bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbapenem heteroresistance of KPC-producing Klebsiella pneumoniae results from tolerance, persistence and resistance
Authors: Chiarelli Adriana , Cabanel Nicolas , Rosinski-Chupin Isabelle , Obadia Thomas , Ruimy Raymond , Naas Thierry , Bonnin Rémy A. , Glaser Philippe
Published: May 2022

Carbapenemase-producing Klebsiella pneumoniae (CPKp) have disseminated globally and represent a major threat in hospitals with few therapeutic options and high mortality rates. Isolates producing the carbapenemase KPC (KPC-Kp) might be classified as susceptible according to clinical breakpoints by antibiotic susceptibility testing (AST), allowing the use of imipenem or meropenem for treatment of infections. However, some KPC-Kp show heteroresistance (HR) to carbapenems, with colonies growing in the inhibition halo of agar-based AST. HR KPC-Kp have been associated with a higher risk of treatment failure. Here, we characterized the diversity of mechanisms behind HR to imipenem of these isolates. By analyzing a diverse collection of CPKp, we showed that HR is frequent among KPC-Kp. By monitoring single HR colony appearance using the ScanLag setup, we discriminated surviving cells in two subpopulations leading to a Gaussian-like distribution of early-appearing colonies, with a delayed emergence compared to colonies arising in the absence of antibiotics, and a long tail of late-appearing colonies. A subset of colonies showed a reduced growth rate. Characterization of surviving populations by AST and whole-genome sequencing of 333 colonies revealed a majority of parental genotypes and a broad landscape of genetic alterations in 28% of the colonies, including gene loss, DNA amplification and point mutations. This unveils the complexity of imipenem HR among KPC-Kp isolates, which involves tolerant and persistent cells, but also resistant bacteria. These observations contribute to a better understanding of reasons behind carbapenem treatment failure of KPC-Kp isolates.

IMPORTANCE

The ability of a bacterium to defeat antibiotics not only depends upon resistance, but also on tolerance and persistence, which allow a bacterial population to temporarily survive high drug doses. Carbapenems are antibiotics of last resort and Klebsiella pneumoniae isolates producing the carbapenemase KPC are a threat to hospitals, although they might remain susceptible to carbapenems. However, seemingly homogeneous populations of KPC-K. pneumoniae isolates frequently show varying degrees of susceptibility to carbapenem, i.e., a phenomenon called heteroresistance. We characterized bacteria surviving a high dose of imipenem, progressively degraded by the released carbapenemase, by monitoring the growth of the resulting colonies using the ScanLag system, their genome sequence and carbapenem susceptibility. We show that the observed phenotypic diversity combines tolerance, persistence and resistance making the treatment with high doses of carbapenems frequently inefficient.
Space-time resolved inference-based whole-brain neurophysiological mechanism imaging: application to resting-state alpha rhythm
Authors: Zhao Yun , Boley Mario , Pelentritou Andria , Karoly Philippa J. , Freestone Dean R. , Liu Yueyang , Muthukumaraswamy Suresh , Woods William , Liley David , Kuhlmann Levin
Published: May 2022

Neural mechanisms are complex and difficult to image. This paper presents a new space-time resolved whole-brain imaging framework, called Neurophysiological Mechanism Imaging (NMI), that identifies neurophysiological mechanisms within cerebral cortex at the macroscopic scale. By fitting neural mass models to electromagnetic source imaging data using a novel nonlinear inference method, population averaged membrane potentials and synaptic connection strengths are efficiently and accurately imaged across the whole brain at a resolution afforded by source imaging. The efficiency of the framework enables return of the augmented source imaging results overnight using high performance computing. This suggests it can be used as a practical and novel imaging tool. To demonstrate the framework, it has been applied to resting-state magnetoencephalographic source estimates. The results suggest that endogenous inputs to cingulate, occipital, and inferior frontal cortex are essential modulators of resting-state alpha power. Moreover, endogenous input and inhibitory and excitatory neural populations play varied roles in mediating alpha power in different resting-state sub-networks. The framework can be applied to arbitrary neural mass models and has broad applicability to image neural mechanisms in different brain states.

Highlights

The whole-brain imaging framework can disclose the neurophysiological substrates of complicated brain functions in a spatiotemporal manner.

