bluuebunny/crossref_metadata_2025 huggingface dataset:
CaMKK2 facilitates Golgi-associated vesicle trafficking to sustain cancer cell proliferation
Authors: Stewart Lorna M. , Gerner Lisa , Rettel Mandy , Stein Frank , Burrows James F. , Mills Ian G. , Evergren Emma
Published: November 2021

Calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2) regulates cell and whole-body metabolism and supports tumorigenesis. The cellular impacts of perturbing CAMKK2 expression are, however, not yet fully characterised. By knocking down CAMKK2 levels, we have identified a number of significant subcellular changes indicative of perturbations in vesicle trafficking within the endomembrane compartment. To determine how they might contribute to effects on cell proliferation, we have used proteomics to identify Gemin4 as a direct interactor, capable of binding CAMKK2 and COPI subunits. Prompted by this, we confirmed that CAMKK2 knockdown leads to concomitant and significant reductions in δ-COP protein. Using imaging, we show that CAMKK2 knockdown leads to Golgi expansion, the induction of ER stress, abortive autophagy and impaired lysosomal acidification. All are phenotypes of COPI depletion. Based on our findings, we hypothesise that CAMKK2 sustains cell proliferation in large part through effects on organelle integrity and membrane trafficking.
Coexistence of structural and magnetic phases in van der Waals magnet CrI3
Authors: Meseguer-Sánchez Jaume , Popescu Catalin , García-Muñoz José Luis , Luetkens Hubertus , Taniashvili Grigol , Navarro-Moratalla Efrén , Guguchia Zurab , Santos Elton J. G.
Published: November 2021

CrI3 has raised as an important system to the emergent field of two-dimensional van der Waals magnetic materials. However, it is still unclear why CrI3 which has a ferromagnetic rhombohedral structure in bulk, changed to anti-ferromagnetic monoclinic at thin layers. Here we show that this behaviour is due to the coexistence of both monoclinic and rhombohedral crystal phases followed by three magnetic transitions at TC1 = 61 K, TC2 = 50 K and TC3 = 25 K. Each transition corresponds to a certain fraction of the magnetically ordered volume as well as monoclinic and rhombohedral proportion. The different phases are continuously accessed as a function of the temperature over a broad range of magnitudes. Our findings suggest that the challenge of understanding the magnetic properties of thin layers CrI3 is in general a coexisting structural-phase problem mediated by the volume-wise competition between magnetic phases already present in bulk.
A comparative analysis of cell surface targeting aptamers
Authors: Kelly Linsley , Maier Keith E. , Yan Amy , Levy Matthew
Published: November 2021

Aptamers represent a potentially important class of ligands for the development of diagnostics and therapeutics. However, it is often difficult to compare the function and specificity of many of these molecules as assay formats and conditions vary greatly. Here, with an interest in developing aptamer targeted therapeutics that could effectively deliver cargoes to cells, we chemically synthesize 15 aptamers that have been reported to target cell surface receptors or cells. Using standardized assay conditions, we assess each aptamer’s binding properties on a panel of 11 different cancer cell lines, correlate aptamer binding to antibody controls and use siRNA transfection to validate each aptamer’s binding to reported target receptors. Using a subset of these molecules known to be expressed on prostate cancers, we use near-infrared in vivo imaging to assess the tumor localization following intravenous injection. Our data demonstrate some surprising differences in the reported specificity and function for many of these molecules and raise concerns regarding their cell targeting capabilities. They also identify an anti-human transferrin aptamer, Waz, as a robust candidate for targeting prostate cancers and for future development of aptamer-based therapeutics.
Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo
Authors: Ibraheim Raed , Tai Phillip W. L. , Mir Aamir , Javeed Nida , Wang Jiaming , Rodríguez Tomás C. , Namkung Suk , Nelson Samantha , Khokhar Eraj Shafiq , Mintzer Esther , Maitland Stacy , Chen Zexiang , Cao Yueying , Tsagkaraki Emmanouela , Wolfe Scot A. , Wang Dan , Pai Athma A. , Xue Wen , Gao Guangping , Sontheimer Erik J.
Published: November 2021

Adeno-associated virus (AAV) vectors are important delivery platforms for therapeutic genome editing but are severely constrained by cargo limits. Simultaneous delivery of multiple vectors can limit dose and efficacy and increase safety risks. Here, we describe single-vector, ~4.8-kb AAV platforms that express Nme2Cas9 and either two sgRNAs for segmental deletions, or a single sgRNA with a homology-directed repair (HDR) template. We also use anti-CRISPR proteins to enable production of vectors that self-inactivate via Nme2Cas9 cleavage. We further introduce a nanopore-based sequencing platform that is designed to profile rAAV genomes and serves as a quality control measure for vector homogeneity. We demonstrate that these platforms can effectively treat two disease models [type I hereditary tyrosinemia (HT-I) and mucopolysaccharidosis type I (MPS-I)] in mice by HDR-based correction of the disease allele. These results will enable the engineering of single-vector AAVs that can achieve diverse therapeutic genome editing outcomes.
The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors
Authors: Gebregiworgis Teklab , Kano Yoshihito , St-Germain Jonathan , Radulovich Nikolina , Udaskin Molly L. , Mentes Ahmet , Huang Richard , Poon Betty P. K. , He Wenguang , Valencia-Sama Ivette , Robinson Claire M. , Huestis Melissa , Miao Jinmin , Yeh Jen Jen , Zhang Zhong-Yin , Irwin Meredith S. , Lee Jeffrey E. , Tsao Ming-Sound , Raught Brian , Marshall Christopher B. , Ohh Michael , Ikura Mitsuhiko
Published: November 2021

Cancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant.
Sustained enzymatic activity and flow in crowded protein droplets
Authors: Testa Andrea , Dindo Mirco , Rebane Aleksander A. , Nasouri Babak , Style Robert W. , Golestanian Ramin , Dufresne Eric R. , Laurino Paola
Published: November 2021

Living cells harvest energy from their environments to drive the chemical processes that enable life. We introduce a minimal system that operates at similar protein concentrations, metabolic densities, and length scales as living cells. This approach takes advantage of the tendency of phase-separated protein droplets to strongly partition enzymes, while presenting minimal barriers to transport of small molecules across their interface. By dispersing these microreactors in a reservoir of substrate-loaded buffer, we achieve steady states at metabolic densities that match those of the hungriest microorganisms. We further demonstrate the formation of steady pH gradients, capable of driving microscopic flows. Our approach enables the investigation of the function of diverse enzymes in environments that mimic cytoplasm, and provides a flexible platform for studying the collective behavior of matter driven far from equilibrium.
Microevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest
Authors: Thom Gregory , Gehara Marcelo , Smith Brian Tilston , Miyaki Cristina Y. , do Amaral Fábio Raposo
Published: November 2021

Tropical mountains hold more biodiversity than their temperate counterparts, and this disparity is often associated with the latitudinal climatic gradient. However, distinguishing the impact of latitude versus the background effects of species history and traits is challenging due to the evolutionary distance between tropical and temperate assemblages. Here, we test whether microevolutionary processes are linked to environmental variation across a sharp latitudinal transition in 21 montane birds of the southern Atlantic Forest in Brazil. We find that effective dispersal within populations in the tropical mountains is lower and genomic differentiation is better predicted by the current environmental complexity of the region than within the subtropical populations. The concordant response of multiple co-occurring populations is consistent with spatial climatic variability as a major process driving population differentiation. Our results provide evidence for how a narrow latitudinal gradient can shape microevolutionary processes and contribute to broader scale biodiversity patterns.
Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues
Authors: Paparella Ashleigh S. , Aboulache Briana L. , Harijan Rajesh K. , Potts Kathryn S. , Tyler Peter C. , Schramm Vern L.
Published: November 2021

Clostridium difficile causes life-threatening diarrhea and is the leading cause of healthcare-associated bacterial infections in the United States. TcdA and TcdB bacterial toxins are primary determinants of disease pathogenesis and are attractive therapeutic targets. TcdA and TcdB contain domains that use UDP-glucose to glucosylate and inactivate host Rho GTPases, resulting in cytoskeletal changes causing cell rounding and loss of intestinal integrity. Transition state analysis revealed glucocationic character for the TcdA and TcdB transition states. We identified transition state analogue inhibitors and characterized them by kinetic, thermodynamic and structural analysis. Iminosugars, isofagomine and noeuromycin mimic the transition state and inhibit both TcdA and TcdB by forming ternary complexes with Tcd and UDP, a product of the TcdA- and TcdB-catalyzed reactions. Both iminosugars prevent TcdA- and TcdB-induced cytotoxicity in cultured mammalian cells by preventing glucosylation of Rho GTPases. Iminosugar transition state analogues of the Tcd toxins show potential as therapeutics for C. difficile pathology.
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface
Authors: Hunter Miranda V. , Moncada Reuben , Weiss Joshua M. , Yanai Itai , White Richard M.
Published: November 2021

During tumor progression, cancer cells come into contact with various non-tumor cell types, but it is unclear how tumors adapt to these new environments. Here, we integrate spatially resolved transcriptomics, single-cell RNA-seq, and single-nucleus RNA-seq to characterize tumor-microenvironment interactions at the tumor boundary. Using a zebrafish model of melanoma, we identify a distinct “interface” cell state where the tumor contacts neighboring tissues. This interface is composed of specialized tumor and microenvironment cells that upregulate a common set of cilia genes, and cilia proteins are enriched only where the tumor contacts the microenvironment. Cilia gene expression is regulated by ETS-family transcription factors, which normally act to suppress cilia genes outside of the interface. A cilia-enriched interface is conserved in human patient samples, suggesting it is a conserved feature of human melanoma. Our results demonstrate the power of spatially resolved transcriptomics in uncovering mechanisms that allow tumors to adapt to new environments.
Structural insights into the clustering and activation of Tie2 receptor mediated by Tie2 agonistic antibody
Authors: Jo Gyunghee , Bae Jeomil , Hong Ho Jeong , Han Ah-reum , Kim Do-Kyun , Hong Seon Pyo , Kim Jung A , Lee Sangkyu , Koh Gou Young , Kim Ho Min
Published: November 2021

