bluuebunny/crossref_metadata_2025 huggingface dataset:
Reliability, validity, and sensitivity of Japanese version of the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument: application to efficacy assessment of intravenous immunoglobulin administration
Authors: Matsuda Kazuki M , Sugimoto Eiki , Ako Yoshiaki , Kitamura Marie , Miyahara Mai , Kotani Hirohito , Norimatsu Yuta , Hisamoto Teruyoshi , Kuzumi Ai , Fukasawa Takemichi , Sato Shinichi , Yoshizaki Ayumi
Published: September 2023

Objective

This study aimed to develop and assess the reliability, validity, and sensitivity of Japanese version of the University of California Los Angeles Scleroderma Clinical Trial Consortium Gastrointestinal Tract (GIT) Instrument 2.0 (the GIT score), as an evaluation tool for GIT symptoms in systemic sclerosis (SSc).

Methods

Japanese version of the GIT score was constructed using the forward-backward method. The reliability and validity of this instrument were evaluated in a cohort of 38 SSc patients. Correlation analysis was conducted to assess the relationship between the GIT score and existing patient-reported outcome measures. Additionally, the sensitivity of the GIT score was examined by comparing GIT scores before and after intravenous immunoglobulin (IVIG) administration in 10 SSc-myositis overlap patients, as IVIG has recently demonstrated effectiveness in alleviating GIT symptoms of SSc.

Results

Japanese version of the GIT score exhibited internal consistency and a significant association with the Frequency Scale for the Symptoms of Gastroesophageal Reflux Disease. Furthermore, the total GIT score, as well as the reflux and distention/bloating subscales, displayed moderate correlations with the EQ-5D pain/discomfort subscale, Short Form-36 body pain subscale, and its physical component summary. Notably, following IVIG treatment, there was a statistically significant reduction in the total GIT score and most of the subscales.

Conclusion

We firstly validated Japanese version of the GIT score in Japanese SSc patients in real-world clinical settings. This instrument holds promise for application in future clinical trials involving this patient population.

Key messages

What is already known about this subject?

Khanna et al. developed the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract (GIT) Instrument (the GIT score) to assess patient-reported GIT symptoms in individuals with systemic sclerosis (SSc).

What does this study add?

We have developed and established the reliability, validity, and sensitivity of the Japanese version of the GIT score in cohorts of Japanese individuals with SSc.

How might this impact on clinical practice?

This tool can effectively evaluate GIT manifestations in Japanese SSc patients in routine clinical settings, and potentially in clinical trial contexts.
Dimeric immunoglobulin A as a novel diagnostic marker of measles infection
Authors: Hanafiah Khayriyyah Mohd , Hiebert Joanne , Zubach Vanessa , Severini Alberto , Anderson David A. , Drummer Heidi E.
Published: September 2023

Despite tremendous measles incidence reduction through universal vaccination, elimination efforts rely on improved surveillance. Detection of anti-measles immunoglobulin M (IgM) by ELISA is the standard laboratory diagnostic method. However, true infection is rare and seroconversion following MMR vaccination also generates IgM, which results in low positive predictive values of assays in elimination settings, thus necessitating confirmatory testing. Improved diagnostic tests for measles infection are a World Health Organization (WHO) research priority. We investigated whether dimeric immunoglobulin A (dIgA), the predominant antibody produced in mucosal immunity, may be a marker of recent or acute measles infection. We examined a serological panel of confirmed measles infection (anti-measles IgM positives, n=50), and non-measles infection with rubella (n=36), roseola (n=40), chikungunya/dengue/zika (n=41), parvovirus (n=35) and other fever-rash illness of unknown cause (n=37). Sera were examined on a Micrommune anti-measles IgM, Euroimmun anti-measles virus lysate (VL) and nucleoprotein (NP) IgM kits. Assays were then modified to detect dIgA using an in-house protocol based on a recombinant chimeric secretory component protein and anti-secretory component monoclonal antibody. We observed significantly higher levels of anti-measles VL dIgA in measles samples than non-measles controls (p<0.001), and there was low correlation with IgM (R2: 0.01, p value:0.487). Unlike IgM, dIgA reactive to measles NP was not detected in most samples. Comparable diagnostic potential of anti-measles dIgA (AUC 0.920 - 0.945) to anti-measles IgM (AUC 0.986 – 0.995), suggests that dIgA may be a new blood-based marker of acute measles, independent of IgM, which merits further investigation and optimization.
A clinical microscopy dataset to develop a deep learning diagnostic test for urinary tract infection
Authors: Liou Natasha , De Trina , Urbanski Adrian , Chieng Catherine , Kong Qingyang , David Anna L , Khasriya Rajvinder , Yakimovich Artur , Horsley Harry
Published: September 2023

