investigate the view of Bangladeshi women toward their own rights and the impact on their access to improved ANC.

Method

To address this gap, a binary logistic regression model was employed by analyzing in IBM SPSS Statistics 25 using Bangladesh Demographic and Health Survey (BDHS) 2017-18 data. The study recruited a diverse sample of women from various social backgrounds, beliefs, and geographical locations in Bangladesh.

Result

It was spotted that a small percentage (6.6%) of women in Bangladesh were under proper ANC coverage. The women who didn’t justify domestic violence were 1.231 times more likely to be under ANC coverage in Bangladesh than those who justified domestic violence in the adjusted model. Moreover, women with no education were .048 times less likely to be under ANC coverage than women with higher education. Women who were not exposed to media were .099 times less likely to be under ANC coverage than those who were exposed to media. Unfortunately, almost one-fifth of all Bangladeshi women (19.6%) justified being

Conclusion

Women’s entitlements enable them to actively engage in their own healthcare programs, leading to improved health outcomes for both mother and child. Through targeted awareness campaigns, educational initiatives, and policy advocacy, beaten by their husbands.

Bangladesh can create an environment where women are aware of their rights and have access to quality ANC services. By ensuring their rights are respected, a society that values reproductive health and the well-being of women and children can strive.
Improved specificity of glutamate decarboxylase 65 autoantibody measurement using luciferase-based immunoprecipitation system (LIPS) assays
Authors: Wyatt R.C. , Grace S.L. , Brigatti C. , Marzinotto I. , Gillard B.T. , Shoemark D. , Chandler K. , Achenbach P. , Piemonti L. ,   The BOX Study Group, Long A.E. , Gillespie K.M. , Lampasona V. , Williams A.J.K.
Published: July 2023

Autoantibodies to glutamate decarboxylase (GADA) are widely used in the prediction and classification of type 1 diabetes. GADA radiobinding assays (RBAs) using N-terminally truncated antigens offer improved specificity but radioisotopes limit the high-throughput potential for population screening. Luciferase-based Immunoprecipitation System (LIPS) assays are sensitive and specific alternatives to RBAs with the potential to improve risk stratification.

The performance of assays using the Luciferase (Nluc-) conjugated GAD65constructs, Nluc-GAD65(96-585) and full length Nluc-GAD65(1-585) were evaluated in 434 well-characterised sera from recent-onset type 1 diabetes patients and first-degree relatives.

Non-radioactive, high-throughput LIPS assays are quicker and require less serum than RBAs. Of 171 relatives previously tested single autoantibody positive for autoantibodies to full-length GAD65by RBA but had not progressed to diabetes, fewer retested positive by LIPS using either truncated (n=72) or full-length (n=111) antigen. The Nluc-GAD65(96-585) truncation demonstrated the highest specificity in LIPS assays overall but in contrast to RBA, N-terminus truncations did not result in a significant increase in disease-specificity compared with the full-length antigen. This suggests that binding of non-specific antibodies is affected by the conformational changes resulting from addition of the Nluc antigen. Nluc-GAD65(96-585) LIPS assays offer low blood volume, high specificity GADA tests for screening and diagnostics.
A comparison of critical speed and critical power in runners using Stryd running power
Authors: van Rassel C. R. , Sales M. K. , Ajayi O. O. , Nagai K. , MacInnis M. J.
Published: July 2023

Purpose

Although running traditionally relies on critical speed (CS) as an indicator of critical intensity, portable inertial measurement units (IMUs) offer a potential solution for estimating running mechanical power to assess critical power (CP) in runners. The purpose of this study was to determine whether CS and CP differ when assessed using the Stryd device, a portable IMU, and if two running bouts are sufficient to determine CS and CP.

Methods

On an outdoor running track, ten trained runners (, 59.0 [4.2] ml·kg-1·min-1) performed three running time-trials (TT) between 1200 and 4400m on separate days. CS and CP were derived from two-parameter hyperbolic speed-time and power-time models, respectively, using two (CS2TTCP2TT) and three (CS3TTCP3TT) time trials. Subsequently, runners performed constant intensity running for 800m at their calculated CS3TTand CP3TT.