Angiopoietin (Angpt)-Tie receptor 2 (Tie2) plays key roles in vascular development and homeostasis as well as pathological vascular remodeling. Therefore, Tie2-agonistic antibody and engineered Angpt1 variants have been developed as potential therapeutics for ischemic and inflammatory vascular diseases. However, their underlying mechanisms for Tie2 clustering and activation remain elusive and the poor manufacturability and stability of Angpt1 variants limit their clinical application. Here, we develop a human Tie2-agonistic antibody (hTAAB), which targets the membrane proximal fibronectin type III domain of Tie2 distinct from the Angpt-binding site. Our Tie2/hTAAB complex structures reveal that hTAAB tethers the preformed Tie2 homodimers into polygonal assemblies through specific binding to Tie2 Fn3 domain. Notably, the polygonal Tie2 clustering induced by hTAAB is critical for Tie2 activation and are resistant to antagonism by Angpt2. Our results provide insight into the molecular mechanism of Tie2 clustering and activation mediated by hTAAB, and the structure-based humanization of hTAAB creates a potential clinical application.
Nuclear S-nitrosylation impacts tissue regeneration in zebrafish
Authors: Matrone Gianfranco , Jung Sung Yun , Choi Jong Min , Jain Antrix , Leung Hon-Chiu Eastwood , Rajapakshe Kimal , Coarfa Cristian , Rodor Julie , Denvir Martin A. , Baker Andrew H. , Cooke John P.
Published: November 2021

Despite the importance of nitric oxide signaling in multiple biological processes, its role in tissue regeneration remains largely unexplored. Here, we provide evidence that inducible nitric oxide synthase (iNos) translocates to the nucleus during zebrafish tailfin regeneration and is associated with alterations in the nuclear S-nitrosylated proteome. iNos inhibitors or nitric oxide scavengers reduce protein S-nitrosylation and impair tailfin regeneration. Liquid chromatography/tandem mass spectrometry reveals an increase of up to 11-fold in the number of S-nitrosylated proteins during regeneration. Among these, Kdm1a, a well-known epigenetic modifier, is S-nitrosylated on Cys334. This alters Kdm1a binding to the CoRest complex, thus impairing its H3K4 demethylase activity, which is a response specific to the endothelial compartment. Rescue experiments show S-nitrosylation is essential for tailfin regeneration, and we identify downstream endothelial targets of Kdm1a S-nitrosylation. In this work, we define S-nitrosylation as an essential post-translational modification in tissue regeneration.
The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model
Authors: Jašarević Eldin , Hill Elizabeth M. , Kane Patrick J. , Rutt Lindsay , Gyles Trevonn , Folts Lillian , Rock Kylie D. , Howard Christopher D. , Morrison Kathleen E. , Ravel Jacques , Bale Tracy L.
Published: November 2021

Newborns are colonized by maternal microbiota that is essential for offspring health and development. The composition of these pioneer communities exhibits individual differences, but the importance of this early-life heterogeneity to health outcomes is not understood. Here we validate a human microbiota-associated model in which fetal mice are cesarean delivered and gavaged with defined human vaginal microbial communities. This model replicates the inoculation that occurs during vaginal birth and reveals lasting effects on offspring metabolism, immunity, and the brain in a community-specific manner. This microbial effect is amplified by prior gestation in a maternal obesogenic or vaginal dysbiotic environment where placental and fetal ileum development are altered, and an augmented immune response increases rates of offspring mortality. Collectively, we describe a translationally relevant model to examine the defined role of specific human microbial communities on offspring health outcomes, and demonstrate that the prenatal environment dramatically shapes the postnatal response to inoculation.
Bridging the gap between in silico and in vivo by modeling opioid disposition in a kidney proximal tubule microphysiological system
Authors: Imaoka Tomoki , Huang Weize , Shum Sara , Hailey Dale W. , Chang Shih-Yu , Chapron Alenka , Yeung Catherine K. , Himmelfarb Jonathan , Isoherranen Nina , Kelly Edward J.
Published: November 2021

Opioid overdose, dependence, and addiction are a major public health crisis. Patients with chronic kidney disease (CKD) are at high risk of opioid overdose, therefore novel methods that provide accurate prediction of renal clearance (CLr) and systemic disposition of opioids in CKD patients can facilitate the optimization of therapeutic regimens. The present study aimed to predict renal clearance and systemic disposition of morphine and its active metabolite morphine-6-glucuronide (M6G) in CKD patients using a vascularized human proximal tubule microphysiological system (VPT-MPS) coupled with a parent-metabolite full body physiologically-based pharmacokinetic (PBPK) model. The VPT-MPS, populated with a human umbilical vein endothelial cell (HUVEC) channel and an adjacent human primary proximal tubular epithelial cells (PTEC) channel, successfully demonstrated secretory transport of morphine and M6G from the HUVEC channel into the PTEC channel. The in vitro data generated by VPT-MPS were incorporated into a mechanistic kidney model and parent-metabolite full body PBPK model to predict CLr and systemic disposition of morphine and M6G, resulting in successful prediction of CLr and the plasma concentration–time profiles in both healthy subjects and CKD patients. A microphysiological system together with mathematical modeling successfully predicted renal clearance and systemic disposition of opioids in CKD patients and healthy subjects.
Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations
Authors: Gunadi  , Hakim Mohamad Saifudin , Wibawa Hendra , Marcellus  , Trisnawati Ika , Supriyati Endah , Afiahayati  , Khair Riat El , Iskandar Kristy , Siswanto  , Irene  , Anggorowati Nungki , Daniwijaya Edwin Widyanto , Nugrahaningsih Dwi Aris Agung , Puspadewi Yunika , Simanjaya Susan , Puspitarani Dyah Ayu , Hanifin Hana Fauzyyah , Setiawan Alvina Alexandra , Tania Irene , Amalia Cita Shafira , Artayasa I. Putu Aditio , Rachman Haries , Mulyawan Herdiyanto , Ananda Nur Rahmi , Arguni Eggi , Nuryastuti Titik , Wibawa Tri
Published: November 2021

