bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precision medicine for developmental and epileptic encephalopathies in Africa – strategies for a resource-limited setting
Authors: Esterhuizen Alina I. , Tiffin Nicki , Riordan Gillian , Wessels Marie , Burman Richard J. , Aziz Miriam C. , Calhoun Jeffrey D. , Gunti Jonathan , Amiri Ezra E. , Ramamurthy Aishwarya , Bamshad Michael J. , Nickerson Deborah A. , Mefford Heather C. , Ramesar Raj , Wilmshurst Jo M. , Carvill Gemma L. 
Published: August 2022

ABSTRACTPurposeSub-Saharan Africa bears the highest burden of epilepsy worldwide. A presumed proportion is genetic, but this aetiology is buried under the burden of infections and perinatal insults, in a setting of limited awareness and few options for testing. Children with developmental and epileptic encephalopathies (DEEs), are most severely affected by this diagnostic gap in Africa, as the rate of actionable findings is highest in DEE-associated genes.MethodsWe tested 235 genetically naïve South African children diagnosed with/possible DEE, using gene panels, exome sequencing and chromosomal microarray. Statistical comparison of electroclinical features in children with and without candidate variants was performed to identify characteristics most likely predictive of a positive genetic finding.ResultsOf 41/235 children with likely/pathogenic variants, 26/235 had variants supporting precision therapy. Multivariate regression modelling highlighted neonatal or infantile-onset seizures and movement abnormalities as predictive of a positive genetic finding. We used this, coupled with an emphasis on precision medicine outcomes, to propose the pragmatic “Think-Genetics” strategy for early recognition of a possible genetic aetiology.ConclusionOur findings emphasise the importance of an early genetic diagnosis in DEE. We designed the “Think-Genetics” strategy for early recognition, appropriate interim management and genetic testing for DEE in resource-constrained settings.
RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex
Authors: Kato Kazuki , Okazaki Sae , Schmitt-Ulms Cian , Jiang Kaiyi , Zhou Wenyuan , Ishikawa Junichiro , Isayama Yukari , Adachi Shungo , Nishizawa Tomohiro , Makarova Kira S. , Koonin Eugene V. , Abudayyeh Omar O. , Gootenberg Jonathan S. , Nishimasu Hiroshi 
Published: August 2022

AbstractThe type III-E Cas7-11 effector nuclease forms a complex with a CRISPR RNA (crRNA) and the putative caspase-like protease Csx29, catalyzes crRNA-guided target RNA cleavage, and has been used for RNA targeting in eukaryotic cells. Here, we report cryo-electron microscopy structures of the Cas7-11–crRNA–Csx29 complex with and without target RNA, and demonstrate that target RNA binding induces a conformational change in Csx29 and results in the protease activation. Biochemical analysis confirmed that Cas7-11-bound Csx29 cleaves Csx30 in a target RNA-dependent manner. Reconstitution of the system in bacteria uncovered Csx30-dependent cellular toxicity regulated by Csx31, and that Csx29-mediated cleavage produces toxic Csx30 fragments, promoting cell death. We find that Csx30 can bind both Csx31 and the associated sigma factor RpoE, suggesting Csx30 can inhibit RpoE and modulate cellular stress response towards infection. Overall, the RNA-guided nuclease-protease activities of the Cas7-11–Csx29 effector complex facilitate protease-based programmed cell death.
The effector recognition by synthetic sensor NLR receptors requires the concerted action of multiple interfaces within and outside the integrated domain
Authors: Zhang Xin , Liu Yang , Yuan Guixin , Wang Dongli , Zhu Tongtong , Wu Xuefeng , Ma Mengqi , Guo Liwei , Guo Hailong , Bhadauria Vijai , Liu Junfeng , Peng You-Liang 
Published: August 2022

