bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleep Disruption in a Mouse Model of Chronic Traumatic Brain Injury
Authors: Morris Andrew R. , Gudenschwager Basso Erwin K. , Gutierrez-Monreal Miguel A. , Arja Rawad Daniel , Kobeissy Firas H. , Janus Christopher G. , Wang Kevin K. W. , Zhu Jiepei , Liu Andrew C.
Published: November 2023

Chronic sleep/wake disturbances are strongly associated with traumatic brain injury (TBI) in patients and are being increasingly recognized. However, the underlying mechanisms are largely understudied and there is an urgent need for animal models of lifelong sleep/wake disturbances. The objective of this study was to develop a chronic TBI rodent model and investigate the lifelong chronic effect of TBI on sleep/wake behavior. We performed repetitive midline fluid percussion injury (rmFPI) in four months old mice and monitored their sleep/wake behavior using the non-invasive PiezoSleep system. The sleep/wake states were recorded before injury (baseline) and then monthly thereafter. We found that TBI mice displayed a significant decrease in sleep duration in both the light and dark phases, beginning at three months post-TBI and continuing throughout the study. Consistent with the sleep phenotype, these TBI mice showed circadian locomotor activity phenotypes and exhibited reduced anxiety-like behavior. TBI mice also gained less weight, and had less lean mass and total body water content, compared to sham controls. Furthermore, TBI mice showed extensive brain tissue loss and increased GFAP and IBA1 levels in the hypothalamus and the vicinity of the injury, indicative of chronic neuropathology. In summary, our study identified a critical time window of TBI pathology and associated circadian and sleep/wake phenotypes. Future studies should leverage this mouse model to investigate the molecular mechanisms underlying the chronic sleep/wake phenotypes following TBI early in life.
Methyl-TWAS: A powerful method forin silicotranscriptome-wide association studies (TWAS) using long-range DNA methylation
Authors: Kim Soyeon , Qin Yidi , Park Hyun Jung , Yue Molin , Xu Zhongli , Forno Erick , Chen Wei , Celedón Juan C.
Published: November 2023

In silicotranscriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-basedin silicoTWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression forin silicoTWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates bothcis-andtrans-CpGs, including various regulatory regions to identify DEGs that would be missed usingcis-methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well asin silicoTWAS in white blood cells. Methyl-TWAS is a valuable tool forin silicoTWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.
Thein vitrofunctional profiles of fentanyl and nitazene analogs at the µ-opioid receptor - high efficacy is dangerous regardless of signaling bias
Authors: Tsai Meng-Hua M. , Chen Li , Baumann Michael H. , Canals Meritxell , Javitch Jonathan A. , Lane J. Robert , Shi Lei
Published: November 2023

Novel synthetic opioids (NSOs), including both fentanyl and non-fentanyl analogs that act as the μ-opioid receptor (MOR) agonists, are associated with serious intoxication and fatal overdose. Previous studies proposed that G protein biased MOR agonists are safer pain medications, while other evidence indicates that low intrinsic efficacy at MOR better explains reduced opioid side effects. Here, we characterized thein vitrofunctional profiles of various NSOs at MOR using adenylate cyclase inhibition and β-arrestin2 recruitment assays, in conjunction with the application of the receptor depletion approach. By fitting the concentration-response data to the operational model of agonism, we deduced the intrinsic efficacy and affinity for each opioid in the Gi protein signaling and β-arrestin2 recruitment pathways. Compared to the reference agonist DAMGO, we found that several fentanyl analogs were more efficacious at inhibiting cAMP production, whereas all fentanyl analogs were less efficacious at recruiting β-arrestin2. In contrast, the non-fentanyl 2-benzylbenzimidazole (i.e., nitazene) analogs were highly efficacious and potent in both the cAMP and β-arrestin2 assays. Our findings suggest that the high intrinsic efficacy of the NSOs in Gi protein signaling is a common property that may underlie their high risk of intoxication and overdose, highlighting the limitation of usingin vitrofunctional bias to predict the adverse effects of opioids. Instead, our results show that, regardless of bias, opioids with sufficiently high intrinsic efficacy can be lethal, especially given the extremely high potency of many of these compounds that are now pervading the illicit drug market.
Hybrid-hybrid correction of errors in long reads with HERO
Authors: Kang Xiongbin , Xu Jialu , Luo Xiao , Schönhuth Alexander
Published: November 2023

Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO, as the first “hybrid-hybrid” approach, to make use of both de Bruijn graphs and overlap graphs for optimal catering to the particular strengths of NGS and TGS reads. Extensive benchmarking experiments demonstrate that HERO improves indel and mismatch error rates by on average 65% (27 95%) and 20% (4 61%). Using HERO prior to genome assembly significantly improves the assemblies in the majority of the relevant categories.
Scaling deep identifiable models enables zero-shot characterization of single-cell biological states
Authors: Dong Mingze , Agrawal Kriti , Fan Rong , Sefik Esen , Flavell Richard A. , Kluger Yuval
Published: November 2023