The outcome of SARS-CoV-2 infection is determined by multiple factors, including the viral, host genetics, age, and comorbidities. This study investigated the association between prognostic factors and disease outcomes of patients infected by SARS-CoV-2 with multiple S protein mutations. Fifty-one COVID-19 patients were recruited in this study. Whole-genome sequencing of 170 full-genomes of SARS-CoV-2 was conducted with the Illumina MiSeq sequencer. Most patients (47%) had mild symptoms of COVID-19 followed by moderate (19.6%), no symptoms (13.7%), severe (4%), and critical (2%). Mortality was found in 13.7% of the COVID-19 patients. There was a significant difference between the age of hospitalized patients (53.4 ± 18 years) and the age of non-hospitalized patients (34.6 ± 19) (p = 0.001). The patients’ hospitalization was strongly associated with hypertension, diabetes, and anticoagulant and were strongly significant with the OR of 17 (95% CI 2–144; p = 0.001), 4.47 (95% CI 1.07–18.58; p = 0.039), and 27.97 (95% CI 1.54–507.13; p = 0.02), respectively; while the patients’ mortality was significantly correlated with patients’ age, anticoagulant, steroid, and diabetes, with OR of 8.44 (95% CI 1.5–47.49; p = 0.016), 46.8 (95% CI 4.63–472.77; p = 0.001), 15.75 (95% CI 2–123.86; p = 0.009), and 8.5 (95% CI 1.43–50.66; p = 0.019), respectively. This study found the clade: L (2%), GH (84.3%), GR (11.7%), and O (2%). Besides the D614G mutation, we found L5F (18.8%), V213A (18.8%), and S689R (8.3%). No significant association between multiple S protein mutations and the patients’ hospitalization or mortality. Multivariate analysis revealed that hypertension and anticoagulant were the significant factors influencing the hospitalization and mortality of patients with COVID-19 with an OR of 17.06 (95% CI 2.02–144.36; p = 0.009) and 46.8 (95% CI 4.63–472.77; p = 0.001), respectively. Moreover, the multiple S protein mutations almost reached a strong association with patients’ hospitalization (p = 0.07). We concluded that hypertension and anticoagulant therapy have a significant impact on COVID-19 outcomes. This study also suggests that multiple S protein mutations may impact the COVID-19 outcomes. This further emphasized the significance of monitoring SARS-CoV-2 variants through genomic surveillance, particularly those that may impact the COVID-19 outcomes.
Intrinsic timescales across the basal ganglia
Authors: Nougaret Simon , Fascianelli Valeria , Ravel Sabrina , Genovesio Aldo
Published: November 2021

Recent studies have shown that temporal stability of the neuronal activity over time can be estimated by the structure of the spike-count autocorrelation of neuronal populations. This estimation, called the intrinsic timescale, has been computed for several cortical areas and can be used to propose a cortical hierarchy reflecting a scale of temporal receptive windows between areas. In this study, we performed an autocorrelation analysis on neuronal populations of three basal ganglia (BG) nuclei, including the striatum and the subthalamic nucleus (STN), the input structures of the BG, and the external globus pallidus (GPe). The analysis was performed during the baseline period of a motivational visuomotor task in which monkeys had to apply different amounts of force to receive different amounts of reward. We found that the striatum and the STN have longer intrinsic timescales than the GPe. Moreover, our results allow for the placement of these subcortical structures within the already-defined scale of cortical temporal receptive windows. Estimates of intrinsic timescales are important in adding further constraints in the development of computational models of the complex dynamics among these nuclei and throughout cortico-BG-thalamo-cortical loops.
Synbiotic (Lactiplantibacillus pentosus GSSK2 and isomalto-oligosaccharides) supplementation modulates pathophysiology and gut dysbiosis in experimental metabolic syndrome
Authors: Khanna Sakshi , Bishnoi Mahendra , Kondepudi Kanthi Kiran , Shukla Geeta
Published: November 2021

Metabolic syndrome a lifestyle disease, where diet and gut microbiota play a prodigious role in its initiation and progression. Prophylactic bio-interventions employing probiotics and prebiotics offer an alternate nutritional approach towards attenuating its progression. The present study aimed to evaluate the protective efficacy of a novel synbiotic (Lactiplantibacillus pentosus GSSK2 + isomalto-oligosaccharides) in comparison to orlistat in an experimental model of metabolic syndrome. It was observed that supplementation of synbiotic for 12 weeks to Sprague Dawley rats fed with high fat diet (HFD), ameliorated the morphometric parameters i.e. weight gain, abdominal circumference, Lee’s index, BMI and visceral fat deposition along with significantly increased fecal Bacteroidetes to Firmicutes ratio, elevated population of Lactobacillus spp., Akkermansia spp., Faecalibacterium spp., Roseburia spp. and decreased Enterobacteriaceae compared with HFD animals. Additionally, synbiotic administration to HFD animals exhibited improved glucose clearance, lipid biomarkers, alleviated oxidative stress, prevented leaky gut phenotype, reduced serum lipopolysaccharides and modulated the inflammatory, lipid and glucose metabolism genes along with restored histomorphology of adipose tissue, colon and liver compared with HFD animals. Taken together, the study highlights the protective potential of synbiotic in comparison with its individual components in ameliorating HFD-induced metabolic complications.
Gait performance of adolescent mice assessed by the CatWalk XT depends on age, strain and sex and correlates with speed and body weight
Authors: Pitzer Claudia , Kurpiers Barbara , Eltokhi Ahmed
Published: November 2021