Urinary tract infection (UTI) is a common disorder. Its diagnosis can be made by microscopic examination of voided urine for cellular markers of infection. This manual technique is technically difficult, time-consuming and prone to inter-observer errors. The application of computer vision to this domain has been slow due to the lack of a clinical image dataset from UTI patients. We present an open dataset containing 300 images and 3,562 manually annotated urinary cells labelled into seven classes of clinically significant cell types. It is an enriched dataset acquired from the unstained and untreated urine of patients with symptomatic UTI using a simple imaging system. We demonstrate that this dataset can be used to train a Patch U-Net, a novel deep learning architecture with a random patch generator to recognise urinary cells. Our hope is that with this dataset UTI diagnosis will be made possible in nearly all clinical settings by using a simple imaging system which leverages advanced machine learning techniques.
Chinese Herbal Medicine Treatment for Alzheimer’s Disease Inpatients in China: Alternative or Complement to Conventional Medicine, a Cross-sectional Study
Authors: Chen Xiaoping , Yan Hao , Nicholas Stephen , Maitland Elizabeth , Huang Zhengwei , Ma Yong , Shi Xuefeng
Published: September 2023

Objectives

Chinese herbal medicine (CHM), a typical type of complementary and alternative medicine (CAM), has been used to treat Alzheimer’s disease (AD) with costs covered by China’s urban basic medical insurance. Previous studies have demonstrated the treatment effectiveness of CHM for intractable disease and CHM’s ability to reduce medical costs. There has been no research exploring the impact of CHM on AD inpatient hospital costs or whether CHM is a complement or alternative to conventional medicine treatments. We compared the medical costs of AD inpatients, CHM users, and non-CHM users to analyze whether CHM has increased or decreased the AD inpatient costs, to assess whether CHM was an alternative or complementary treatment.

Methods

Our cross-sectional research was based on a 5% random sample from the 2010 to 2016 Urban Employee Basic Medical Insurance (UEBMI) and Urban Resident Basic Medical Insurance (URBMI) claim data, yielding information on 1507 urban AD inpatients. Wilcoxon rank sum test and chi square test were applied to the medical cost data with an abnormal distribution. To control for confounding factors, such as demographic (age and sex) and medical costs, the influence between CHM costs and conventional medicine costs were analyzed by quantile regression.

Results

CHM users accounted for 79.83% (1203/1507) of the total inpatients. The median inpatient cost of CHM users was RMB13293.95 (USD2084.49), which was higher than non-CHM users’ (RMB8428.10/USD1321.53, P<0.001). The median CHM cost was RMB721.00 (USD113.05). Positive correlations between CHM users and CHM costs were found after controlling for confounder variables (Coef.=0.09, P<0.001).

Conclusion

During 2010-2016, nearly 80% of AD inpatients in our sample used CHM. Participation in CHM increased the total inpatient costs, pharmacy costs, and conventional medicine costs of AD inpatients over non-CHM users. CHM mainly plays a complementary or less alternative role to conventional medicine for AD treatment.
Micro-Scale Control of Oligodendrocyte Morphology and Myelination by the Intellectual Disability-Linked Protein Acyltransferase ZDHHC9
Authors: Jeong Hey-Kyeong , Gonzalez-Fernandez Estibaliz , Crawley Ilan , Hwang Jinha , Martin Dale David Orr , Bamji Shernaz X , KIM JONG-IL , Kang Shin-Hyeok , Thomas Gareth
Published: September 2023

Mutations in the X-linked ZDHHC9 gene cause cognitive deficits in humans, with a subset of patients suffering from epilepsy. X-linked intellectual disability (XLID) is often ascribed to neuronal deficits, but here we report that expression of human and mouse ZDHHC9 orthologs is far higher in myelinating oligodendrocytes (OLs) than in other CNS cell types. ZDHHC9 codes for a protein acyltransferase (PAT), and we found that ZDHHC9 is the most highly expressed PAT in OLs. Wild type ZDHHC9 localizes to Golgi outposts in OL processes, but other PATs and XLID mutant forms of ZDHHC9 are restricted to OL cell bodies. Using genetic tools for OL progenitor fate tracing and sparse cell labeling, we show that mice lacking Zdhhc9 have grossly normal OL development but display extensive morphological and structural myelin abnormalities. Consistent with the hypothesis that these deficits are OL-autonomous, they are broadly phenocopied by acute Zdhhc9 knockdown in cultured conditions. Finally, we found that ZDHHC9 palmitoylates Myelin Basic Protein (MBP) in heterologous cells, and that palmitoylation of MBP is impaired in the Zdhhc9 knockout brain. Our findings provide critical insights into the mechanisms of ZDHHC9-associated XLID and shed new light on the palmitoylation-dependent control of myelination.
Optimal Social Group Size in Spotted Hyaenas (Crocuta crocuta): Insights into a Multilevel Society
Authors: Dunbar R.I.M.
Published: September 2023