Developed a semi-analytical Kalman filter to estimate neurophysiological variables in the nonlinear neural mass model efficiently and accurately from large-scale electromagnetic time-series.

The semi-analytical Kalman filter is 7.5 times faster and 5% more accurate in estimating model parameters than the unscented Kalman filter.

Provided several group-level statistical observations based on neurophysiological variables and visualised them in a whole-brain manner to show different perspectives of neurophysiological mechanisms.

Applied the framework to study resting-state alpha oscillation and found novel relationships between local neurophysiological variables in specific brain regions and alpha power.
Sensitivity of novel SARS-CoV-2 Omicron subvariants, BA.2.11, BA.2.12.1, BA.4 and BA.5 to therapeutic monoclonal antibodies
Authors: Yamasoba Daichi , Kosugi Yusuke , Kimura Izumi , Fujita Shigeru , Uriu Keiya , Ito Jumpei , Sato Kei ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium
Published: May 2022

As of May 2022, Omicron BA.2 variant is the most dominant variant in the world. Thereafter, Omicron subvariants have emerged and some of them began outcompeting BA.2 in multiple countries. For instance, Omicron BA.2.11, BA.2.12.1 and BA.4/5 subvariants are becoming dominant in France, the USA and South Africa, respectively. In this study, we evaluated the sensitivity of these new Omicron subvariants (BA.2.11, BA.2.12.1 and BA.4/5) to eight therapeutic monoclonal antibodies (bamlanivimab, bebtelovimab, casirivimab, cilgavimab, etesevimab, imdevimab, sotrovimab and tixagevimab). Notably, we showed that although cilgavimab is antiviral against BA.2, BA.4/5 exhibits higher resistance to this antibody compared to BA.2. Since mutations are accumulated in the spike proteins of newly emerging SARS-CoV-2 variants, we suggest the importance of rapid evaluation of the efficiency of therapeutic monoclonal antibodies against novel SARS-CoV-2 variants.
Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH
Authors: Mattioli Edoardo Jun , Rossi Jacopo , Meloni Maria , De Mia Marcello , Marchand Christophe H. , Tagliani Andrea , Fanti Silvia , Falini Giuseppe , Trost Paolo , Lemaire Stéphane D. , Fermani Simona , Calvaresi Matteo , Zaffagnini Mirko
Published: May 2022

S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols. GSNO can also induce protein S-glutathionylation but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes enzyme inhibition by specifically inducing S-nitrosylation. Treatment with reducing agents restores CrGAPA activity completely. While the cofactor NADP+ only partially protects from GSNO-mediated S-nitrosylation, the resultant inactivation is completely blocked by the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible of CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP+ and NAD+ reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. Quantum mechanical/molecular mechanical calculations were performed to investigate the reaction mechanism of GSNO with CrGAPA Cys149 and to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.
Cellular reprogramming with ATOH1, GFI1, and POU4F3 implicate epigenetic changes and cell-cell signaling as obstacles to hair cell regeneration in mature mammals
Authors: Iyer Amrita A. , Hosamani Ishwar , Nguyen John D. , Cai Tiantian , Singh Sunita , Beyer Lisa , Zhang Hongyuan , Jen Hsin-I , Yousaf Rizwan , Birol Onur , Sun Jenny J. , Ray Russell S. , Raphael Yehoash , Segil Neil , Groves Andrew K.
Published: May 2022

Reprogramming of the cochlea with hair cell-specific transcription factors such as ATOH1 has been proposed as a potential therapeutic strategy for hearing loss. ATOH1 expression in the developing cochlea can efficiently induce hair cell regeneration but the efficiency of hair cell reprogramming declines rapidly as the cochlea matures. We developed Cre-inducible mice to compare hair cell reprogramming with ATOH1 alone or in combination with two other hair cell transcription factors, GFI1 and POU4F3. In newborn mice, all transcription factor combinations tested produced large numbers of cells with the morphology of hair cells and rudimentary mechanotransduction properties. However, one week later, only a combination of ATOH1, GFI1 and POU4F3 could reprogram non-sensory cells of the cochlea to a hair cell fate, and these new cells were less mature than cells generated by reprogramming one week earlier. We used scRNA-seq and combined scRNA-seq and ATAC-seq to suggest at least two impediments to hair cell reprogramming in older animals. First, hair cell gene loci become less epigenetically accessible in non-sensory cells of the cochlea with increasing age. Second, signaling from hair cells to supporting cells, including Notch signaling, can prevent reprogramming of many supporting cells to hair cells, even with three hair cell transcription factors. Our results shed light on the molecular barriers that must be overcome to promote hair cell regeneration in the adult cochlea.
Bioprinting microporous functional living materials from protein-based core-shell microgels
Authors: Ou Yangteng , Cao Shixiang , Zhang Yang , Zhu Hongjia , Guo Chengzhi , Yan Wei , Xin Fengxue , Dong Weiliang , Zhang Yanli , Narita Masashi , Yu Ziyi , Knowles Tuomas
Published: May 2022