AbstractPlant sensor nucleotide-binding leucine-rich repeat (NLR) receptors detect pathogen effectors through their integrated domains (IDs). The RGA5 sensor NLR recognizes its corresponding effectors AVR-Pia and AVR1-CO39 from the blast fungus Magnaporthe oryzae through direct binding to its heavy metal-associated (HMA) ID to trigger the RGA4 helper NLR-dependent resistance in rice. Here we report a mutant of RGA5 named RGA5HMA5 that confers complete resistance in transgenic rice plants to the M. oryzae strains expressing the noncorresponding effector AVR-PikD. RGA5HMA5 carries three engineered interfaces, two of which lie in the HMA ID and the other in the C-terminal Lys-rich stretch tailing the ID. However, the RGA5 variants having one or two of the three interfaces, including replacing all the Lys residues with Glu residues in the Lys-rich stretch, failed to activate RGA4-dependent cell death of rice protoplasts. Altogether, this work demonstrates that sensor NLRs require a concerted action of multiple surfaces within and outside the IDs to both recognize noncorresponding effectors and activate helper NLR-mediated resistance, and has implications in structure-guided designing of sensor NLRs.
Modeling concentration-dependent phase separation processes involving peptides and RNA via residue-based coarse-graining
Authors: Valdes-Garcia Gilberto , Heo Lim , Lapidus Lisa J. , Feig Michael 
Published: August 2022

ABSTRACTBiomolecular condensation, especially liquid-liquid phase separation, is an important physical process with relevance for a number of different aspects of biological functions. Key questions of what drives such condensation, especially in terms of molecular composition, can be addressed via computer simulations, but the development of computationally efficient, yet physically realistic models has been challenging. Here, the coarse-grained model COCOMO is introduced that balances the polymer behavior of peptides and RNA chains with their propensity to phase separate as a function of composition and concentration. COCOMO is a residue-based model that combines bonded terms with short- and long-range terms, including a Debye-Hückel solvation term. The model is highly predictive of experimental data on phase-separating model systems. It is also computationally efficient and can reach the spatial and temporal scales on which biomolecular condensation is observed with moderate computational resources.
Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import
Authors: Nashed S , El Barbry H , Benchouaia M , Dijoux-Maréchal A , Ruiz Gutierrez N , Gaulier L , Chevreux G , Le Crom S , Palancade B , Devaux F , Laine E , Garcia M 
Published: August 2022

ABSTRACTN-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified inS. cerevisiaemore than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their modification by NatC as critical features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.
Ecology drives the observed spectrum of hydrophobin protein diversity across Kingdom Fungi
Authors: Lovett Brian , Kasson Matt T. , Gandier Julie-Anne 
Published: August 2022

1.AbstractHydrophobins mediate the interactions between fungi and the elements of their ecosystem via assembly at interfaces serving a wide range of diverse functions. As such, these proteins can be seen as a means by which fungi not only adapt to a pre-existing environment, but also actively participate in the construction of their own ecological niches. Through this lens, we provide an expansive hydrophobin survey across the ecological breadth of Kingdom Fungi and advance the view that hydrophobins are best defined as a generic molecular structure with shared core structural features that accommodate a remarkable diversity of amino acid sequences. We examine the relationship between hydrophobin sequences, fungus phylogeny, and associated ecology from 45 fungal proteomes predicted from genomes spanning eight phyla and more than 25 orders. To capture the full spectrum of the hydrophobin amino acid sequence space mapped by our study, we describe the family as a continuum of overlapping hidden Markov models (HMMs), each HMM representing clusters of sequence similarity spanning existing hydrophobin classes. Overall, our approach uncovered ecology as a major driver of hydrophobin diversification, further expanded the known hydrophobins beyond Dikarya, and uncovered evidence extending the possibilities for their function from exclusively extracellular to include intracellular. In addition, we identified novel core groups of cysteine-rich proteins whose conservation across fungi suggest they play key ecological roles. Together, our work offers an ontological framework that captures the diversity of hydrophobin amino acid sequences and highlights the need to revisit challenging fundamental questions regarding hydrophobins to achieve a mechanistic understanding of their function as emerging from assembly within an ecosystem.
Remarkable sex-specific differences at Single-Cell Resolution in Neonatal Hyperoxic Lung Injury
Authors: Cantu A , Cantu M , Dong X , Leek C , Sajti E , Lingappan K 
Published: August 2022