How to identify true biological differences across samples while overcoming batch effects has been a persistent challenge in single-cell RNA-seq data analysis, hindering analyses across datasets for transferable biological findings. In this work, we show that scaling up deep identifiable models leads to a surprisingly effective solution for this challenging task. We developed scShift, a deep variational inference framework with theoretical support in disentangling batch-dependent and independent variations. By training the model with compendiums of scRNA-seq atlases, scShift shows remarkablezero-shotcapabilities in revealing representations of cell types and biological states in single-cell data while overcoming batch effects. We employed scShift to systematically compare lung fibrosis states across different datasets, tissues and experimental systems. scShift uniquely extrapolates lung fibrosis states to previously unseen post-COVID-19 fibrosis, characterizing universal myeloid-fibrosis signatures, potential repurposing drug targets and fibrosis-associated cell interactions. Evaluations of over 200 trained scShift models demonstrate emergent zero-shot capabilities and a scaling law beyond a transition threshold, with respect to dataset diversity. With its scaling performance on massive single-cell compendiums and exceptional zero-shot capabilities, scShift represents an important advance toward next-generation computational models for single-cell analysis.
Testing of putative antiseizure drugs in a preclinical Dravet syndrome zebrafish model
Authors: Whyte-Fagundes P , Vance A , Carroll A , Figueroa F , Manukyan C , Baraban S.C.
Published: November 2023

Dravet syndrome (DS) is a severe genetic epilepsy primarily caused byde novomutations in a voltage-activated sodium channel gene (SCN1A). Patients face life-threatening seizures that are largely resistant to available anti-seizure medications (ASM). Preclinical DS animal models are a valuable tool to identify candidate ASMs for these patients. Among these,scn1labmutant zebrafish exhibiting spontaneous seizure-like activity are particularly amenable to large-scale drug screening. Prior screening in ascn1labmutant zebrafish line generated using N-ethyl-N-nitrosourea (ENU) identified valproate, stiripentol, and fenfluramine e.g., Federal Drug Administration (FDA) approved drugs with clinical application in the DS population. Successful phenotypic screening inscn1labmutant zebrafish consists of two stages: (i) a locomotion-based assay measuring high-velocity convulsive swim behavior and (ii) an electrophysiology-based assay, usingin vivolocal field potential (LFP) recordings, to quantify electrographic seizure-like events. Using this strategy more than 3000 drug candidates have been screened inscn1labzebrafish mutants. Here, we curated a list of nine additional anti-seizure drug candidates recently identified in preclinical models: 1-EBIO, AA43279, chlorzoxazone, donepezil, lisuride, mifepristone, pargyline, soticlestat and vorinostat. First-stage locomotion-based assays inscn1labmutant zebrafish identified only 1-EBIO, chlorzoxazone and lisuride. However, second-stage LFP recording assays did not show significant suppression of spontaneous electrographic seizure activity for any of the nine anti-seizure drug candidates. Surprisingly, soticlestat induced frank electrographic seizure-like discharges in wild-type control zebrafish. Taken together, our results failed to replicate clear anti-seizure efficacy for these drug candidates highlighting a necessity for strict scientific standards in preclinical identification of ASMs.
Temporal and spatial analysis of astrocytes following stroke identifies novel drivers of reactivity
Authors: Kim Rachel D , Marchildon Anne E , Frazel Paul W , Hasel Philip , Guo Amy X , Liddelow Shane A
Published: November 2023

Astrocytes undergo robust gene expression changes in response to a variety of perturbations, including ischemic injury. How these transitions are affected by time, and how heterogeneous and spatially distinct various reactive astrocyte populations are, remain unclear. To address these questions, we performed spatial transcriptomics as well as single nucleus RNAseq of ∼138,000 mouse forebrain astrocytes at 1, 3, and 14 days after ischemic injury. We observed a widespread and temporally diverse response across many astrocyte subtypes. We identified astrocyte clusters unique in injury, including a transiently proliferative substate that may be BRCA1-dependent. We also found an interferon-responsive population that rapidly expands to the perilesion cortex at 1 day and persists up to 14 days post stroke. These lowly abundant, spatially restricted populations are likely functionally important in post-injury stabilization and resolution. These datasets offer valuable insights into injury-induced reactive astrocyte heterogeneity and can be used to guide functional interrogation of biologically meaningful reactive astrocyte substates to understand their pro- and anti-reparative functions following acute injuries such as stroke.
Photobody formation spatially segregates two opposing phytochrome B signaling actions to titrate plant environmental responses
Authors: Kim Ruth Jean Ae , Fan De , He Jiangman , Kim Keunhwa , Du Juan , Chen Meng
Published: November 2023

Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear photobodies (PBs). However, the function of PBs remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. These results reveal a PB-mediated light and temperature sensing mechanism, in which PHYB condensation confers the co-occurrence and competition of two antagonistic phase-separated PHYB signaling actions—PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm— thereby enabling an environmentally-sensitive counterbalancing mechanism to titrate nucleoplasmic PIF5 and its transcriptional output. This PB-enabled signaling mechanism provides a framework for regulating a plethora of PHYB-interacting signaling molecules in diverse plant environmental responses.
SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain
Authors: Bennett Corbett , Ouellette Ben , Ramirez Tamina , Cahoon Alex , Cabasco Hannah , Browning Yoni , Lakunina Anna , Lynch Galen F. , McBride Ethan , Belski Hannah , Gillis Ryan , Grasso Conor , Howard Robert , Johnson Tye , Loeffler Henry , Smith Heston , Sullivan David , Williford Allison , Caldejon Shiella , Durand Severine , Gale Samuel , Guthrie Alan , Ha Vivian , Han Warren , Hardcastle Ben , Mochizuki Chris , Sridhar Arjun , Suarez Lucas , Swapp Jackie , Wilkes Joshua , Siegle Joshua H. , Farrell Colin , Groblewski Peter A. , Olsen Shawn R.
Published: November 2023

To understand the neural basis of behavior, it is essential to measure spiking dynamics across many interacting brain regions. While new technologies, such as Neuropixels probes, facilitate multi-regional recordings, significant surgical and procedural hurdles remain for these experiments to achieve their full potential. Here, we describe a novel 3D-printed cranial-replacement implant (SHIELD) enabling electrophysiological recordings from distributed areas of the mouse brain. This skull-shaped implant is designed with customizable insertion holes, allowing dozens of cortical and subcortical structures to be recorded in a single mouse using repeated multi-probe insertions over many days. We demonstrate the procedure’s high success rate, biocompatibility, lack of adverse effects on behavior, and compatibility with imaging and optogenetics. To showcase the scientific utility of the SHIELD implant, we use multi-probe recordings to reveal novel insights into how alpha rhythms organize spiking activity across visual and sensorimotor networks. Overall, this method enables powerful large-scale electrophysiological measurements for the study of distributed brain computation.
Stereotyped goal-directed manifold dynamics in the insular cortex
Authors: Talpir Itay , Livneh Yoav
Published: November 2023

The insular cortex is involved in diverse processes including bodily homeostasis, emotions, and cognition. Yet we lack a comprehensive understanding of how it processes information at the level of neuronal populations. We leveraged recent advances in unsupervised machine learning to study insular cortex population activity patterns (i.e., neuronal manifold) in mice performing goal-directed behaviors. We find that the insular cortex activity manifold is remarkably consistent across different animals and under different motivational states. Activity dynamics within the neuronal manifold are highly stereotyped during rewarded trials, enabling robust prediction of single-trial outcomes across different mice, and across various natural and artificial motivational states. Comparing goal-directed behavior with self-paced free consumption, we find that the stereotyped activity patterns reflect task-dependent goal-directed reward anticipation, and not licking, taste, or positive valence. These findings reveal a core computation in insular cortex that could explain its involvement in pathologies involving aberrant motivations.
Pyruvate Oxidation Sustains B Cell Antigen-Specific Activation to Exacerbate MASH
Authors: Barrow Fanta , Wang Haiguang , Fredrickson Gavin , Florczak Kira , Ciske Erin , Khanal Shalil , Parthiban Preethy , Nguyen Huy , Rios Enrique , Kostallari Enis , Revelo Xavier S.
Published: November 2023

B cells play a crucial role in the pathogenesis of metabolic dysfunction-associated steatohepatitis (MASH), a severe form of steatotic liver disease that if persistent can lead to cirrhosis, liver failure, and cancer. Chronic inflammation and fibrosis are key features of MASH that determine disease progression and outcomes. Recent advances have revealed that pathogenic B cell-derived cytokines and antibodies promote the development of MASH. However, the mechanisms through which B cells promote fibrosis and the metabolic adaptations underlying their pathogenic responses remain unclear. Here, we report that a subset of mature B cells with heightened cytokine responses accumulate in the liver and promote inflammation in MASH. To meet the increased energetic demand of effector responses, B cells increase their ATP production via oxidative phosphorylation (OXPHOS) fueled by pyruvate oxidation in a B cell receptor (BCR)-specific manner. Blocking pyruvate oxidation completely abrogated the inflammatory capacity of MASH B cells. Accordingly, the restriction of the BCR led to MASH attenuation, including reductions in steatosis, hepatic inflammation, and fibrosis. Mechanistically, BCR restriction decreased B cell maturation, activation, and effector responses in the liver, accompanied by decreased T cell- and macrophage-mediated inflammation. Notably, attenuated liver fibrosis in BCR-restricted mice was associated with lower IgG production and decreased expression of Fc-gamma receptors on hepatic stellate cells. Together, these findings indicate a key role for B cell antigen-specific responses in promoting steatosis, inflammation, and fibrosis during MASH.
Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies
Authors: Williams Matthew P. , Flegontov Pavel , Maier Robert , Huber Christian D.
Published: November 2023

Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and thef3-statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate andP-values of qpAdm models, andf3-statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-lengthf2-statistics, demonstrating the improved demographic inference that could be achieved with advancements inf-statistic estimations.
Generation of salivary glands derived from pluripotent stem cells via conditional blastocyst complementation
Authors: Tanaka Junichi , Miura Akihiro , Shimamura Yuko , Hwang Youngmin , Shimizu Dai , Kondo Yuri , Sawada Anri , Sarmah Hemanta , Ninish Zurab , Mishima Kenji , Mori Munemasa
Published: November 2023

Various patients suffer from dry mouth due to salivary gland dysfunction. Whole salivary gland generation and transplantation is a potential therapy to resolve this issue. However, the lineage permissible to design the entire salivary gland generation has been enigmatic. Here, we discovered Foxa2 as a lineage critical for generating a salivary gland via conditional blastocyst complementation (CBC). Foxa2 linage, but not Shh nor Pitx2, initiated to label between the boundary region of the endodermal and the ectodermal oral mucosa before primordial salivary gland formation, resulting in marking the entire salivary gland. The salivary gland was agenesis by depleting Fgfr2 under the Foxa2 lineage in the mice. We rescued this phenotype by injecting donor pluripotent stem cells into the mouse blastocysts. Those mice survived until adulthood with normal salivary glands compatible in size compared with littermate controls. These results indicated that CBC-based salivary gland generation is promising for next-generation cell-based therapy.
Chemical Tools for the Gid4 Subunit of the Human E3 Ligase C-terminal to LisH (CTLH) Degradation Complex
Authors: Yazdi Aliakbar Khalili , Perveen Sumera , Song Xiaosheng , Dong Aiping , Szewczyk Magdalena M. , Calabrese Matthew F. , Casimiro-Garcia Agustin , Chakrapani Subramanyam , Dowling Matthew S. , Ficici Emel , Lee Jisun , Montgomery Justin I. , O’Connell Thomas N. , Skrzypek Grzegorz J. , Tran Tuan P. , Troutman Matthew D. , Wang Feng , Young Jennifer A. , Min Jinrong , Barsyte-Lovejoy Dalia , Brown Peter J. , Santhakumar Vijayaratnam , Arrowsmith Cheryl H. , Vedadi Masoud , Owen Dafydd R.
Published: November 2023

We have developed a novel chemical handle (PFI-E3H1) and a chemical probe (PFI-7) as ligands for the Gid4 subunit of the human E3 ligase CTLH degradation complex. Through an efficient initial hit-ID campaign, structure-based drug design (SBDD) and leveraging the sizeable Pfizer compound library, we identified a 500 nM ligand for this E3 ligase through file screening alone. Further exploration identified a vector that is tolerant to addition of a linker for future chimeric molecule design. The chemotype was subsequently optimized to sub-100 nM Gid4 binding affinity for a chemical probe. These novel tools, alongside the suitable negative control also identified, should enable the interrogation of this complex human E3 ligase macromolecular assembly.
MdHY5 and MdHY5S form a positive transcription loop to regulate browning and phenolics synthesis in fresh-cut apple under purple LED light
Authors: Jin Juntong , Qi Liyong , Shen Shurong , Yang Shuran , Yuan Hui , Wang Aide
Published: November 2023

Enzymatic browning significantly affects the appearance and quality of fresh-cut fruit. Light treatment can effectively inhibit fresh-cut apple browning via unknown molecular mechanisms. Here, we found that the application of purple LED light decreased the browning index of fresh-cut apple, delaying browning as compared to that of fresh-cut apple placed in the dark, and suggesting that purple LED light suppresses browning. In addition, the expression levels ofMdHY5andMdHY5S, important BASIC LEUCINE ZIPPER DOMAIN (bZIP) transcription factors that are involved in the light signaling pathway, were increased by purple LED light treatment. SilencingMdHY5andMdHY5Sin apple meant that purple LED light treatment no longer inhibited fresh-cut apple browning, the expression levels of the browning-related genesPOLYPHENOL OXIDASE(MdPPO) andPEROXIDASE(MdPOD) increased, and the expression of the phenolic synthesis genePHENYLALANINE AMMONIALYASE(MdPAL) decreased. Further study revealed thatMdHY5andMdHY5Sbind to theMdPPOandMdPODpromoters, reducing their transcription. In contrast,MdHY5andMdHY5Sbind to theMdPALpromoter, enhancing transcription. Further research revealed that MdHY5 and MdHY5S also bind directly to each other’s promoters to form a positive transcriptional loop that activates their transcription. Our findings revealed that purple LED light inhibits browning and increases phenolics synthesis in fresh-cut apple by activatingMdHY5andMdHY5S. The results provide a theoretical basis upon which the new methods for improving the appearance and quality of fresh-cut apple can be based.
The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogenParastagonospora nodorum
Authors: Morikawa Shota , Verdonk Callum , John Evan , Lenzo Leon , Sbaraini Nicolau , Turo Chala , Li Hang , Jiang David , Chooi Yit-Heng , Tan Kar-Chun
Published: November 2023