Living materials bring together material science and biology to allow the engineering and augmenting of living systems with novel functionalities. Bioprinting promises accurate control over the formation of such complex materials through programmable deposition of cells in soft materials, but current approaches had limited success in fine-tuning cell microenvironments while generating robust macroscopic morphologies. Here, we address this challenge through the use of core-shell microgel ink to decouple cell microenvironments from the structural shell for further processing. Cells are microfluidically immobilized in the viscous core that can promote the formation of both microbial populations and mammalian cellular spheroids, followed by interparticle annealing to give covalently stabilized functional scaffolds with controlled microporosity. The results show that the core-shell strategy mitigates cell leakage while affording a favorable environment for cell culture. Furthermore, we demonstrate that different microbial consortia can be printed into scaffolds for a range of applications. By compartmentalizing microbial consortia in separate microgels, the collective bioprocessing capability of the scaffold is significantly enhanced, shedding light on strategies to augment living materials with bioprocessing capabilities.
Impact of Pericytes on the Stabilisation of Microvascular Networks in Microfluidic Systems in Response to Nanotoxicity
Authors: Dibble Matthew , Di Cio Stefania , Luo Piaopiao , Balkwill Frances , Gautrot Julien E.
Published: May 2022

Recapitulating the normal physiology of the microvasculature is pivotal in the development of more complex in vitro models and organ-on-chip design. Pericytes are an important component of the vasculature, promoting vessel stability, inhibiting vascular permeability and maintaining the vascular hierarchical architecture. This report presents a microfluidic model exploring interactions between endothelial cells and pericytes. We identify basal conditions required to form stable and reproducible endothelial networks. We then investigate interactions between endothelial cells and pericytes via direct co-culture. In our system, pericytes inhibited vessel hyperplasia and maintained vessel length in prolonged culture (>10 days). In addition, these vessels displayed barrier function and expression of junction markers associated with vessel maturation, including VE-cadherin, β-catenin and ZO-1. Furthermore, pericytes maintained vessel integrity following stress (nutrient starvation) and inhibited vessel regression, in contrast to the striking dissociation of networks in endothelial monocultures. This response was also observed when endothelial/pericyte co-cultures were exposed to high concentrations of moderately toxic cationic nanoparticles used for gene delivery. This study highlights the importance of pericytes in protecting vascular networks from stress and external agents and their importance to the design of advancedin vitromodels, including for the testing of nanotoxicity, to better recapitulate physiological response and avoid false positives.
Clair3-Trio: high-performance Nanopore long-read variant calling in family trios with Trio-to-Trio deep neural networks
Authors: Su Junhao , Zheng Zhenxian , Ahmed Syed Shakeel , Lam Tak-Wah , Luo Ruibang
Published: May 2022

Accurate identification of genetic variants from family child-mother-father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read sequencing data. For better trio variant calling, we introduce Clair3-Trio, the first variant caller tailored for family trio data from Nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model, which allows it to input the trio sequencing information and output all of the trio’s predicted variants within a single model to improve variant calling. We also present MCVLoss, a novel loss function tailor-made for variant calling in trios, leveraging the explicit encoding of the Mendelian inheritance. Clair3-Trio showed comprehensive improvement in experiments. It predicted far fewer Mendelian inheritance violation variations than current state-of-the-art methods. We also demonstrated that our Trio-to-Trio model is more accurate than competing architectures. Clair3-Trio is accessible as a free, open-source project at https://github.com/HKU-BAL/Clair3-Trio.
The damage-independent evolution of ageing by selective destruction
Authors: Wordsworth James , O’ Keefe Hannah , Clark Peter , Shanley Daryl
Published: May 2022