The automatization of behavioral tests assessing motor activity in rodent models is important for providing robust and reproducible results and evaluating new therapeutics. The CatWalk system is an observer-independent, automated and computerized technique for the assessment of gait performance in rodents. This method has previously been used in adult rodent models of CNS-based movement disorders such as Parkinson’s and Huntington’s diseases. As motor and gait abnormalities in neuropsychiatric disorders are observed during infancy and adolescence, it became important to validate the CatWalk XT in the gait analysis of adolescent mice and unravel factors that may cause variations in gait performance. Three adolescent wild-type inbred mouse strains, C57BL/6N, DBA/2 and FVB/N, were tested using the CatWalk XT (Version 10.6) for suitable detection settings to characterize several gait parameters at P32 and P42. The same detection settings being suitable for C57BL/6N and DBA/2 mice allowed a direct comparison between the two strains. On the other hand, due to their increased body weight and size, FVB/N mice required different detection settings. The CatWalk XT reliably measured the temporal, spatial, and interlimb coordination parameters in the investigated strains during adolescence. Additionally, significant effects of sex, development, speed and body weight within each strain confirmed the sensitivity of motor and gait functions to these factors. The CatWalk gait analysis of rodents during adolescence, taking the effect of age, strain, sex, speed and body weight into consideration, will decrease intra-laboratory discrepancies and increase the face validity of rodent models of neuropsychiatric disorders.
Women and other risk factors for chronic kidney disease of unknown etiology in Thailand: National Health Examination V Survey
Authors: Aekplakorn Wichai , Chariyalertsak Suwat , Kessomboon Pattapong , Assanangkornchai Sawitri , Taneepanichskul Surasak , Neelapaichit Nareemarn , Chittamma Anchalee , Kitiyakara Chagriya
Published: November 2021

There are limited data on chronic kidney disease of unknown etiology (CKDu) from Southeast Asia. Initially described in working age men, a common approach to detect CKDu that includes all adults has recently been proposed. We determined the prevalence, and risk factors for CKDu using data from a cross-sectional, nationally representative survey of the adult population of Thailand. We used a proxy for CKDu as age < 70 with impaired kidney function (eGFR < 60) in the absence of diabetes and hypertension (CKDu1) and heavy proteinuria (CKDu2). Prevalence estimates were probability-weighted for the Thai population. The associations between risk factors and CKDu or elderly subjects with eGFR < 60 without traditional causes were assessed by multivariable logistic regression. Of 17,329 subjects, the prevalence were: eGFR < 60, 5.3%; CKDu1 0.78%; CKDu2, 0.75%. CKDu differed by 4.3-folds between regions. Women, farmers/laborers, older age, gout, painkillers, rural area, and stones were independent risk factors for CKDu. Women, age, rural, gout, painkillers were significant risk factors for both CKDu and elderly subjects. These data collected using standardized methodology showed that the prevalence of CKDu in Thailand was low overall, although some regions had higher risk. Unlike other countries, Thai women had a two-fold higher risk of CKDu.
Probabilistic modelling of effects of antibiotics and calendar time on transmission of healthcare-associated infection
Authors: Laager Mirjam , Cooper Ben S. , Eyre David W. ,   the CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare)
Published: November 2021

Healthcare-associated infection and antimicrobial resistance are major concerns. However, the extent to which antibiotic exposure affects transmission and detection of infections such as MRSA is unclear. Additionally, temporal trends are typically reported in terms of changes in incidence, rather than analysing underling transmission processes. We present a data-augmented Markov chain Monte Carlo approach for inferring changing transmission parameters over time, screening test sensitivity, and the effect of antibiotics on detection and transmission. We expand a basic model to allow use of typing information when inferring sources of infections. Using simulated data, we show that the algorithms are accurate, well-calibrated and able to identify antibiotic effects in sufficiently large datasets. We apply the models to study MRSA transmission in an intensive care unit in Oxford, UK with 7924 admissions over 10 years. We find that falls in MRSA incidence over time were associated with decreases in both the number of patients admitted to the ICU colonised with MRSA and in transmission rates. In our inference model, the data were not informative about the effect of antibiotics on risk of transmission or acquisition of MRSA, a consequence of the limited number of possible transmission events in the data. Our approach has potential to be applied to a range of healthcare-associated infections and settings and could be applied to study the impact of other potential risk factors for transmission. Evidence generated could be used to direct infection control interventions.
Development of surface engineered antigenic exosomes as vaccines for respiratory syncytial virus
Authors: Hong Suyeon , Ruan Shaobo , Greenberg Zachary , He Mei , McGill Jodi L.
Published: November 2021