The spotted hyaena lives in unusually large social groups for a carnivore. Since the infertility trap normally limits the size of social groups in mammals, it seems likely that this species has evolved some way of mitigating the stresses involved. In primates, this usually takes the form of female-female alliances, often embedded in multilevel social systems. I show (1) that the distribution of hyaena clan sizes is multimodal, with a fractal scaling close to 3 and a base unit of 12-15 individuals (3-5 reproductive females) and (2) that fertility is a trade off between the benefits of having more males in the group and the costs incurred by having more females, with 4-5 as the limit on the number of females that can live together without their reproductive rates falling below the demographic replacement rate. I present evidence that females buffer themselves against the infertility trap by forming matrilineal alliances that in turn create a multilevel structure. In this respect, hyaena resemble cercopithecine primates in using social strategies to enable animals to live in larger groups than they would otherwise be able to do.
Use of CRISPR interference for efficient and rapid gene inactivation inFusobacterium nucleatum
Authors: Zhou Peng , G C Bibek , Stolte Flynn , Wu Chenggang
Published: September 2023

Gene inactivation via creating in-frame deletion mutations inFusobacterium nucleatumis time-consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPRi system. This system employs the nuclease-inactiveStreptococcus pyogenesCas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes,ftsX,andradD, pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline,ftsXsuppression caused filamentous cell formation akin to chromosomalftsXdeletion, while targetingradDsignificantly reduced RadD protein levels, abolishing coaggregation. The system was then extended to probe essential genesbamAandftsZ, vital for outer membrane biogenesis and cell division. Impressively,bamAsuppression disrupted membrane integrity and bacterial separation, stalling growth, whileftsZ-targeting yielded elongated cells in broth with compromised agar growth. Further studies onF. nucleatumclinical strain CTI-2 andFusobacterium periodonticumrevealed reduced indole synthesis when targetingtnaA. Moreover, silencingclpBinF. periodonticumdecreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains.

IMPORTANCE

How can we effectively investigate the gene functions inFusobacterium nucleatum, given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPRi system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and sgRNA expression is driven by the robust, constitutiverpsJpromoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered resistant strains like CTI-2 andFusobacterium periodontium. With CRISPRi’s potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
Biofoundry-scale DNA assembly validation using cost-effective high-throughput long read sequencing
Authors: Vegh Peter , Donovan Sophie , Rosser Susan , Stracquadanio Giovanni , Fragkoudis Rennos
Published: September 2023

Biofoundries are automated high-throughput facilities specialising in the design, construction and testing of engineered/synthetic DNA constructs (plasmids), often from genetic parts. A critical step of this process is assessing the fidelity of the assembled DNA construct to the desired design. Current methods utilised for this purpose are restriction digest or PCR followed by fragment analysis, and sequencing. The Edinburgh Genome Foundry (EGF) has recently established a single-molecule sequencing quality control step using the Oxford Nanopore sequencing technology, along with a companion Nextflow pipeline and a Python package to perform in-depth analysis and generate a detailed report. Our software enables biofoundry scientists and end-users to rapidly analyse sequencing data, without specialised bioinformatics knowledge. In conclusion, we have created a laboratory and software protocol that validates assembled, cloned or edited plasmids, using Nanopore long reads, which can serve as a useful resource for the genetics, synthetic biology and sequencing communities.

Author information

All authors contributed to the design of the sequencing quality control step and pipeline, and the preparation of the manuscript. P.V. wrote the manuscript, designed and implemented the bioinformatics pipeline and interpreted results. S.D. wrote the manuscript, implemented the laboratory protocol and interpreted results. G.S. designed the bioinformatics pipeline. R.F. wrote the manuscript and contributed to the design of the laboratory protocol and pipeline.

Address: Edinburgh Genome Foundry (University of Edinburgh), Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom

Graphical abstract
Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions
Authors: Sivadas Athira , McDonald Eli Fritz , Shuster Sydney O. , Davis Caitlin M. , Plate Lars
Published: September 2023

Phosphofructokinase is the central enzyme in glycolysis and constitutes a highly regulated step. The liver isoform (PFKL) compartmentalizes during activation and inhibitionin vitroandin vivorespectively. Compartmentalized PFKL is hypothesized to modulate metabolic flux consistent with its central role as the rate limiting step in glycolysis. PFKL tetramers self-assemble at two interfaces in the monomer (interface 1 and 2), yet how these interfaces contribute to PFKL compartmentalization and drive protein interactions remains unclear. Here, we used site-specific incorporation of noncanonical photocrosslinking amino acids to identify PFKL interactors at interface 1, 2, and the active site. Tandem mass tag-based quantitative interactomics reveals interface 2 as a hotspot for PFKL interactions, particularly with cytoskeletal, glycolytic, and carbohydrate derivative metabolic proteins. Furthermore, PFKL compartmentalization into puncta was observed in human cells using citrate inhibition. Puncta formation attenuated crosslinked protein-protein interactions with the cytoskeleton at interface 2. This result suggests that PFKL compartmentalization sequesters interface 2, but not interface 1, and may modulate associated protein assemblies with the cytoskeleton.
Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos
Authors: Yang Jian , Cook Lauryn , Chen Zhiyuan
Published: September 2023