The fungusParastagonospora nodorumcauses septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA inP. nodorumdevelopment and virulence was investigated here. Deletion of theP. nodorum VeAortholog,PnVeA, resulted in growth abnormalities including pigmentation, abolished asexual sporulation and highly reduced virulence on wheat. Comparative RNA-Seq and RT-PCR analyses revealed that the deletion ofPnVeAalso decoupled the expression of major necrotrophic effector genes. In addition, the deletion ofPnVeAresulted in an up-regulation of four predicted secondary metabolite (SM) gene clusters. Using liquid-chromatography mass-spectrometry, it was observed that one of the SM gene clusters led to an accumulation of the mycotoxin alternariol. PnVeA is essential for asexual sporulation, full virulence, secondary metabolism and necrotrophic effector regulation.
The Magnitude, Distribution Patterns, and Risk Factors of AIDS-Related Illnesses in Adults on Combined Antiretroviral Therapy in Malawi.
Authors: Salema Hemson H
Published: November 2023

This study describes the burden and spectrum of AIDS-related opportunistic diseases (ODs) in adults living with HIV (ALHIV) receiving combined antiretroviral therapy since the scale-up of free HIV treatment in Malawi. Data on AIDS-related ODs were abstracted from the 2004-2015 medical records and analysed using logistic regression models. 9,953 patients, with median age of 40 years (interquartile range (IQR): 33-48 years), of which 60.8% were females and 86.8% were within active sexual age (15-54 years), were included in the analysis. 65.1% were urban residents and 59.6% were from Southern region. 12,814 AIDS-related opportunistic episodes were extracted: 56.5% were prevalent AIDS-defining conditions and 43.5% were incident and recurrent cases. 7.7% of patients did not manifest any OD. Mycobacterial (36.3%), bacterial (20.8%), fungal (15.8%) and viral (15.1%) aetiological agents were most identified common pathogens. Tuberculosis (34.4%), bacterial pneumonia (11.2%), nontyphoid Salmonella bacteraemia (9.6%), HIV-wasting syndrome (8.9%), candidiasis (6.8%), isosporiasis (5.2%), pneumocystis pneumonia (4.2%) and cryptococcal meningitis (3.7%) were overall, most prevalent ODs. In the multivariate regression, healthcare facility types, gender, age-group, residential area, CD4 count, viral load, treatment initiation eligibility criteria and socio-economic status were identifiable risk factors of AIDS-related opportunistic diseases. The high prevalence of ODs among ALHIV in Malawi regardless of ART status requires establishing and strengthening of efficient strategies for effective prevention, early detection, and proactive management of AIDS-related ODs across all patient groups, regions, and health facilities. Keywords: HIV; AIDS; ART; ALHIV; CD4; Viral Load; AIDS-related opportunistic conditions/diseases.
An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal
Authors: Padane Abdou , Tegally Houriiyah , Ramphal Yajna , Seyni Ndiaye , Sarr Mariéma , Diop Mame Matar , Diedhiou Cyrille Kouligueul , Mboup Aminata , Diouf Ndèye Dieyna , Souaré Abdoulaye , Diagne Ndéye Diabou , Aza-Gnandji Marilyne , Dabo Ndèye Astou , Dia Yacine Amet , Diaw Ndeye Aminata , Leye Nafissatou , Diaw Papa Alassane , Ahouidi Ambroise , Cissé Badara , Diallo Abdoulaye Samba , Diop Ousmane , Diallo Abdou Aziz , Ndoye Souadou , Sanko Tomasz J. , Baxter Cheryl , Wilkinson Eduan , San James E. , Tshabuila Derek , Naidoo Yeshnee , Pillay Sureshnee , Lessells Richard , Cissé Khady , Leye Abdoulaye , Mbaye Khalifa Ababacar , Kania Dramane , Tinto Bachirou , Traoré Isidore , Kagone Sampawendé Thérèse , Ouedraogo Abdoul Salam , Gifford Robert J. , Lourenço José , Giovanetti Marta , Giandhari Jennifer , de Oliveira Tulio , Mboup Souleymane
Published: November 2023

Chikungunya (CHIKV) is a re-emerging endemic arbovirus in West Africa. Since July 2023, Senegal and Burkina Faso have been experiencing an ongoing outbreak, with over 300 confirmed cases detected so far in the regions of Kédougou and Tambacounda in Senegal, the largest recorded outbreak yet. CHIKV is typically maintained in a sylvatic cycle in Senegal but its evolution and factors contributing to re-emergence are so far unknown in West Africa, leaving a gap in understanding and responding to recurrent epidemics. We produced, in real-time, the first locally-generated and publicly available CHIKV whole genomes in West Africa, to characterize the genetic diversity of circulating strains, along with phylodynamic analysis to estimate time of emergence and population growth dynamics. A novel strain of the West African genotype, phylogenetically distinct from strains circulating in previous outbreaks, was identified. This suggests a likely new spillover from sylvatic cycles in rural Senegal and potential of seeding larger epidemics in urban settings in Senegal and elsewhere.
Cost-effective boosting allocations in the post-Omicron era of COVID-19 management
Authors: Le Thao P , Conway Eamon , Akpan Edifofon , Abell Isobel , Abraham Patrick , Baker Christopher M , Campbell Patricia T , Cromer Deborah , Lydeamore Michael J , McDonough Yasmine , Mueller Ivo , Ryan Gerard , Walker Camelia , Wang Yingying , Carvalho Natalie , McVernon Jodie
Published: November 2023