Respiratory syncytial virus (RSV) is one of the main pathogens associated with lower respiratory tract infections in infants and young children worldwide. Exosomes secreted by antigen presenting cells (APCs) can elicit immune responses by carrying major histocompatibility complex (MHC) class I molecules complexed with antigenic peptides and other co-stimulating factors. Therefore, we developed novel immunomagnetic nanographene particles to sequentially isolate, surface engineer, and release intact dendritic cell (DC) exosomes for use as a potential vaccine platform against RSV. The H-2Db-restricted, immunodominant peptides from RSV (M187–195 and NS161–75) were introduced to MHC-I on DC-derived exosomes to express peptide/MHC-I (pMHC-I) complexes. A mouse model of RSV infection was used to define the immunogenicity of surface engineered exosomes for activating virus-specific immune responses. Ex vivo assays demonstrated that engineered exosomes carrying RSV-specific peptides can elicit interferon-gamma (IFN-γ) production by virus-specific CD8+ T cells isolated from RSV-infected C57BL/6 mice. In vivo assays demonstrated that subcutaneous administration of both M187–195 and NS161–75 engineered exosomes to mice, with or without additional adjuvant, appeared safe and well tolerated, however, did not prime antigen-specific CD8+ T cell responses. Surface engineered exosomes are immunogenic and promising for further development as a vaccine platform.
Prediction of primary venous thromboembolism based on clinical and genetic factors within the U.K. Biobank
Authors: Kolin David A. , Kulm Scott , Elemento Olivier
Published: November 2021

Both clinical and genetic factors drive the risk of venous thromboembolism. However, whether clinically recorded risk factors and genetic variants can be combined into a clinically applicable predictive score remains unknown. Using Cox proportional-hazard models, we analyzed the association of risk factors with the likelihood of venous thromboembolism in U.K. Biobank, a large prospective cohort. We then created a polygenic risk score of 36 single nucleotide polymorphisms and a clinical score determined by age, sex, body mass index, previous cancer diagnosis, smoking status, and fracture in the last 5 years. Participants were at significantly increased risk of venous thromboembolism if they were at high clinical risk (subhazard ratio, 4.37 [95% CI, 3.85–4.97]) or high genetic risk (subhazard ratio, 3.02 [95% CI, 2.63–3.47]) relative to participants at low clinical or genetic risk, respectively. The combined model, consisting of clinical and genetic components, was significantly better than either the clinical or the genetic model alone (P < 0.001). Participants at high risk in the combined score had nearly an eightfold increased risk of venous thromboembolism relative to participants at low risk (subhazard ratio, 7.51 [95% CI, 6.28–8.98]). This risk score can be used to guide decisions regarding venous thromboembolism prophylaxis, although external validation is needed.
Poly(N,N-dimethylacrylamide)-coated upconverting NaYF4:Yb,Er@NaYF4:Nd core–shell nanoparticles for fluorescent labeling of carcinoma cells
Authors: Oleksa Viktoriia , Macková Hana , Engstová Hana , Patsula Vitalii , Shapoval Oleksandr , Velychkivska Nadiia , Ježek Petr , Horák Daniel
Published: November 2021

Upconverting luminescent lanthanide-doped nanoparticles (UCNP) belong to promising new materials that absorb infrared light able to penetrate in the deep tissue level, while emitting photons in the visible or ultraviolet region, which makes them favorable for bioimaging and cell labeling. Here, we have prepared upconverting NaYF4:Yb,Er@NaYF4:Nd core–shell nanoparticles, which were coated with copolymers of N,N-dimethylacrylamide (DMA) and 2-(acryloylamino)-2-methylpropane-1-sulfonic acid (AMPS) or tert-butyl [2-(acryloylamino)ethyl]carbamate (AEC-Boc) with negative or positive charges, respectively. The copolymers were synthesized by a reversible addition-fragmentation chain transfer (RAFT) polymerization, reaching Mn ~ 11 kDa and containing ~ 5 mol% of reactive groups. All copolymers contained bisphosphonate end-groups to be firmly anchored on the surface of NaYF4:Yb,Er@NaYF4:Nd core–shell nanoparticles. To compare properties of polymer coatings, poly(ethylene glycol)-coated and neat UCNP were used as a control. UCNP with various charges were then studied as labels of carcinoma cells, including human hepatocellular carcinoma HepG2, human cervical cancer HeLa, and rat insulinoma INS-1E cells. All the particles proved to be biocompatible (nontoxic); depending on their ξ-potential, the ability to penetrate the cells differed. This ability together with the upconversion luminescence are basic prerequisites for application of particles in photodynamic therapy (PDT) of various tumors, where emission of nanoparticles in visible light range at ~ 650 nm excites photosensitizer.
No aftereffects of high current density 10 Hz and 20 Hz tACS on sensorimotor alpha and beta oscillations
Authors: Lafleur Louis-Philippe , Murray Audrey , Desforges Manon , Pacheco-Barrios Kevin , Fregni Felipe , Tremblay Sara , Saint-Amour Dave , Lepage Jean-François , Théoret Hugo
Published: November 2021

Application of transcranial alternating current stimulation (tACS) is thought to modulate ongoing brain oscillations in a frequency-dependent manner. However, recent studies report various and sometimes inconsistent results regarding its capacity to induce changes in cortical activity beyond the stimulation period. Here, thirty healthy volunteers participated in a randomized, cross-over, sham-controlled, double-blind study using EEG to measure the offline effects of tACS on alpha and beta power. Sham and high current density tACS (1 mA; 10 Hz and 20 Hz; 0.32 mA/cm2) were applied for 20 min over bilateral sensorimotor areas and EEG was recorded at rest before and after stimulation for 20 min. Bilateral tACS was not associated with significant changes in local alpha and beta power frequencies at stimulation sites (C3 and C4 electrodes). Overall, the present results fail to provide evidence that bilateral tACS with high current density applied over sensorimotor regions at 10 and 20 Hz reliably modulates offline brain oscillation power at the stimulation site. These results may have implications for the design and implementation of future protocols aiming to induce sustained changes in brain activity, including in clinical populations.
Effect of Au substrate and coating on the lasing characteristics of GaAs nanowires
Authors: Aman Gyanan , Mohammadi Fatemesadat , Fränzl Martin , Lysevych Mykhaylo , Tan Hark Hoe , Jagadish Chennupati , Schmitzer Heidrun , Cahay Marc , Wagner Hans Peter
Published: November 2021