In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we employed epigenome editing to perturb the long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in ∼2667 insertions throughout the mouse genome. CRISPRi robustly repressed 2485 (∼ 93%) MT2_Mm insertions and 1090 (∼55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused down-regulation of hundreds of ZGA genes at the 2-cell stage and embryonic arrest mostly at the morula stage. Mechanistically, MT2_Mm/MT2C_Mm primarily served as alternative ZGA promoters activated by OBOX proteins. Thus, through unprecedented large-scale epigenome editing, we addressed to what extent MT2_Mm/MT2C_Mm regulates ZGA and preimplantation development. Our approach could be adapted to systematically perturb retrotransposons in other mammalian embryos as it doesn’t require transgenic animals.
A genome-wide association study identifies genetic variants associated with hip pain in the UK Biobank cohort (N=221,127)
Authors: Pan Qi , Cai Tengda , Veluchamy Abi , Hebert Harry L , Zhu Peixi , Haque Mainul , Dottorini Tania , Colvin Lesley A , Smith Blair H , Meng Weihua
Published: September 2023

Hip pain is a common musculoskeletal complaint that leads many people to seek medical attention. Approximately 14.3% of the population aged 60 and above have reported substantial hip pain persisting for most days over a six-week period. Our research aimed to identify the genetic variants associated with hip pain by conducting a genome-wide association study (GWAS) on the hip pain phenotype, utilizing data from 221,127 participants from the UK Biobank cohort. We found 7 different loci associated with hip pain, with the most significant SNP being rs77641763, which is situated within theEXD3gene (pvalue = 2.20 x 10-13). We utilized publicly available summary statistics from a previous GWAS meta-analysis on hip osteoarthritis as a replication cohort. Two loci (rs12042579 and rs9597759) were suggestively replicated. Further analysis of tissue expression revealed significant associations between brain tissues and hip pain. Additionally, we found strong genetic correlations between hip pain and other pain phenotypes. This research has therefore identified multiple genetic loci associated with hip pain, which may potentially pave the way for medical interventions that can alleviate the burden of hip pain.
Effect of Acute Kidney Injury on In-hospital Mortality in Non-critical Medical Patients in a Sub-Saharan African Country
Authors: Mekonnen Nahom Desalegn , Leulseged Tigist Workneh , Mera Nebiat Adane , Berhe Helen Surafeal , Beyene Anteneh Abera , Yemaneberhan Kidus Haile , Hassen Buure Ayderuss , Abriha Feven Negasi , Getachew Lidiya Zenebe , Habtezgi Birukti Gebreyohannes
Published: September 2023

Background

AKI is a major global public health problem that affects millions of people each year and has been linked to poor prognosis in critically ill patients. As being a common complication in hospitalized patients, understanding its effect on non-critical patients is equally crucial, but there is a paucity of knowledge in this area, particularly in Africa. Therefore, the aim of this study was to assess the effect of AKI on in-hospital morality in non-critical medical patients admitted to a large tertiary hospital in Ethiopia.

Methods

A retrospective cohort study of 319 non-critical medical patients (113 with AKI and 206 without AKI) admitted between July 2019 and January 2022 was conducted. The in-hospital mortality rate was estimated using incidence density with a 95% CI. The two groups’ comparability was assessed using chi-square and Fisher’s exact tests. The effect of AKI on in-hospital mortality was analyzed using a log binomial regression model with a p-value of ≤ 0.05 determining a significant effect, and the effect was measured using adjusted relative risk (ARR) and its 95% CI.

Results

The in-hospital mortality rate was 6.8 per 1000 person-days of observation (95% CI=4.9-9.4). AKI did not show a significant effect on in-hospital mortality (ARR = 0.72, 95% CI=0.30-1.71, p=0.450). On the other hand, sepsis was found to be a significant predictor, with over a threefold increase in risk of in-hospital mortality (ARR=3.47, 95% CI=1.60-7.52, p=0.002).