Ageing is currently believed to reflect the accumulation of molecular damage due to energetic costs of maintenance, as proposed in disposable soma theory (DST). Here we use agent-based modelling to describe an alternative theory by which ageing could undergo positive selection independent of energetic costs. We suggest that the selective advantage of aberrant cells with fast growth might necessitate a mechanism of counterselection we name selective destruction that specifically removes the faster cells from tissues, preventing the morbidity and mortality risks they pose. The resulting survival advantage of slower mutants could switch the direction of selection, allowing them to outcompete both fast mutants and wildtype cells, causing them to spread and induce ageing in the form of a metabolic slowdown.

Selective destruction could therefore provide a proximal cause of ageing that is both consistent with the gene expression hallmarks of ageing, and independent of accumulating damage. Furthermore, negligible senescence would acquire a new meaning of increased basal mortality.
Mass photometric detection and quantification of nanoscale α-synuclein phase separation
Authors: Ray Soumik , Mason Thomas O. , Boyens-Thiele Lars , Jahnke Nadin , Buell Alexander K.
Published: May 2022

α-Synuclein (α-Syn) liquid-liquid phase separation (LLPS) leads to irreversible amyloid fibril formation associated with Parkinson’s disease pathogenesis. Critical concentrations of α-Syn LLPS are relatively high under physiological solution conditions. Moreover, α-Syn exhibits delayed LLPS kinetics under certain conditions which deviates from the behaviour predicted by classical homogeneous nucleation theory. In the current body of work, using interferometric light scattering (iSCAT), also known as mass photometry, we experimentally probe that α-Syn can form nanoscale phase separated assemblies/clusters, containing tens to hundreds of molecules— both above and below the critical LLPS concentration down to physiologically relevant scales. The formation of these clusters is instantaneous, even under conditions where the formation of microscopically visible droplets takes several days. However, they account for a very small volume fraction below saturation concentration. The slow growth of the nanoclusters can be attributed to a kinetic barrier which can be overcome by increasing the solution temperature to just below the droplet melting point. We provide reasons for caution in quantifying dilute phase concentrations for α-Syn LLPS samples containing nanoscale droplets—which can only be separated using ultracentrifugation. In addition, we also delineate that the presence of certain surfaces facilitates α-Syn droplet nucleation under conditions of delayed kinetics but is not a mandatory prerequisite for nanocluster formation. Taken together, our findings reveal that phase separation of α-Syn occurs at a wider range of solution conditions than predicted so far and provides an important step towards understanding α-Syn LLPS within physiological scales.

Abstract Figure
Quantum CART(qCART), apiggyBac-basedsystem for development and production of virus-free multiplex CAR-T cell therapy
Authors: Chen Yi-Chun , Hua Wei-Kai , Hsu Jeff C. , Chang Peter S. , Wen Kuo-Lan Karen , Huang Yi-Wun , Tsai Jui-Cheng , Kao Yi-Hsin , Wu Pei-Hua , Wang Po-Nan , Chen Ke-Fan , Liao Wan-Ting , Wu Sareina Chiung-Yuan
Published: May 2022

Chimeric antigen receptor T (CAR-T) cell therapy has the potential to transform cancer treatment. However, CAR-T therapy application is currently limited to certain types of relapsed/refractory B cell lymphomas. To unlock the full potential of CAR-T therapy, technologic breakthroughs will be needed in multiple areas, including optimization of autologous CAR-T development, shortening the innovation cycle, and further manufacturing advancement of next-generation CAR-T therapies. Here, we established a simple and robust virus-free multiplexQuantum CART™system that seamlessly and synergistically integrates four platforms: 1.GTailor™for rapid identification of lead CAR construct design, 2.Quantum Nufect™for effective but gentle electroporation-based gene delivery, 3.Quantum pBac™, featuring a virus-free transposon-based vector with large payload capacity and integration profile similar to retrovirus, and 4.iCellar™for robust and high-quality CAR+T memory stem cell expansion. This robust, virus-free multiplexQuantum CART™system is expected to unleash the full potential of CAR-T therapy for treating diseases.
Neurotransmitter content heterogeneity within an interneuron class shapes inhibitory transmission at a central synapse
Authors: Dumontier Dimitri , Mailhes-Hamon Caroline , Supplisson Stéphane , Dieudonné Stéphane
Published: May 2022