Results

Running at the calculated CS3TTspeed (3.88 [0.44] m·s-1) elicited an average Stryd running power (271 [28] W) not different from the calculated CP3TT(270 [28]; p=0.940; d=0.02), with excellent agreement between the two values (ICC=0.980). The CS2TT(3.97 [0.42] m·s-1) was not significantly higher than CS3TT(3.89 [0.44] m·s-1; p=0.178; d=0.46); however, CP2TT(278 [29] W) was significantly greater than CP3TT(p=0.041; d=0.75).

Conclusion

The running intensities at CS and CP were similar, supporting the use of running power (Stryd) as a metric of aerobic fitness and exercise prescription, and two trials provided a reasonable, albeit higher, estimate of CS and CP.
Single-cell RNAseq identifies clonally expanded antigen-specific T-cells following intradermal injection of gold nanoparticles loaded with diabetes autoantigen in humans
Authors: Hanna Stephanie J. , Thayer Terri C. , Robinson Emma J.S. , Vinh Ngoc-Nga , Williams Nigel , Landry Laurie , Andrews Robert , Siah Qi Zhuang , Leete Pia , Wyatt Rebecca , McAteer Martina A. , Nakayama Maki , Wong F. Susan , Yang Jennie H.M. , Tree Tim I.M. , Ludvigsson Johnny , Dayan Colin M. , Tatovic Danijela
Published: July 2023

Gold nanoparticles (GNPs) have been used in the development of novel therapies as a way of delivery of both stimulatory and tolerogenic peptide cargoes. Here we report that intradermal injection of GNPs loaded with the proinsulin peptide C19-A3, in patients with type 1 diabetes, results in recruitment and retention of immune cells in the skin. These include large numbers of clonally expanded T-cells sharing the same paired T-cell receptors (TCRs) with activated phenotypes, half of which, when the TCRs were re-expressed in a cell-based system, were confirmed to be specific for either GNP or proinsulin. All the identified gold-specific clones were CD8+, whilst proinsulin-specific clones were both CD8+and CD4+. Proinsulin-specific CD8+clones had a distinctive cytotoxic phenotype with overexpression of granulysin (GNLY) and KIR receptors. Clonally expanded antigen-specific T cells remainedin situfor months to years, with a spectrum of tissue resident memory and effector memory phenotypes.

As the T-cell response intradermally is divided between targeting the gold core and the antigenic cargo, this offers a route to improving Trm formation in response to vaccines. In addition, our scRNAseq data indicate that focussing on clonally expanded skin infiltrating T-cells recruited to intradermally injected antigen is a highly efficient method to enrich and identify antigen-specific cells. This approach has the potential to be used to monitor the intradermal delivery of antigens and nanoparticles for immune modulation in humans.
Novel co-culture strategies of tumor organoids with autologous T-cells reveal clinically relevant combinations of immune-checkpoint and targeted therapies
Authors: Podaza Enrique , Capuano Jared , Assaad Majd Al , Kuo Hui-Hsuan , Markowitz Geoffrey , Irizarry Adriana , Ravichandran Hiranmayi , Ackermann Sarah , Kane Troy , Manohar Jyothi , Sigouros Michael , Moyer Jenna , Bhinder Bhavneet , Chandra Pooja , Malbari Murtaza , Boehnke Karsten , Mosquera Juan Miguel , Mittal Vivek , Sboner Andrea , Gokozan Hamza , Altorki Nasser , Elemento Olivier , Martin M. Laura
Published: July 2023