Background Following widespread exposure to Omicron variants, COVID-19 has transitioned to endemic cir- culation. Populations now have diverse infection and vaccination histories, resulting in heterogeneous immune landscapes. Careful consideration of vaccination is required through the post-Omicron phase of COVID-19 management to minimise disease burden. We assess the impact and cost-effectiveness of targeted COVID-19 vaccination strategies to support global vaccination recommendations. Methods We integrated immunological, transmission, clinical and cost-effectiveness models, and simulated populations with different characteristics and immune landscapes. We calculated the expected number of infections, hospitalisations and deaths for different vaccine scenarios. Costs (from a healthcare perspective) were estimated for exemplar country income level groupings in the Western Pacific Region. Results are reported as incremental costs and disability-adjusted life years averted compared to no additional vaccination. Parameter and stochastic uncertainty were captured through scenario and sensitivity analysis. Findings Across different population demographics and income levels, we consistently found that annual elder-targeted boosting strategies are most likely to be cost-effective or cost-saving, while paediatric programs are unlikely to be cost-effective. Results remained consistent while accounting for uncertain- ties in the epidemiological and economic models. Half-yearly boosting may only be cost-effective in higher income settings with older population demographics and higher cost-effectiveness thresholds. Interpretation These results demonstrate the value of continued booster vaccinations to protect against severe COVID-19 disease outcomes across high and middle-income settings and show that the biggest health gains relative to vaccine costs are achieved by targeting older age-groups. Funding Funded by the World Health Organization.
Association Between Beta Blocker and Clinical Outcome in Adult Patients with Sepsis or Septic Shock: Protocol of a Systematic Review and Meta- Analysis of Randomized Controlled Trials
Authors: Bhattacharjee Sulagna , Ernest Emmanuel Easterson , Maitra Souvik
Published: November 2023

Use of beta-blockers as a part of heart rate control strategy is sepsis and septic shock patients is of great debate. Despite of early encouraging results, no large trial was performed and several subsequent small studies reported conflicting results. This meta-analysis and systematic review will be conducted and published as per PRISMA guidelines. In this review, randomized controlled trials comparing short-acting beta-blockers with ‘standard of care’ in adult patients with sepsis and septic shock will be included. Primary outcome will be 28-day mortality and secondary outcomes will be duration of intensive care unit stay, duration of hospital stay, ICU mortality, hospital mortality and reported adverse events. A random effect model will be used for all analysis.

Source of Support

Nil

Conflict of interests

None
Midkine and Ptprz1b act upstream of Wnt planar cell polarity to establish a midline in the developing zebrafish hindbrain
Authors: Le Yao , Rajasekhar Kavitha , Loo Tricia Y.J. , Saunders Timothy E. , Wohland Thorsten , Winkler Christoph
Published: November 2023

A midline in the developing central nervous system (CNS) is essential for the symmetric distribution of neural progenitors that later establish functional, bilaterally symmetric neural circuits. In the zebrafish hindbrain, a midline forms early during neurulation and requires a coordinated interplay of cell convergence and midline-crossing cell divisions (C-divisions). These two processes are controlled by the Wnt/planar cell polarity (PCP) pathway. However, upstream cues that control the timely production of PCP components remain unknown. Midkine (Mdk) and pleiotrophin (Ptn) are structurally related heparin-binding growth factors that are dynamically expressed in the developing zebrafish hindbrain. We used proximity ligation assays (PLAs) and fluorescence cross correlation spectroscopy (FCCS)in vivoto show that two zebrafish Mdks, Mdka and Mdkb, as well as Ptn interact with protein tyrosine phosphatase receptors type Z1, Ptprz1a and Ptprz1b, with distinct affinities. Ligand binding triggered Ptprz1b internalization and thereby determined the availability of signaling receptor on cell membranes. In zebrafishmdka, ptnandptprz1bmutants, cell migration and convergence were significantly impaired during hindbrain neurulation. Impaired convergence led to misplaced C-divisions, defective cell polarity and consequently duplicated midlines. These duplications were rescued by overexpression ofDrosophilaPrickle, a key component of the Wnt/PCP pathway. Here, we provide evidence that zygotic Mdka controls the distribution of maternally provided Ptprz1b, which in turn is needed for transcription of zebrafishprickle1b. Our findings thus reveal a role for Mdka and Ptprz1b upstream of Wnt/PCP to coordinate neural plate convergence, neural progenitor positioning and midline formation.
Dietary restriction and life-history trade-offs: insights into mTOR pathway regulation and reproductive investment in Japanese quails
Authors: Reda Gebrehaweria Kidane , Ndunguru Sawadi Fransisco , Csernus Brigitta , Gulyás Gabriella , Knop Renáta , Szabó Csaba , Czeglédi Levente , Lendvai Ádám Z.
Published: November 2023