Conclusion

With early detection and proper management, non-critical patients with AKI can have a similar prognosis as those without AKI, unlike the critical setting. However, sepsis was found to be a significant predictor of in-hospital mortality implying the need to pay special attention to the management of these cases.
A transcriptionally active lipid vesicle encloses the injectedChimalliviridaegenome in early infection
Authors: Armbruster Emily G. , Rani Phoolwanti , Lee Jina , Klusch Niklas , Hutchings Joshua , Hoffman Lizbeth Y. , Buschkaemper Hannah , Enustun Eray , Adler Benjamin A. , Inlow Koe , VanderWal Arica R. , Hoffman Madelynn Y. , Daksh Daksh , Aindow Ann , Deep Amar , Rodriguez Zaida K. , Morgan Chase J. , Ghassemian Majid , Laughlin Thomas G. , Charles Emeric , Cress Brady F. , Savage David F. , Doudna Jennifer A. , Pogliano Kit , Corbett Kevin D. , Villa Elizabeth , Pogliano Joe
Published: September 2023

Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses1–3. Bacteriophages of theChimalliviridaefamily sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA4–10. Previously, we observed lipid membrane-bound vesicles in cells infected byChimalliviridae, but due to the paucity of genetics tools for these viruses it was unknown if these vesicles represented unproductive, abortive infections or abona fidestage in the phage life cycle. Using the recently-developed dRfxCas13d-based knockdown system CRISPRi-ART11in combination with fluorescence microscopy and cryo-electron tomography, we show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. We demonstrate that early phage genes are transcribed by the virion-associated RNA polymerase from the genome within the compartment, making the EPI vesicle the first known example of a lipid membrane-bound organelle that separates transcription from translation in prokaryotes. Further, we show that the phage nucleus is essential for the phage life cycle, with genome replication only beginning after the injected DNA is transferred from the EPI vesicle to the newly assembled phage nucleus. Our results show thatChimalliviridaerequire two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive stages of the viral life cycle.
Dissociable roles of thalamic nuclei in the refinement of reaches to spatial targets
Authors: Sibener LJ , Mosberger AC , Chen TX , Athalye VR , Murray JM , Costa RM
Published: September 2023

Reaches are complex movements that are critical for survival, and encompass the control of different aspects such as direction, speed, and endpoint precision. Complex movements have been postulated to be learned and controlled through distributed motor networks, of which the thalamus is a highly connected node. Still, the role of different thalamic circuits in learning and controlling specific aspects of reaches has not been investigated. We report dissociable roles of two distinct thalamic nuclei – the parafascicular (Pf) and ventroanterior/ventrolateral (VAL) nuclei – in the refinement of spatial target reaches in mice. Using 2-photon calcium imaging in a head-fixed joystick task where mice learned to reach to a target in space, we found that glutamatergic neurons in both areas were most active during reaches early in learning. Reach-related activity in both areas decreased late in learning, as movement direction was refined and reaches increased in accuracy. Furthermore, the population dynamics of Pf, but not VAL, covaried in different subspaces in early and late learning, but eventually stabilized in late learning. The neural activity in Pf, but not VAL, encoded the direction of reaches in early but not late learning. Accordingly, bilateral lesions of Pf before, but not after learning, strongly and specifically impaired the refinement of reach direction. VAL lesions did not impact direction refinement, but instead resulted in increased speed and target overshoot. Our findings provide new evidence that the thalamus is a critical motor node in the learning and control of reaching movements, with specific subnuclei controlling distinct aspects of the reach early in learning.
Comparative single-cell regulome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis
Authors: Liu Yuting , Luo Xin , Sun Yiming , Chen Kaimin , Hu Ting , You Benhui , Xu Jiahao , Zhang Fengyun , Meng Xiaoyu , Li Xiang , He Xiechao , Li Cheng , Su Bing
Published: September 2023

The cellular and genetic mechanism underlying the human-specific features of cortex development remains unclear. We generated a cell-type resolved atlas of transcriptome and regulome of the developing macaque and mouse prefrontal cortex, and conducted evolutionary analyses with the published complementary human data. We discovered a primate-specific expansion of two neural progenitor subclasses, glia-committed radial glia (RG) and truncated RG. Specifically, the human neural progenitors show extensive transcriptional rewiring in the growth factor and extracellular matrix pathways. Expression of the human-specific progenitor markerITGA2in the cortex of fetal mouse promotes progenitor proliferation and an increased upper-layer neuron proportion. We demonstrate that these transcriptional divergences are primarily driven by the activity changes of the distal regulatory elements in the genome. Markedly, the chromatin regions with human-gained accessibility enrich the human-fixed sequence changes, as well as sequence polymorphisms associated with intelligence and neuropsychiatric disorders. Our results uncover evolutionary innovations in neural progenitors and gene regulatory mechanism during primate cortex evolution.
Robust Small Molecule-Aided Cardiac Reprogramming Systems Selective to Cardiac Fibroblasts
Authors: Tao Yanmeng , Yang Yang , Yang Zhenghao , Wang Lipeng , Wang Shi-Qiang , Zhao Yang
Published: September 2023