Optically pumped lasing from highly Zn-doped GaAs nanowires lying on an Au film substrate and from Au-coated nanowires has been demonstrated up to room temperature. The conically shaped GaAs nanowires were first coated with a 5 nm thick Al2O3 shell to suppress atmospheric oxidation and band-bending effects. Doping with a high Zn concentration increases both the radiative efficiency and the material gain and leads to lasing up to room temperature. A detailed analysis of the observed lasing behavior, using finite-difference time domain simulations, reveals that the lasing occurs from low loss hybrid modes with predominately photonic character combined with electric field enhancement effects. Achieving low loss lasing from NWs on an Au film and from Au coated nanowires opens new prospects for on-chip integration of nanolasers with new functionalities including electro-optical modulation, conductive shielding, and polarization control.
EZH1/2 inhibition augments the anti-tumor effects of sorafenib in hepatocellular carcinoma
Authors: Kusakabe Yuko , Chiba Tetsuhiro , Oshima Motohiko , Koide Shuhei , Rizq Ola , Aoyama Kazumasa , Ao Junjie , Kaneko Tatsuya , Kanzaki Hiroaki , Kanayama Kengo , Maeda Takahiro , Saito Tomoko , Nakagawa Ryo , Kobayashi Kazufumi , Kiyono Soichiro , Nakamura Masato , Ogasawara Sadahisa , Suzuki Eiichiro , Nakamoto Shingo , Yasui Shin , Mikata Rintaro , Muroyama Ryosuke , Kanda Tatsuo , Maruyama Hitoshi , Kato Jun , Mimura Naoya , Ma Anqi , Jin Jian , Zen Yoh , Otsuka Masayuki , Kaneda Atsushi , Iwama Atsushi , Kato Naoya
Published: November 2021

Both EZH2 and its homolog EZH1 function as histone H3 Lysine 27 (H3K27) methyltransferases and repress the transcription of target genes. Dysregulation of H3K27 trimethylation (H3K27me3) plays an important role in the development and progression of cancers such as hepatocellular carcinoma (HCC). This study investigated the relationship between the expression of EZH1/2 and the level of H3K27me3 in HCC. Additionally, the role of EZH1/2 in cell growth, tumorigenicity, and resistance to sorafenib were also analyzed. Both the lentiviral knockdown and the pharmacological inhibition of EZH1/2 (UNC1999) diminished the level of H3K27me3 and suppressed cell growth in liver cancer cells, compared with EZH1 or EZH2 single knockdown. Although a significant association was observed between EZH2 expression and H3K27me3 levels in HCC samples, overexpression of EZH1 appeared to contribute to enhanced H3K27me3 levels in some EZH2lowH3K27me3high cases. Akt suppression following sorafenib treatment resulted in an increase of the H3K27me3 levels through a decrease in EZH2 phosphorylation at serine 21. The combined use of sorafenib and UNC1999 exhibited synergistic antitumor effects in vitro and in vivo. Combination treatment canceled the sorafenib-induced enhancement in H3K27me3 levels, indicating that activation of EZH2 function is one of the mechanisms of sorafenib-resistance in HCC. In conclusion, sorafenib plus EZH1/2 inhibitors may comprise a novel therapeutic approach in HCC.
Practical approach to detection and surveillance of emerging highly resistant Mycobacterium tuberculosis Beijing 1071-32-cluster
Authors: Mokrousov Igor , Vyazovaya Anna , Sinkov Viacheslav , Gerasimova Alena , Ioannidis Panayotis , Jiao Weiwei , Khromova Polina , Papaventsis Dimitrios , Pasechnik Oksana , Perdigão João , Rastogi Nalin , Shen Adong , Skiba Yuriy , Solovieva Natalia , Suffys Philip , Tafaj Silva , Umpeleva Tatiana , Vakhrusheva Diana , Yarusova Irina , Zhdanova Svetlana , Zhuravlev Viacheslav , Ogarkov Oleg
Published: November 2021