Resources are needed for growth, reproduction and survival, and organisms must trade-off limited resources among competing processes. Nutritional availability in organisms is sensed and monitored by nutrient-sensing pathways that can trigger physiological changes or alter gene expression. Previous studies have proposed that one such signalling pathway, the mechanistic target of rapamycin (mTOR), underpins a form of adaptive plasticity when individuals encounter constraints in their energy budget. Despite the fundamental importance of this process in evolutionary biology, how nutritional limitation is regulated through the expression of genes governing this pathway and its consequential effects on fitness remains understudied, particularly in birds. We used dietary restriction to simulate resource depletion and examined its effects on body mass, reproduction and gene expression in Japanese quails (Coturnix japonica). Quails were subjected toad libitum(ADL) feeding or 20%, 30%, and 40% restriction levels for two weeks. All restricted groups exhibited reduced body mass, whereas reductions in the number and mass of eggs were observed only under more severe restrictions. Dietary restriction led to decreased expression ofmTORand insulin-like growth factor 1 (IGF1), whereas the ribosomal protein S6 kinase 1 (RPS6K1) and autophagy-related genes (ATG9AandATG5) were upregulated. The pattern in which mTOR respond to restriction was similar to what has been seen in body mass. Regardless of the treatment, proportionally higher reproductive investment was associated with individual variation inmTORexpression. These findings reveal the connection between dietary intake and the expression ofmTORand related genes in this pathway.
Neopolyploidy-induced changes in the giant duckweed (Spirodela polyrhiza) alter herbivore preference, performance, and plant population performance
Authors: Assour Hannah R. , Ashman Tia-Lynn , Turcotte Martin M.
Published: November 2023

Premise

Polyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their animal associates. Yet, knowledge of whether ploidy affects plant-herbivore dynamics is scarce. Here, we test whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether ploidy impacts plant and herbivore performance, and whether these interactions depend on plant genetic background.

Methods

Using multiple pairs of independently synthesized neotetraploid greater duckweed (Spirodela polyrhiza) and their diploid progenitors, we evaluated the effect of neopolyploidy on duckweed’s interaction with the water-lily aphid (Rhopalosiphum nymphaeae). Using two-way choice experiments, we first evaluated feeding preference by the herbivore. We then evaluated the consequences of ploidy on aphid and plant performance by measuring population growth over multiple generations.

Key Results

Aphids preferred neopolyploids over diploids when the plants were provided at equal abundances but not when they were provided at equal surface area, indicating the role of plant size in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was highly dependent on the genetic lineage of the plant. Lastly, the impact of herbivory on neopolyploids vs. diploid duckweed varied greatly with genetic lineage, but overall, neopolyploids appeared to be generally less tolerant than diploids.

Conclusions

We conclude that polyploidization can impact the preference and performance of herbivores on their plant hosts, whereas plant performance depends on complex interactions between herbivory, ploidy, and genetic lineage. These results have significant implications for the establishment and persistence of plants and herbivores in nature.
Structural basis for VLDLR recognition by eastern equine encephalitis virus
Authors: Yang Pan , Li Wanyu , Fan Xiaoyi , Pan Junhua , Mann Colin J. , Varnum Haley , Clark Lars E. , Clark Sarah A. , Coscia Adrian , Smith Katherine Nabel , Brusic Vesna , Abraham Jonathan
Published: November 2023

Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, including paralysis and intellectual disability. The spike proteins of alphaviruses comprise trimers of heterodimers of their envelope glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), two closely related proteins that are expressed in the brain, as cellular receptors for EEEV and a distantly related alphavirus, Semliki forest virus (SFV)1. The EEEV and SFV spike glycoproteins have low sequence homology, and how they have evolved to bind the same cellular receptors is unknown. Here, we used single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain. The structures reveal that EEEV and SFV use distinct surfaces to bind VLDLR; EEEV uses a cluster of basic residues on the E2 subunit of its spike glycoprotein, while SFV uses two basic residues at a remote site on its E1 glycoprotein. Our studies reveal that different alphaviruses interact with the same cellular receptor through divergent binding modes. They further suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses.
Development of LRRK2 designed ankyrin-repeat proteins
Authors: Dederer Verena , Murillo Marta Sanz , Karasmanis Eva P , Hatch Kathryn S , Chatterjee Deep , Preuss Franziska , Abdul Azeez Kamal R , Nguyen Landon Vu , Galicia Christian , Dreier Birgit , Plückthun Andreas , Versees Wim , Mathea Sebastian , Leschziner Andres E , Reck-Peterson Samara L , Knapp Stefan
Published: November 2023