Patient derived tumor organoids (PDTOs) have become relevant pre-clinical models for therapeutic modelling since they highly recapitulate patients’ response to treatment. Nevertheless, their value for immunotherapy modelling has not been fully explored. We developed a tumor processing protocol that enable the establishment of PDTOs and tumor infiltrating lymphocytes (TILs) isolation. By the optimization of functional assays, we compared the T-cells effector functions of matching PBMCs and TILs, demonstrating that PBMCs after co-culture and TILs after initial expansion display similar responses. In addition, the evaluation of cytokine production by fluorospot in combination with an image-based killing assay enable the screening of different immune-checkpoint inhibitors as well as its combination with target inhibitors. Our proof-of-concept functional assays showed the potential and versatility of PDTOs and T-cells co-culture systems for immunotherapy screening. The optimization of scalable functional assays downstream co-culture represents a significant step forward to increase the value of PDTOs as pre-clinical models for immunotherapeutic screens.
ESGq: Alternative Splicing events quantification across conditions based on Event Splicing Graphs
Authors: Cozzi Davide , Bonizzoni Paola , Denti Luca
Published: July 2023

Alternative Splicing (AS) is a regulation mechanism that contributes to protein diversity and is also associated to many diseases and tumors. Alternative splicing events quantification from RNA-Seq reads is a crucial step in understanding this complex biological mechanism. However, tools for AS events detection and quantification show inconsistent results. This reduces their reliability in fully capturing and explaining alternative splicing. We introduce ESGq, a novel approach for the quantification of AS events across conditions based on read alignment against Event Splicing Graphs. By comparing ESGq to two state-of-the-art tools on real RNA-Seq data, we validate its performance and evaluate the statistical correlation of the results. ESGq is freely available athttps://github.com/AlgoLab/ESGq.
Overcoming PARP inhibitor resistance by inducing a homologous recombination repair defective phenotype with ATR, CHK1 and WEE1 inhibitors
Authors: Smith Hannah L , Willmore Elaine , Prendergast Lisa , Curtin Nicola J
Published: July 2023

Purpose

PARP inhibitors (PARPi) are effective in homologous recombination repair (HRR) defective (HRD) cancers. To (re)sensitise HRR proficient (HRP) tumours to PARPi combinations with other drugs are being explored. Our aim was to determine the mechanism underpinning the sensitisation to PARPi by inhibitors of cell cycle checkpoint kinase ATR, CHK1 and WEE1.

Experimental design

A panel of HRD and HRP cells (including matched BRCA1 or 2 mutant and corrected pairs) and ovarian cancer ascites cells were used. Rucaparib (PARPi) induced replication stress (RS) and HRR (immunofluorescence microscopy for γH2AX and RAD51 foci, respectively), cell cycle changes (flow cytometry), activation of ATR, CHK1 and WEE1 (Western Blot for pCHK1S345, pCHK1S296 and pCDK1Y15, respectively) and cytotoxicity (colony formation assay) was determined, followed by investigations of the impact on all of these parameters by inhibitors of ATR (VE-821, 1 μM), CHK1 (PF-477736, 50 nM) and WEE1 (MK-1775, 100 nM).

Results

Rucaparib induced RS (3 to10-fold), S-phase accumulation (2-fold) and ATR, CHK1 and WEE1 activation (up to 3-fold), and VE-821, PF-477736 and MK-1775 inhibited their targets and abrogated these rucaparib-induced cell cycle changes in HRP and HRD cells. Rucaparib activated HRR in HRP cells only and was (60-1,000x) more cytotoxic to HRD cells. VE-821, PF-477736 and MK-1775 blocked HRR and sensitised HRP but not HRD cells and primary ovarian ascites to rucaparib.

Conclusions

Our data indicate that, rather than acting via abrogation of cell cycle checkpoints, ATR, CHK1 and WEE1 inhibitors cause an HRD phenotype and hence synthetic lethality with PARPi.
Label-free imaging of DNA interactions with 2D materials
Authors: Sülzle Jenny , Yang Wayne , Shimoda Yuta , Ronceray Nathan , Mayner Eveline , Manley Suliana , Radenovic Aleksandra
Published: July 2023

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a Focused Ion Beam (FIB) technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.
msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
Authors: Demeulemeester Nina , Gébelin Marie , Gomes Lucas Caldi , Lingor Paul , Carapito Christine , Martens Lennart , Clement Lieven
Published: July 2023

In the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis and ageing. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by the inherently low abundance of many PTMs and the confounding of PTM intensities with its parent protein abundance.