Direct cardiac reprogramming to induce cardiomyocyte-like cells, e.g. by GMT (Gata4, Mef2c and Tbx5), is a promising route for regenerating damaged heartin vivoand disease modellingin vitro. Supplementation with additional factors and chemical agents can enhance efficiency but raises concerns regarding selectivity to cardiac fibroblasts and complicates delivery for in situ cardiac reprogramming. Here, we screened 2000 chemicals with known biological activities and found that a combination of 2C (SB431542 and Baricitinib) significantly enhances cardiac reprogramming by GMT. Without Gata4, MT (Mef2c and Tbx5) plus 2C could selectively reprogram cardiac fibroblasts with enhanced efficiency, kinetics, and cardiomyocyte function. Moreover, 2C significantly enhanced cardiac reprogramming in human cardiac fibroblasts. 2C synergistically enhances cardiac reprogramming by inhibiting Alk5, Tyk2 and downregulating Oas2, Oas3, Serpina3n and Tgfbi. 2C enables selective and robust cardiac reprogramming that can greatly facilitate disease modellingin vitroand advance clinical therapeutic heart regenerationin vivo.
The Implant-Induced Foreign Body Response is Limited by CD13-Dependent Regulation of Ubiquitination of Fusogenic Proteins
Authors: Ghosh Mallika , McGurk Fraser , Norris Rachael , Dong Andy , Nair Sreenidhi , Jellison Evan , Murphy Patrick , Verma RajKumar , Shapiro Linda H
Published: September 2023

Implanted medical devices from artificial heart valves, arthroscopic joints to implantable sensors often induce a Foreign Body Response (FBR), a form of chronic inflammation resulting from the inflammatory reaction to a persistent foreign stimulus. The FBR is characterized by a subset of multinucleated giant cells (MGCs) formed by macrophage fusion, the Foreign Body Giant cells (FBGCs), accompanied by inflammatory cytokines, matrix deposition and eventually, deleterious fibrotic implant encapsulation. Despite efforts to improve biocompatibility, implant-induced FBR persists, compromising the utility of devices and making efforts to control the FBR imperative for long-term function. Controlling macrophage fusion in FBGC formation presents a logical target to prevent implant failure, but the actual contribution of FBGCs to FBR-induced damage is controversial. CD13 is a molecular scaffold andin vitroinduction of CD13KObone-marrow progenitors generates many more MGCs than WT, suggesting CD13 regulates macrophage fusion. Moreover, in the mesh implant model of FBR, CD13KOmice produced significantly more peri-implant FBGCs with enhanced TGFβ expression and increased collagen deposition vs. WT. Pre-fusion, increased protrusion and microprojection formation accompanies hyperfusion in the absence of CD13. Expression of fusogenic proteins driving cell-cell fusion was aberrantly sustained at high levels in CD13KOMGCs, which we show is due to a novel CD13 function, regulating ubiquitin/proteasomal protein degradation. By controlling protein degradation, CD13 becomes a physiologic brake preventing aberrant macrophage fusion and may be a novel therapeutic target to improve success of implanted medical devices. Furthermore, our data directly implicates FBGCs in the detrimental fibrosis that characterizes the FBR.
Structure and dynamics of a pentameric KCTD5/Cullin3/Gβγ E3 ubiquitin ligase complex
Authors: Nguyen Duc Minh , Rath Deanna H. , Devost Dominic , Pétrin Darlaine , Rizk Robert , Ji Alan X. , Narayanan Naveen , Yong Darren , Zhai Andrew , Kuntz Douglas A. , Mian Maha U.Q. , Pomroy Neil C. , Keszei Alexander F.A. , Benlekbir Samir , Mazhab-Jafari Mohammad T. , Rubinstein John L. , Hébert Terence E. , Privé Gilbert G.
Published: September 2023

Heterotrimeric G proteins can be regulated by post-translational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain (CTD), engages CUL3 to form the central scaffold of a cullin- RING E3 ligase complex (CRL3KCTD5) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3NTD/Gβ1γ2assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5BTB/CUL3NTDand KCTD5CTD/Gβγ moieties of the structure. CRL3KCTD5engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 super-assembly, and extension of the structure to include full- length CUL3 with RBX1 and an ARIH1∼ubiquitin conjugate reveals that some conformational states position the ARIH1∼ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3NTD/Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex.

Significance Statement

In humans, ∼600 enzyme complexes can carry out protein ubiquitylation, and the most abundant class of these are the cullin3-RING-ligase complexes (CRL3s). CRL3s are multiprotein complexes built around a BTB/cullin3 core, and the incorporation of different BTB proteins into this scaffold results in distinct architectures that ubiquitylate a wide range of substrates. In most cases, it is not known how the complexes are tuned to their substrates. We show that the BTB protein KCTD5 is the central organizer in a CRL3KCTD5complex, and that the architecture and internal dynamics of KCTD5 are essential for positioning a Gβγ substrate protein near an activated ubiquitin for the transfer reaction. This explains how KCTD5 targets Gβγ for proteasomal degradation and regulates cellular activities.
Effect of alpha-tubulin acetylation on the doublet microtubule structure
Authors: Yang Shun Kai , Kubo Shintaroh , Black Corbin , Peri Katya , Dai Daniel , Valente Melissa , Gaertig Jacek , Bui Khanh Huy
Published: September 2023