Neurotransmitter content is deemed the most basic defining criterion for neuronal classes, contrasting with the intercellular heterogeneity of many other molecular and functional features. Here we show, in the adult mouse brain, that neurotransmitter content variegation within a neuronal class is a component of its functional heterogeneity. Most Golgi cells (GoCs), the well-defined class of cerebellar interneurons inhibiting granule cells (GrCs), contain cytosolic glycine, accumulated by the neuronal transporter GlyT2, and GABA in various proportions. To assess the functional consequence of this neurotransmitter variation, we paired GrCs recordings with optogenetic stimulations of single GoCs, which preserve the intracellular transmitter mixture. We show that the strength and decay kinetics of GrCs IPSCs, which are entirely mediated by GABAA receptors are negatively correlated to the presynaptic expression of GlyT2 by GoCs. We isolate a slow spillover component of GrCs inhibition that is also affected by the expression of GlyT2, leading to a 56 % decrease in relative charge. Acute manipulations of cytosolic GABA and glycine supply recapitulate the modulation of IPSC charge, supporting the hypothesis that presynaptic loading of glycine negatively impact the GABAergic transmission in mixed interneurons through a competition for vesicular filling. Our results suggest that heterogeneity of neurotransmitter supply within the GoC class may provide a presynaptic mechanism to tune the gain of the stereotypic granular layer microcircuit, thereby expanding the realm of possible dynamic behavior.
Cell detoxification of secondary metabolites by P4-ATPase mediated vesicle transport
Authors: Li Yujie , Ren Hui , Wang Fanlong , Chen Jianjun , Ma Lian , Chen Yang , Li Xianbi , Fan Yanhua , Jin Dan , Hou Lei , Zhou Yonghong , Keyhani Nemat O. , Pei Yan
Published: May 2022

Mechanisms for cellular detoxification of drug compounds are of significant interest in human health. Cyclosporine A (CsA) and tacrolimus (FK506) are widely known antifungal and immunosuppressive microbial natural products. However, both compounds can result in significant side effects when used as immunosuppressants. The insect pathogenic fungusBeauveria bassianashows resistance to CsA and FK506. However, the mechanisms underlying the resistance have remained unknown. Here, we identify a P4-ATPase gene,BbCRPA, from the fungus, which confers resistanceviaa unique vesicle mediated transport pathway that targets the compounds into detoxifying vacuoles. Interestingly, the expression ofBbCRPAin plants promotes resistance to the phytopathogenic fungusVerticillium dahliae viadetoxification of the mycotoxin cinnamyl acetate using a similar pathway. Our data reveal a new function for a subclass of P4-ATPases in cell detoxification. The P4-ATPases conferred cross-species resistance can be exploited for plant disease control and human health protection.
Regional context for balancing sagebrush- and woodland-dependent songbird needs with targeted pinyon-juniper management in the sagebrush biome
Authors: Tack Jason D. , Smith Joseph T. , Doherty Kevin E. , Donnelly Patrick J. , Maestas Jeremy D. , Allred Brady W. , Reinhardt Jason , Morford Scott L. , Naugle David E.
Published: May 2022