ABSTRACTExposure to supraphysiological concentrations of oxygen (hyperoxia) predisposes to bronchopulmonary dysplasia (BPD), which is characterized by abnormal alveolarization and pulmonary vascular development, in preterm neonates. Neonatal hyperoxia exposure is used to recapitulate the phenotype of human BPD in murine models. Male sex is considered an independent predictor for the development of BPD, but the main mechanisms underlying sexually dimorphic outcomes are unknown. Our objective was to investigate sex-specific and cell-type specific transcriptional changes that drive injury in the neonatal lung exposed to hyperoxia at single-cell resolution and delineate the changes in cell-cell communication networks in the developing lung. We used single cell RNA sequencing (scRNAseq) to generate transcriptional profiles of >35000 cells isolated from the lungs of neonatal male and female C57BL/6 mice exposed to 95% FiO2 between PND1-5 (saccular stage of lung development) or normoxia and euthanized at PND7 (alveolar stage of lung development). ScRNAseq identified 22 cell clusters with distinct populations of endothelial, epithelial, mesenchymal, and immune cells. Our data identified that the distal lung vascular endothelium (composed of aerocytes and general capillary endothelial cells) is exquisitely sensitive to hyperoxia exposure with the emergence of an intermediate capillary endothelial population with both aCaP and gCaP markers. We also identified a myeloid derived suppressor cell population from the lung neutrophils. Sexual dimorphism was evident in all lung cell subpopulations but was striking among the lung immune cells. Finally, we identified that the specific intercellular communication networks and the ligand-receptor pairs that are impacted by neonatal hyperoxia exposure.
SARS-CoV-2 Airway Infection Results in Time-dependent Sensory Abnormalities in a Hamster Model
Authors: Serafini Randal A. , Frere Justin J. , Zimering Jeffrey , Giosan Ilinca M. , Pryce Kerri D. , Golynker Ilona , Panis Maryline , Ruiz Anne , tenOever Benjamin , Zachariou Venetia 
Published: August 2022

ABSTRACTDespite being largely confined to the airways, SARS-CoV-2 infection has been associated with sensory abnormalities that manifest in both acute and long-lasting phenotypes. To gain insight on the molecular basis of these sensory abnormalities, we used the golden hamster infection model to characterize the effects of SARS-CoV-2 versus Influenza A virus (IAV) infection on the sensory nervous system. Efforts to detect the presence of virus in the cervical/thoracic spinal cord and dorsal root ganglia (DRGs) demonstrated detectable levels of SARS-CoV-2 by quantitative PCR and RNAscope uniquely within the first 24 hours of infection. SARS-CoV-2-infected hamsters demonstrated mechanical hypersensitivity during acute infection; intriguingly, this hypersensitivity was milder, but prolonged when compared to IAV-infected hamsters. RNA sequencing (RNA-seq) of thoracic DRGs from acute infection revealed predominantly neuron-biased signaling perturbations in SARS-CoV-2-infected animals as opposed to type I interferon signaling in tissue derived from IAV-infected animals. RNA-seq of 31dpi thoracic DRGs from SARS-CoV-2-infected animals highlighted a uniquely neuropathic transcriptomic landscape, which was consistent with substantial SARS-CoV-2-specific mechanical hypersensitivity at 28dpi. Ontology analysis of 1, 4, and 30dpi RNA-seq revealed novel targets for pain management, such as ILF3. Meta-analysis of all SARS-CoV-2 RNA-seq timepoints against preclinical pain model datasets highlighted both conserved and unique pro-nociceptive gene expression changes following infection. Overall, this work elucidates novel transcriptomic signatures triggered by SARS-CoV-2 that may underlie both short- and long-term sensory abnormalities while also highlighting several therapeutic targets for alleviation of infection-induced hypersensitivity.One Sentence SummarySARS-CoV-2 infection results in an interferon-associated transcriptional response in sensory tissues underlying time-dependent hypersensitivity.
RNA Immunoprecipitation and Sequencing of Isolated RNAs (RIP-SIR) Identifies Endogenous miRNA-Target Interactions
Authors: Wells Julie , Srivastava Anuj , Maser Richard S. , Kesharwani Rupesh , Sarsani Vishal Kumar , Daigle Sandra L. , Lynch Ryan P. , Munger Heidi J. , Doty Rosalinda , Saxl Ruth L. , Bult Carol J. 
Published: August 2022

AbstractMicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression in species ranging from plants to mammals. Unraveling the complex networks of miRNA-mediated regulation of gene expression requires the ability to identify the mRNA targets of individual miRNAs in native cellular contexts. Here we describe RIP-SIR, an unbiased genome-wide method for identifying interactions between endogenous miRNAs and their targets in almost any tissue or cell type.
Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning
Authors: Lei Zhengyang , Lian Lijin , Zhang Likun , Wei Jiazhang , Liu Changyue , Liu Hong , Liu Ying , Du Zhicheng , Yuan Xi , Zhong Xiaoyun , Gul Ijaz , Zhang Haihui , Wang Chuhui , Zhai Shiyao , Pandey Vijay , Zhang Canyang , Xing Xinhui , Deng Lin , Yu Dongmei , He Qian , Qin Peiwu 
Published: August 2022

AbstractFrog virus 3 (FV3, generaRanavirus, familyIridoviridae), a double-stranded DNA virus, results in irreparable damage to biodiversity and significant economic losses to aquaculture. Although the existing FV3 detection methods are of high sensitivity and specificity, the complex procedure and requirement of expensive instruments limit their practical implantation. Herein, we develop a fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for FV3. Combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, we achieve a limit of detection (LoD) of 100 aM (60.2 copies/μL) by optimizing RPA primers and CRISPR RNAs (crRNAs). For POC detection, we build a smartphone microscopy (SPM) and achieve an LoD of 10 aM within 40 minutes. Four positive animal-derived samples with a quantitation cycle (Cq) value of quantitative PCR (qPCR) in the range of 13 to 32 are detectable by the proposed system. In addition, we deploy deep learning models for binary classification (positive or negative samples) and multiclass classification (different concentrations of FV3 and negative samples), achieving 100% and 98.75% accuracy, respectively. Without temperature regulation and expensive equipment, RPA-CRISPR/Cas12a combined with a smartphone readout and artificial intelligence (AI) assisted classification shows great potential for FV3 detection. This integrated system holds great promise for POC detection of aquatic DNA pathogens.HighlightsAn integrated DNA detection system is developed by combining RPA, CRISPR/Cas12a, smartphone microscopy, and deep learning.The LoD of frog virus 3 is 10 aM within 40 min.The detection system shows good performance on animal-derived samples.
Prognostic accuracy of triage tools for adults with suspected COVID-19 in a middle-income setting: an observational cohort study
Authors: Marincowitz Carl , Sbaffi Laura , Hodkinson Peter , McAlpine David , Fuller Gordon , Goodacre Steve , Bath Peter A. , Hasan Madina , Omer Yasein , Wallis Lee 
Published: August 2022