Acetylation of α-tubulin at the lysine 40 residue (αK40) by ATAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule in the cilia ofTetrahymena thermophilausing a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the doublet microtubule structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.
Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis
Authors: Imoto Yuuta , Xue Jing , Luo Lin , Raychaudhuri Sumana , Itoh Kie , Ma Ye , Craft George E. , Kwan Ann H. , Mackay Joel P. , Ha Taekjip , Watanabe Shigeki , Robinson Phillip J.
Published: September 2023

Dynamin 1 (Dyn1) has two major splice variants, xA and xB, with unique C-terminal extensions of 20 and 7 amino acids, respectively. Of these, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that the long tail variant, Dyn1xA, achieves this localization by preferentially binding to Endophilin A through a newly defined Class II binding site overlapping with its extension, at a site spanning the splice boundary. Endophilin binds this site at higher affinity than the previously reported site, and this affinity is determined by amino acids outside the binding sites acting as long distance elements within the xA tail. Their interaction is regulated by the phosphorylation state of two serine residues specific to the xA variant. Dyn1xA and Endophilin colocalize in patches near the active zone of synapses. Mutations selectively disrupting Endophilin binding to the long extension cause Dyn1xA mislocalization along axons. In these mutants, endocytic pits are stalled on the plasma membrane during ultrafast endocytosis. These data suggest that the specificity for ultrafast endocytosis is defined by the phospho-regulated interaction of Endophilin A through a newly identified site of Dyn1xA’s long tail.
Making your raw data available to the macromolecular crystallography community
Authors: Kroon-Batenburg Loes M. J.
Published: September 2023

A recent editorial in the IUCr macromolecular crystallography journals [Helliwell et al. (2019), Acta Cryst. D75, 455–457] called for the implementation of the FAIR data principles. This implies that the authors of a paper that describes research on a macromolecular structure should make their raw diffraction data available. Authors are already used to submitting the derived data (coordinates) and the processed data (structure factors, merged or unmerged) to the PDB, but may still be uncomfortable with making the raw diffraction images available. In this paper, some guidelines and instructions on depositing raw data to Zenodo are given.
Grounding, framing, and problematising research in online, distance and digital education
Authors: Lim David C.L. , Zawacki-Richter Olaf , Jung Insung
Published: September 2023

Purpose

This paper engages Olaf Zawacki-Richter and Insung Jung in a frank and penetrating conversation that seeks to ground, frame, and problematise research in the field conceptualised as “open, distance and digital education” (ODDE). Taking as starting point the recent publication of the landmark Handbook of Open, Distance, and Digital Education (2022), it segues into a broad critique of the shortcomings of ODDE research, the importance of knowledge production on the meso- and macro-levels, the autonomy of ODDE as a field coming into its own, the place of postfoundationalism in ODDE discourse, and related topics that are pivotal in ODDE today.

Design/methodology/approach

The semi-structured interview was employed as the primary qualitative research method.

Findings

The research imperative of the relatively young but complex field of ODDE today is not the incessant reiteration of the same but rather a strategic reorientation that, first, circumvents the well-documented yet too-often-overlooked shortcomings of ODDE research and, second, promotes transboundary collaborations with the potential for system-wide impact.

Originality/value

This novel interview-based critique of ODDE research demonstrates that extending the scholarly discourse beyond the conventional report format is a productive method for enriching conversations on ODDE and vitalising the field itself.
The impact of integrating a compulsory community-oriented research program within undergraduate medical curriculum on graduates' scientific publications: perspectives from Arabian Gulf University
Authors: Alzayani Salman , Al-Roomi Khaldoon , Jaradat Ahmed , Hamdi Ali M. , Shehata Mohamed H.
Published: September 2023

Purpose

Medical schools aspire to graduate doctors who are competent in interpreting, conducting and publishing scientific research. Hence, the purpose of the paper is explore the impact of a structured compulsory community-oriented, project-based research program in the undergraduate medical curriculum on medical graduates’ future careers, publications and motivation for scientific research.

Design/methodology/approach

An online questionnaire was sent through the Alumni Association of the Arabian Gulf University (AGU) to medical graduates who have valid email addresses, seeking information on their scientific productivity along with demographic and current employment data. Responses were collated and analyzed using a standard statistical software package. The chi-square test and p-value were calculated. P-value <0.05 was considered statistically significant.

Findings

Completed forms were received from 91 medical graduates. In this sample, almost a quarter of the respondents have published a research paper out of their undergraduate research project, and about 50% have published at least one paper (as main or co-author) after graduation. Both demographic and medical specialty was not related to the doctor's perception of the benefits they have attained from the compulsory undergraduate research program. However, medical graduates who are at senior levels in their medical careers and those who are employed in secondary healthcare are significantly more likely to publish research papers.