Tree expansion among historic grassland and shrubland systems is a global phenomenon, which results in dramatic influences on ecosystem processes and wildlife populations. In the western US, pinyon-juniper woodlands have expanded by as much as six-fold among sagebrush steppe landscapes since the late nineteenth century, with demonstrated negative impacts to the behavior, demography, and population dynamics of species that rely on intact sagebrush rangelands. Notably, greater sage-grouse (Centrocercus urophasianus) are unable to tolerate even low conifer cover, which can result in population declines and local extirpation. Removing expanding conifer cover has been demonstrated to increase sage grouse population growth rates and sagebrush-obligate songbird abundance. However, advances in restoring sagebrush habitats have been met with concern about unintended impacts to species that rely on conifer woodlands, notably the pinyon jay (Gymnorhinus cyanocephalus) whose population declines are distinctive among birds breeding in pinyon-juniper woodlands. We modeled indices to abundance in relation to multi-scale habitat features for nine songbirds reliant on both sagebrush and pinyon-juniper woodlands for breeding. Findings demonstrate that targeted sage grouse habitat restoration under the Sage Grouse Initiative is not at odds with protection of pinyon jay populations. Rather, conifer management has largely occurred in the northern sagebrush ecosystem where models suggest that past cuts likely benefit Brewer’s sparrow and sage thrasher while avoiding pinyon jay habitat. Extending our spatial modeling further south beyond the sagebrush biome could better equip conservationists with more comprehensive decision-support, particularly where pinyon jays face additional pressures of drought-induced tree mortality.
The Colon Mucosal Sialylglycome Is Redox-Regulated by the Golgi Enzyme QSOX1
Authors: Ilani Tal , Reznik Nava , Yeshaya Noa , Feldman Tal , Vilela Patrick , Lansky Zipora , Javitt Gabriel , Shemesh Michal , Brenner Ori , Elkis Yoav , Varsano Neta , Murray Nathan , Azadi Parastoo , Jaramillo Ana M. , Evans Christopher M. , Fass Deborah
Published: May 2022

Mucus shields the intestinal epithelium from pathogens and provides a supportive environment for commensal bacteria. Mucus is composed of enormous, heavily glycosylated proteins called mucins, which become disulfide crosslinked in a multi-step biosynthetic pathway culminating in the Golgi apparatus and secretory granules of goblet cells. We observed that knockout mice lacking the Golgi-localized disulfide catalyst QSOX1 produced poorly protective colon mucus, were hypersensitive to induced colitis, and had an altered microbiome. The initial hypothesis arising from these observations was that QSOX1 catalyzes disulfide crosslinking of mucins. Contrary to this hypothesis, the disulfide-mediated polymerization of mucins and related glycoproteins proceeded normally without QSOX1. Instead, we found that QSOX1 forms regulatory disulfides in Golgi glycosyltransferases and thereby promotes effective sialylation of the colon glycome. Our findings reveal that enzymatic control of Golgi redox state impacts glycan elaboration in goblet cells, and that this pathway is crucial for maintaining mucosal function.
Right inferior frontal cortex damage impairs the initiation of inhibitory control, but not its implementation
Authors: Choo Yoojeong , Matzke Dora , Bowren Mark D. , Tranel Daniel , Wessel Jan R.
Published: May 2022

Inhibitory control is one of the most important control functions in the human brain. Much of our understanding of its neural basis comes from seminal work showing that lesions to the right inferior frontal cortex (rIFC) increase stop-signal reaction time (SSRT), a latent variable that expresses the speed of inhibitory control. However, recent work has identified substantial limitations of the SSRT method. Notably, SSRT is confounded by trigger failures: stop-signal trials in which inhibitory control was never initiated. Such trials inflate SSRT, but are typically indicative of attentional, rather than inhibitory deficits. Here, we used hierarchical Bayesian modeling to identify stop-signal trigger failures in human rIFC lesion patients, non-rIFC lesion patients, and healthy comparisons. Furthermore, we measured scalp-EEG to detect β-bursts, a neurophysiological index of inhibitory control. rIFC lesion patients showed a more than five-fold increase in trigger failure trials and did not exhibit the typical increase of stop-related frontal β- bursts. However, on trials in which such β-bursts did occur, rIFC patients showed the typical subsequent upregulation of β over sensorimotor areas, indicating that their ability to implement inhibitory control, once triggered, is intact. These findings suggest that the role of rIFC in inhibitory control has to be fundamentally reinterpreted.
Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations
Authors: Hutchinson Keino , Silva Dina Buitrago , Bohlke Joshua , Clausen Chase , Thomas Allen A. , Bonomi Massimiliano , Schlessinger Avner
Published: May 2022