Therefore, we have developed msqrob2PTM, a new workflow in the msqrob2 universe capable of differential abundance analysis at the PTM, and at the peptidoform level. The latter is important for validating PTMs found as significantly differential. Indeed, as our method can deal with multiple PTMs per peptidoform, there is a possibility that significant PTMs stem from one significant peptidoform carrying another PTM, hinting that it might be the other PTM driving the perceived differential abundance.

Our workflows can flag both Differential Peptidoform (PTM) Abundance (DPA) and Differential Peptidoform (PTM) Usage (DPU). This enables a distinction between direct assessment of differential abundance of peptidoforms (DPA) and differences in the relative usage of peptidoforms corrected for corresponding protein abundances (DPU). For DPA, we directly model the log2-transformed peptidoform (PTM) intensities, while for DPU, we correct for parent protein abundance by an intermediate normalisation step which calculates the log2-ratio of the peptidoform (PTM) intensities to their summarized parent protein intensities.

We demonstrated the utility and performance of msqrob2PTM by applying it to datasets with known ground truth, as well as to biological PTM-rich datasets. Our results show that msqrob2PTM is on par with, or surpassing the performance of, the current state-of-the-art methods. Moreover, msqrob2PTM is currently unique in providing output at the peptidoform level.
The receptor binding domain of SARS-CoV-2 spike protein fused with the type IIbE. coliheat-labile enterotoxin A subunit as an intranasal booster after mRNA vaccination
Authors: Hsieh He-Chin , Chen Chung-Chu , Chou Pin-Han , Liu Wen-Chun , Wu Suh-Chin
Published: July 2023

The outbreak of SARS-CoV-2 infections had led to the COVID-19 pandemic which has a significant impact on global public health and the economy. The spike (S) protein of SARS-CoV-2 contains the receptor binding domain (RBD) which binds to human angiotensin-converting enzyme 2 receptor. Numerous RBD-based vaccines have been developed and recently focused on the induction of neutralizing antibodies against the immune evasive Omicron BQ.1.1 and XBB.1.5 subvariants. In this preclinical study, we reported the use of a direct fusion of the type IIbEscherichia coliheat-labile enterotoxin A subunit with SARS CoV-2 RBD protein (RBD-LTA) as an intranasal vaccine candidate. The results showed that intranasal immunization with the RBD-LTA fusion protein in BALB/c mice elicited potent neutralizing antibodies against the Wuhan-Hu-1 and several SARS-CoV-2 variants as well as the production of IgA antibodies in bronchoalveolar lavage fluids (BALFs). Furthermore, the RBD-LTA fusion protein was used as a second-dose booster after bivalent mRNA vaccination. The results showed that the neutralizing antibody titers elicited by the intranasal RBD-LTA booster were similar to the bivalent mRNA booster, but the RBD-specific IgA titers in sera and BALFs significantly increased. Overall, this preclinical study suggests that the RBD-LTA fusion protein could be a promising candidate as a mucosal booster COVID-19 vaccine.
Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome
Authors: Cozzolino Kira , Sanford Lynn , Hunter Samuel , Molison Kayla , Erickson Benjamin , Courvan Meaghan C.S. , Jones Taylor , Ajit Deepa , Galbraith Matthew D. , Espinosa Joaquin M. , Bentley David L. , Allen Mary A. , Dowell Robin D. , Taatjes Dylan J.
Published: July 2023