Study ObjectiveTools proposed to triage acuity in suspected COVID-19 in the ED have been derived and validated in higher-income settings during early waves of the pandemic. We estimated the accuracy of seven risk-stratification tools recommended to predict severe illness in the Western Cape, South Africa.MethodsAn observational cohort study using routinely collected data from EDs across the Western Cape, from the 27th of August 2020 to 11th March 2022 was conducted to assess performance of the PRIEST tool, NEWS2, TEWS, the WHO algorithm, CRB-65, Quick COVID-19 Severity Index and PMEWS in suspected COVID-19. The primary outcome was death or ICU admission.ResultsOf 446,084 patients, 15,397 patients (3.45%, 95% CI:34% to 35.1%) experienced the primary outcome. Clinical decision-making for inpatient admission achieved a sensitivity of 0.77 (95% CI 0.76 to 0.78), specificity 0.88 (95% CI 0.87 to 0.88) and the negative predictive value (NPV) 0.99 (95% CI 0.99 to 0.99). NEWS2, PMEWS and PRIEST tool algorithm identified patients at risk of adverse outcomes at recommended cut-offs with moderate sensitivity (>0.8) and specificity ranging from 0.47 (NEWS2) to 0.65 (PRIEST tool). Use of the tools at recommended thresholds would have more than doubled admissions with only a 0.01% reduction in false negative triage.ConclusionUse of the PRIEST score, NEWS2 and PMEWS at a threshold of a point higher would achieve similar accuracy to current clinical admission decision, with possible gains in transparency and speed of decision-making.
Strategies for reducing healthcare supply chain inventory costs
Authors: Essila Jean C. 
Published: August 2022

PurposeThis study aims to identify empirically proven strategies for reducing healthcare supply chain inventory costs.Design/methodology/approachThe author conducted in-depth interviews in 80 hospitals covering different supply chains. The author treated the healthcare firm as the unit of analysis and examined Vrat's taxonomy of inventory models based on the static and dynamic complexity theories of inventory models to identify an appropriate approach. The author addressed 33 highly priced and moderately priced stock-keeping units from 1,432 items and test several inventory policies. Next, the author applied combinations of inventory models, testing probabilistic hybrid inventory models.FindingsThe study finds that medical supplies, equipment, and medications are indispensable for a quality healthcare system. Hence, healthcare supply chain management (SCM) professionals must adopt basic inventory cost-reduction strategies, implementing inventory software functionalities effectively and efficiently. This study shows that probabilistic hybrid inventory techniques in healthcare SCM effectively determine an optimal stocking level, significantly reducing costs.Research limitations/implicationsThis study analyzes data from primary care and (to some extent) secondary care institutions. Although tertiary and quaternary care systems do not represent a large portion of the healthcare system, future research should also address these highly specialized organizations' needs.Practical implicationsThis study proposes practical strategies to help continuously improve supply chain operations in healthcare organizations worldwide.Originality/valueThis study suggests probabilistic hybrid inventory models as empirically proven solutions for evaluating stock-keeping units in the healthcare sector. In doing so, the study provides a new healthcare supply chain approach, proposing a modified taxonomy of inventory models.
Performance measurement framework for the oil and gas supply chain
Authors: Menhat Masha , Yusuf Yahaya , Gunasekaran Angappa , Mohammad Al Montaser 
Published: August 2022

PurposeThere is evidence in the literature suggesting the usage of performance measurement framework (PMF) has a positive impact on organisational performance. This is in line with resource based view (RBV) theory, which argues attaining competitive advantage through internal resources and capabilities. In this regard, PMF can be viewed as a “resource” that can be explored in enabling organisational performance. This paper is aimed at developing PMF for the oil and gas supply chain (SC) as a resource and strategic capability.Design/methodology/approachDrawing on RBV theory, a questionnaire survey was designed based on prior literature review and exploratory interview with five SC experts. Following this, the questionnaires were distributed to 550 companies in the UK and 120 companies in Malaysia, which resulted in 15% overall response rate.FindingsThis study presents the prevalence of performance measures (PM) for the oil and gas industry based on the level of importance. It also reveals the impact of the usage of PMF on overall organisational performance. In addition, it identifies the challenges in managing SC performance and factors to be considered in choosing PM.Originality/valueThis study identifies the challenges in managing SC performance and establishes distinctive factors to consider when choosing PM in the oil and gas SC.