The human L-type amino acid transporter 1 (LAT1; SLC7A5) is a membrane transporter of amino acids, thyroid hormones, and drugs such as the Parkinson’s disease drug L-Dopa. LAT1 is found in the blood-brain-barrier (BBB), testis, bone marrow, and placenta, and its dysregulation has been associated with various neurological diseases such as autism and epilepsy as well as cancer. In this study, we combine metainference molecular dynamics (MD) simulations, molecular docking, and experimental testing, to characterize LAT1-inhibitor interactions. We first conducted a series of molecular docking experiments to identify the most relevant interactions between LAT1’s substrate binding site and ligan ds, including both inhibitors and substrates. We then performed metainference MD simulations using cryo-EM structures in different conformations of LAT1 with the electron density map as a spatial restraint, to explore the inherent heterogeneity in the structures. We analyzed the LAT1 substrate binding site to map important LAT1-ligand interactions as well as newly described druggable pockets. Finally, this analysis guided the discovery of previously unknown LAT1 ligands using virtual screening and cellular uptake experiments. Our results improve our understanding of LAT1-inhibitor recognition, providing a framework for rational design of future lead compounds targeting this key drug target.

Statement of Significance

LAT1 is a membrane transporter of amino acids, thyroid hormones, and therapeutic drugs, that is primarily found in the BBB and placenta, as well as in tumor cells of several cancer types. We combine metainference MD simulations, molecular docking, and experimental testing, to characterize LAT1-inhibitor interactions. Our computational analysis predicts S66, G67, F252, G255, Y259, W405 are critical residues for inhibitor binding and druggable sub-pockets in the outward-occluded conformation that are ideal for LAT1 inhibitor discovery. Using virtual screening and functional testing, we discovered multiple LAT1 inhibitors with diverse scaffolds and binding modes. Our results improve our understanding of LAT1’s structure and function, providing a framework for development of future therapeutics targeting LAT1 and other SLC transporters.
HSP90-CDC37-PP5 forms a structural platform for kinase dephosphorylation
Authors: Oberoi Jasmeen , Aran-Guiu Xavi , Outwin Emily A. , Schellenberger Pascale , Roumeliotis Theodoros I. , Choudhary Jyoti S. , Pearl Laurence H.
Published: May 2022

Activation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, on the kinase specific co-chaperone CDC37, and the kinase client itself. Removal of regulatory phosphorylation from client kinases and their release from the HSP90-CDC37 system depends on a Ser/Thr phosphatase PP5, which associates with HSP90 via its N-terminal TPR domain. Here we present the cryoEM structure of the oncogenic protein kinase client BRAFV600E bound to HSP90-CDC37, showing how the V600E mutation favours BRAF association with HSP90-CDC37. Structures of HSP90-CDC37-BRAFV600E complexes with PP5, in autoinhibited and activated conformations, together with proteomic analysis of its phosphatase activity, reveal how PP5 is activated by recruitment to HSP90 complexes to comprehensively dephosphorylate client proteins.
Principled feature attribution for unsupervised gene expression analysis
Authors: Janizek Joseph D. , Spiro Anna , Celik Safiye , Blue Ben W. , Russell Josh C. , Lee Ting-I , Kaeberlin Matt , Lee Su-In
Published: May 2022

As interest in unsupervised deep learning models for the analysis of gene expression data has grown, an increasing number of methods have been developed to make these deep learning models more interpretable. These methods can be separated into two groups: (1)post hocanalyses of black box models through feature attribution methods and (2) approaches to build inherently interpretable models through biologically-constrained architectures. In this work, we argue that these approaches are not mutually exclusive, but can in fact be usefully combined. We propose a novel unsupervised pathway attribution method, which better identifies major sources of transcriptomic variation than prior methods when combined with biologically-constrained neural network models. We demonstrate how principled feature attributions aid in the analysis of a variety of single cell datasets. Finally, we apply our approach to a large dataset of post-mortem brain samples from patients with Alzheimer’s disease, and show that it identifies Mitochondrial Respiratory Complex I as an important factor in this disease.
A model of decentralized vision in the sea urchinDiadema africanum
Authors: Li Tianshu , Kirwan John , Arnone Maria Ina , Nilsson Dan-Eric , La Camera Giancarlo
Published: May 2022