Originality/value

The compulsory community-oriented, project-based research program in AGU has positively contributed to the research productivity of graduates, and it would be worthwhile to include such programs as an integral part of the undergraduate medical curriculum.
Explore, eat and revisit: does local food consumption value influence the destination’s food image?
Authors: Gupta Vikas , Galati Antonino , Sharma Savita
Published: September 2023

Purpose

This research investigates how foreign tourists' revisit intentions are influenced by their local food consumption (LFC) value by emphasizing their attitude towards the local food and the corresponding destination food image. It will also reveal the foreign tourists' food consumption value and explore its influences on the destination's food image.

Design/methodology/approach

The data collection was performed from 433 foreign tourists who visited Delhi, India, using a structured survey instrument and chief constructs were measured as the first-order reflective variables. The 39 items associated with the LFC value underwent both exploratory and confirmatory evaluations. The authors employed partial least square structural equation modeling (PLS-SEM). The model's discriminant and convergent validity, consistency and overall fit were evaluated using confirmatory factor analysis (CFA).

Findings

The findings revealed that “tourists' attitudes and behaviors toward the local cuisine” had a significant and positive influence on their “intention to visit/revisit” and “intention to recommend”. Also, “destination food image” significantly and positively influenced the “intention of tourist to visit/revisit”; however, it negatively and insignificantly influenced the “intention of tourists to recommend”.

Research limitations/implications

This research used five variables related to LFC—quality, health/nutrition, emotion, prestige and price—that impact tourists' attitudes and behaviors toward local foods in Delhi. However, in addition to these constructs, other factors or constructs may be involved that could affect the tourists' attitudes and behaviors. Future studies might explore and include these constructs to provide a more comprehensive image of Delhi's LFC value.

Originality/value

Understanding tourists' food-linked behaviors is critical for effective market conduct. However, the interrelations between travelers' destination food image, LFC value, their perceptions of the local cuisine and behavioral intentions are still unknown, and this will be one of the first attempts to discuss these behaviors.
Factors influencing the individual investors of Bangladesh to opt for investment in ṣukūk
Authors: Chowdhury Tasruma Sharmeen , Salema S.M. Kalbin
Published: September 2023

Purpose

This study aims to identify the factors that influence the willingness of Bangladeshi retail investors to invest in ṣukūk.

Design/methodology/approach

The authors surveyed Bangladeshi retail investors using a structured questionnaire to understand their perspectives on potential investment in ṣukūk. The authors considered the behavioral aspects of retail investors and the desired ṣukūk features to analyze the demand side. Factors and regression analyses were performed to identify the persuading factors.

Findings

The results indicate that investor awareness is a fundamental factor in potential investments in ṣukūk. Investors perceive the security represented by government and third-party guarantees as a persuasive feature of ṣukūk. The tradability and tenor of ṣukūk also affect the investment intention. Sharīʿah consciousness of the investors also plays a significant role in their investment decisions.

Research limitations/implications

One limitation of this study is that it incorporates potential individual investors only, and precludes institutional investors. In the future, there is scope for research to explore the demand factors impacting institutional investors of ṣukūk in Bangladesh.

Practical implications

The authors expect that the study will aid policymakers and ṣukūk issuers in crafting strategies to cater to the needs of Bangladeshi retail investors.

Originality/value

This study is the earliest research conducted in Bangladesh to determine the factors impacting the willingness of individual investors to make their potential investments in ṣukūk. To the best of the authors' knowledge, no study has analyzed the desired ṣukūk features from the perspective of Bangladeshi retail investors.
A four-node rectangular plate finite element using Airy functions with transverse shear
Authors: Abderrahmani Sifeddine
Published: September 2023

Purpose

Among different types of engineering structures, plates play a significant role. Their analysis necessitates numerical modeling with finite elements, such as triangular, quadrangular or sector plate elements, owing to the intricate geometrical shapes and applied loads. The scope of this study is the development of a new rectangular finite element for thin plate bending based on the strain approach using Airy's function. It is called a rectangular plate finite element using Airy function (RPFEUAF) and has four nodes. Each node had three degrees of freedom: one transverse displacement (w) and two normal rotations (x, y).

Design/methodology/approach

Equilibrium conditions are used to generate the interpolation functions for the fields of strain, displacements and stresses. The evolution of the Airy function solutions yielded the selection of these polynomial bi-harmonic functions. The variational principle and the analytical integration approach are used to evaluate the basic stiffness matrix.

Findings

The numerical findings for thin plates quickly approach the Kirchhoff solution. The results obtained are compared to the analytical solution based on Kirchhoff theory.

Originality/value

The efficiency of the strain based approach using Airy's function is confirmed, and the robustness of the presented element RPFEUAF is demonstrated. Because of this, the current element is more reliable, better suited for computations and especially intriguing for modeling this kind of structure.