Ancient sublineage of the Mycobacterium tuberculosis Beijing genotype is endemic and prevalent in East Asia and rare in other world regions. While these strains are mainly drug susceptible, we recently identified a novel clonal group Beijing 1071-32 within this sublineage emerging in Siberia, Russia and present in other Russian regions. This cluster included only multi/extensive drug resistant (MDR/XDR) isolates. Based on the phylogenetic analysis of the available WGS data, we identified three synonymous SNPs in the genes Rv0144, Rv0373c, and Rv0334 that were specific for the Beijing 1071-32-cluster and developed a real-time PCR assay for their detection. Analysis of the 2375 genetically diverse M. tuberculosis isolates collected between 1996 and 2020 in different locations (European and Asian parts of Russia, former Soviet Union countries, Albania, Greece, China, Vietnam, Japan and Brazil), confirmed 100% specificity and sensitivity of this real-time PCR assay. Moreover, the epidemiological importance of this strain and the newly developed screening assay is further stressed by the fact that all identified Beijing 1071-32 isolates were found to exhibit MDR genotypic profiles with concomitant resistance to additional first-line drugs due to a characteristic signature of six mutations in rpoB450, rpoC485, katG315, katG335, rpsL43 and embB497. In conclusion, this study provides a set of three concordant SNPs for the detection and screening of Beijing 1071-32 isolates along with a validated real-time PCR assay easily deployable across multiple settings for the epidemiological tracking of this significant MDR cluster.
Accuracy of high-frequency oscillations recorded intraoperatively for classification of epileptogenic regions
Authors: Weiss Shennan A. , Staba Richard J. , Sharan Ashwini , Wu Chengyuan , Rubinstein Daniel , Das Sandhitsu , Waldman Zachary , Orosz Iren , Worrell Gregory , Engel Jerome , Sperling Michael R.
Published: November 2021

To see whether acute intraoperative recordings using stereo EEG (SEEG) electrodes can replace prolonged interictal intracranial EEG (iEEG) recording, making the process more efficient and safer, 10 min of iEEG were recorded following electrode implantation in 16 anesthetized patients, and 1–2 days later during non-rapid eye movement (REM) sleep. Ripples on oscillations (RonO, 80–250 Hz), ripples on spikes (RonS), sharp-spikes, fast RonO (fRonO, 250–600 Hz), and fast RonS (fRonS) were semi-automatically detected. HFO power and frequency were compared between the conditions using a generalized linear mixed-effects model. HFO rates were compared using a two-way repeated measures ANOVA with anesthesia type and SOZ as factors. A receiver-operating characteristic (ROC) curve analysis quantified seizure onset zone (SOZ) classification accuracy, and the scalar product was used to assess spatial reliability. Resection of contacts with the highest rate of events was compared with outcome. During sleep, all HFOs, except fRonO, were larger in amplitude compared to intraoperatively (p < 0.01). HFO frequency was also affected (p < 0.01). Anesthesia selection affected HFO and sharp-spike rates. In both conditions combined, sharp-spikes and all HFO subtypes were increased in the SOZ (p < 0.01). However, the increases were larger during the sleep recordings (p < 0.05). The area under the ROC curves for SOZ classification were significantly smaller for intraoperative sharp-spikes, fRonO, and fRonS rates (p < 0.05). HFOs and spikes were only significantly spatially reliable for a subset of the patients (p < 0.05). A failure to resect fRonO areas in the sleep recordings trended the most sensitive and accurate for predicting failure. In summary, HFO morphology is altered by anesthesia. Intraoperative SEEG recordings exhibit increased rates of HFOs in the SOZ, but their spatial distribution can differ from sleep recordings. Recording these biomarkers during non-REM sleep offers a more accurate delineation of the SOZ and possibly the epileptogenic zone.
Maternal vaccination with a type-III glycoconjugate protects mouse neonates against Group B Streptococcus intranasal infection
Authors: Chiarot Emiliano , Naimo Eleonora , Corrado Alessia , Giannetti Patrizia , Ros Immaculada Margarit Y. , Bensi Giuliano
Published: November 2021

Group B Streptococcus (GBS) is generally an asymptomatic colonizer of human mucosa but it occasionally infects pregnant women and neonates through vertical transmission, causing disease during the first weeks of life with frequent and severe complications. Preclinical studies have shown that maternal vaccination with polysaccharide-based vaccines protects mothers and offspring from GBS mucosal colonization and consecutive infection. In these models, bacteria were inoculated in mouse either intravaginally in the last trimester of pregnancy or systemically in pups. Here, we investigated whether maternal vaccination with glycoconjugate vaccines may also prevent GBS-mediated colonization and disease in neonates using an infection route that more closely mimics inhalation or ingestion of bacteria during human delivery. To address this point, mice aged less than two days were intranasally challenged with epidemiologically relevant GBS strains. Bacteria were found to colonize nose and intestine, reaching in some cases lungs and blood during the first days of life. Bacteria were also found in vagina of a fraction of colonized female mice within the first month of life. GBS-specific IgG induced by maternal vaccination with a glycoconjugate vaccine formulation were found in blood and mucosal tissues of newborns. Finally, when intranasally challenged with GBS serotype III strains, pups delivered by vaccinated mothers were partially protected against mucosal colonization and deeper infection.
Strain induced localization to delocalization transition on a Lieb photonic ribbon lattice
Authors: Román-Cortés Diego , Fadic Guillermo , Cid-Lara Christofer , Guzmán-Silva Diego , Real Bastián , Vicencio Rodrigo A.
Published: November 2021

Ribbon lattices are kind of transition systems in between one and two dimensions, and their study is crucial to understand the origin of different emerging properties. In this work, we study a Lieb ribbon lattice and the localization–delocalization transition occurring due to a reduction of lattice distances (compression) and the corresponding flat band deformation. We observe how above a critical compression ratio the energy spreads out and propagates freely across the lattice, therefore transforming the system from being a kind of insulator into a conductor. We implement an experiment on a photonic platform and show an excellent agreement with the predicted phenomenology. Our findings suggest and prove experimentally the use of compression or mechanical deformation of lattices to switch the transport properties of a given system.