Leucine rich repeat kinase 2 (LRRK2) is a large multidomain protein containing two catalytic domains, a kinase and a GTPase, as well protein interactions domains, including a WD40 domain. The association of increased LRRK2 kinase activity with both the familial and sporadic forms of Parkinson’s disease (PD) has led to intense interest in determining its cellular function. However, small molecule probes that can bind to LRRK2 and report on or affect its activity are needed. Here, we identified a series of high-affinity LRRK2-binding designed ankyrin-repeat proteins (DARPins). One of these DARPins (E11) bound to the LRRK2 WD40 domain with high affinity. LRRK2 bound to DARPin E11 showed improved behavior on cryo-EM grids, resulting in higher resolution LRRK2 structures. DARPin E11 did not affect the catalytic activity of a truncated form of LRRK2 in vitro but decreased the phosphorylation of Rab8A, a LRRK2 substrate, in cells. We also found that DARPin E11 disrupts the formation of microtubule-associated LRRK2 filaments in cells, which are known to require WD40-based dimerization. Thus, DARPin E11 is a new tool to explore the function and dysfunction of LRRK2 and guide the development of LRRK2 kinase inhibitors that target the WD40 domain instead of the kinase.
Meaningful outcomes of specialist leisure activities for children with complex disabilities: the views of parents, professionals and young people
Authors: Collins Bethan , McGrath Nicole , Astill Fiona , Hurt Lisa , Maguire Sabine , Kemp Alison
Published: November 2023

Leisure activities during childhood are vital to quality of life and wellbeing, however parents report poor quality of life and infrequent leisure participation for children with complex disabilities. Sparkle, a charity in South Wales, delivers specialist leisure activities aimed at providing children with disabilities with access to the same opportunities as any other child. We explored the impact of this provision on psychosocial domains of quality of life for children with complex disabilities.

Multi-source qualitative case studies including interviews and observations were conducted with: four children/young people - aged 8-15 years with diagnoses including autism, Down’s syndrome and cerebral palsy - accessing Sparkle’s leisure activities; their parents/carers and leisure staff supporting them. Data were analysed using coding reliability thematic analysis.

Three themes were generated: self-development, friendship and social interaction, and self and family wellbeing. An overarching theme of the need for a specialist provision enabled the other themes linked to positive outcomes for the children.

We concluded that a specialist provision contributes to positive psychosocial outcomes linked to leisure participation for children with complex disabilities. Limitations, future research and implications for policy and practice are discussed.
How optimal is Ghana's single-digit inflation targeting? An assessment of monetary policy effectiveness in Ghana
Authors: Amoatey Richard , Ayisi Richard K. , Osei-Assibey Eric
Published: November 2023

Purpose

The purpose of this study is twofold. First, to estimate an optimal inflation rate for Ghana and second, to investigate factors that account for the differences between observed and target inflation.

Design/methodology/approach

The paper explored the questions within two econometric frameworks, the Autoregressive Distributed Lag (ARDL) and Threshold Regression Models using data spanning the period 1965–2019.

Findings

The study estimated a range of 5–7% optimal inflation for Ghana. While this confirms the single-digit inflation targeting by the Bank of Ghana, the range is lower than the central bank's band of 6–10%. The combined behaviours of the central bank, banks and external outlook influence inflation target misses.

Practical implications

The study urges the central bank to continue pursuing its single-digit inflation targeting. However, it implies that there is still room for the Bank to further lower the current inflation band to achieve an optimal outcome on growth and welfare. Again, the Bank should commit to increased transparency and accountability to enhance its credibility in attaining the targeted inflation.

Originality/value

The study is one of the first attempts in Africa in Ghana to estimate an optimal inflation target and investigate the underlying factors for deviation from the targets.
The influence of brand personality on brand love, perceived quality and purchase intention: a study of e-retailing sites
Authors: Kukreti Rajat , Yadav Mayank
Published: November 2023

Purpose

This study aims to understand how brand personality affects purchase intention through brand love and perceived quality in e-commerce.

Design/methodology/approach

Three hundred forty-eight users of e-commerce sites in New Delhi, India, were surveyed for the study. The data set was examined using confirmatory factor analysis, and the research hypotheses were assessed using structural equation modeling.

Findings

Two important conclusions emerged from the study. First, brand love and perceived quality have been considerably and favorably influenced by all six dimensions of brand personality of e-commerce brands. Second, the purchase intention toward the e-commerce sites is significantly and positively impacted by brand love and perceived quality.

Practical implications

This study by exploring various dimensions of brand personality, will assist e-commerce executives in increasing purchase intention toward the e-retailing sites.

Originality/value

This research is supposed to be the foremost to look at how brand personality, through brand love and perceived quality affects purchase intention toward e-commerce websites. The attachment theory is used in this study as a theoretical foundation for linking e-commerce brand personality to customers’ purchase intentions via brand love and perceived quality.