Hyperactive interferon (IFN) signaling is a hallmark of Down syndrome (DS), a condition caused by trisomy 21 (T21); strategies that normalize IFN signaling could benefit this population. Mediator-associated kinases CDK8 and CDK19 drive inflammatory responses through incompletely understood mechanisms. Using sibling-matched cell lines with/without T21, we investigated Mediator kinase function in the context of hyperactive IFN in DS over a 75min - 24h timeframe. Activation of IFN-response genes was suppressed in cells treated with the CDK8/CDK19 inhibitor cortistatin A (CA), via rapid suppression of IFN-responsive transcription factor (TF) activity. We also discovered that CDK8/CDK19 affect splicing, a novel means by which Mediator kinases control gene expression. To further probe Mediator kinase function, we completed cytokine screens and metabolomics experiments. Cytokines are master regulators of inflammatory responses; by screening 105 different cytokine proteins, we show that Mediator kinases help drive IFN-dependent cytokine responses at least in part through transcriptional regulation of cytokine genes and receptors. Metabolomics revealed that Mediator kinase inhibition altered core metabolic pathways in cell type-specific ways, and broad up-regulation of anti-inflammatory lipid mediators occurred specifically in kinase-inhibited cells during hyperactive IFNγ signaling. A subset of these lipids (e.g. oleamide, desmosterol) serve as ligands for nuclear receptors PPAR and LXR, and activation of these receptors occurred specifically during hyperactive IFN signaling in CA-treated cells, revealing mechanistic links between Mediator kinases, lipid metabolism, and nuclear receptor function. Collectively, our results establish CDK8/CDK19 as context-specific metabolic regulators, and reveal that these kinases control gene expression not only via TFs, but also through metabolic changes and splicing. Moreover, we establish that Mediator kinase inhibition antagonizes IFN signaling through transcriptional, metabolic, and cytokine responses, with implications for DS and other chronic inflammatory conditions.
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis
Authors: von der Dunk Samuel H. A. , Hogeweg Paulien , Snel Berend
Published: July 2023

The complex eukaryotic cell resulted from a merger between simpler prokaryotic cells, yet the relative timing and the role of the mitochondrial endosymbiosis with respect to other eukaryotic innovations has remained under dispute. Although expansion of the regulatory repertoire has been inferred from phylogenetic studies, gene regulation has not been taken into account in current scenarios of the mitochondrial endosymbiosis which mostly focus on the complementary energetic and ecological perspectives. The endosymbiotic state introduced several unique challenges to cells such as coordination of host and symbiont cell cycles and its disruption by leaking gene products and DNA fragments between host and symbionts. To investigate how these unique challenges impacted genome and network evolution during eukaryogenesis, we study a constructive computational model where two simple cells are forced into an obligate endosymbiosis.

Across multiplein silicoevolutionary replicates, we observe the emergence of different mechanisms for the coordination of host and symbiont cell cycles, stabilizing the endosymbiotic relationship. The most commonly evolved mechanism, implicit control, works without signaling between host and symbiont. Signaling only evolves under the influence of leaking gene products, while such regulatory interference is inherently harmful. In the fittest evolutionary replicate, the host controls the symbiont cell cycle entirely through signaling, mimicking the regulatory dominance of the nucleus over the mitochondrion that evolved during eukaryogenesis.
Theoretical principles explain the structure of the insect head direction circuit
Authors: Aceituno Pau Vilimelis , Dall’Osto Dominic , Pisokas Ioannis
Published: July 2023

To navigate their environment, insects need to keep track of their orientation. Previous work has shown that insects encode their head direction as a sinusoidal activity pattern around a ring of neurons arranged in an eight-column structure. However, it is unclear whether this sinusoidal encoding of head direction is just an evolutionary coincidence or if it offers a particular functional advantage. To address this question, we establish the basic mathematical requirements for direction encoding and show that it can be performed by many circuits, all with different activity patterns. Among these activity patterns, we prove that the sinusoidal one is the most noise-resilient, but only when coupled with a sinusoidal connectivity pattern between the encoding neurons. We compare this predicted optimal connectivity pattern with anatomical data from the head direction circuits of the locust and the fruit fly, finding that our theory agrees with experimental evidence. Furthermore, we demonstrate that our predicted circuit can emerge using Hebbian plasticity, implying that the neural connectivity does not need to be explicitly encoded in the genome of the insect but rather can emerge during development. Finally, we illustrate that in our theory, the consistent presence of the eight-column organisation of head direction circuits across multiple insect species is not a chance artefact but instead can be explained by basic evolutionary principles.