Abstract

Sea urchins can detect light and move in relation to luminous stimuli despite lacking eyes. They presumably detect light through photoreceptor cells distributed on their body surface. However, there is currently no mechanistic explanation of how these animals can process light to detect visual stimuli and produce oriented movement. Here, we present a model of decentralized vision in echinoderms that includes all known processing stages, from photoreceptor cells to radial nerve neurons to neurons contained in the oral nerve ring encircling the mouth of the animals. In the model, light stimuli captured by photoreceptor cells produce neural activity in the radial nerve neurons. In turn, neural activity in the radial nerves is integrated in the oral nerve ring to produce a profile of neural activity reaching spatially across several ambulacra. This neural activity is read out to produce a model of movement. The model captures previously published data on the behavior of sea urchinDiadema africanumprobed with a variety of physical stimuli. The specific pattern of neural connections used in the model makes testable predictions on the properties of single neurons and aggregate neural behavior inDiadema africanumand other echinoderms, offering a potential understanding of the mechanism of visual orientation in these animals.
Selection and validation of reference genes for quantitative real-time polymerase chain reaction in Serratia ureilytica DW2
Authors: Bai Fenglin , Bai Bianxia , Jin Tingting , Zhang Guiping , Ren Jiahong
Published: May 2022

Serratia ureilytica DW2 is a highly efficient phosphate-solubilizing bacterium isolated from Codonopsis pilosula rhizosphere soil that can promote the growth of C. pilosula. However, no validated reference genes from the genus Serratia for use in quantitative real-time polymerase chain reaction (RT–qPCR) normalization have been reported. To screen stable reference genes in S. ureilytica DW2, the expression of eight candidate reference genes (16S rRNA, ftsZ, ftsA, mreB, recA, slyD, thiC, and zipA) under different treatment conditions (pH, temperature, culture time, and salt content) was assayed by RT–qPCR. The expression stability of these genes was analyzed with different algorithms (geNorm, NormFinder, and BestKeeper). To verify the reliability of the data, the most stably expressed reference gene was used to quantify expression of the glucose dehydrogenase (gdh) gene under different soluble phosphate levels. The results showed that the zipA and 16S rRNA genes were the most stable reference genes, and the least stable were thiC and recA. The expression of gdh was consistent with the phosphate solubilization ability on plates containing National Botanical Research Institute phosphate (NBRIP) growth medium. Therefore, this study provides a stable and reliable reference gene for Serratia, which is vital for the accurate quantification of functional gene expression in future studies.
On the economic evaluation of online learning in higher education during the COVID-19 pandemic: a willingness-to-accept approach
Authors: del Saz-Salazar Salvador , Gil-Pareja Salvador , García-Grande María José
Published: May 2022

Purpose

This study, using a contingent valuation approach, aims to shed light on the economic evaluation of online learning during the first wave of the pandemic.

Design/methodology/approach

A sample of 959 higher education students was asked about their willingness-to-accept (WTA) a monetary compensation for the loss of well-being resulting from the unexpected and mandatory transition to the online space. In explaining WTA determinants, the authors test the appropriateness of the double-hurdle model against the alternative of a Tobit model and find that the factors affecting the participation decision are not the same as those that affect the quantity decision.

Findings

Results show that a vast majority of the respondents think that the abrupt transition to online learning is detrimental to them, while those willing to accept a monetary compensation account for 77% of the sample, being the mean WTA between €448 and €595. As expected, WTA decreases with income and age, and it increases if some member of the family unit is unemployed. By aggregating the mean WTA by the population affected, total loss of well-being is obtained.

Originality/value

To the best of the authors’ knowledge, to date, this method has not been used to value online learning in a WTA framework, much less in the particular context of the pandemic. Thus, based on the understanding that the economic evaluation of online learning could be very useful in providing guidance for decision-making, this paper contributes to the literature on the economic evaluation of higher education.
Semisupervised fault diagnosis of aeroengine based on denoising autoencoder and deep belief network
Authors: Lv Defeng , Wang Huawei , Che Changchang
Published: May 2022

Purpose

The purpose of this study is to analyze the intelligent semisupervised fault diagnosis method of aeroengine.

Design/methodology/approach

A semisupervised fault diagnosis method based on denoising autoencoder (DAE) and deep belief network (DBN) is proposed for aeroengine. Multiple state parameters of aeroengine with long time series are processed to form high-dimensional fault samples and corresponding fault types are taken as sample labels. DAE is applied for unsupervised learning of fault samples, so as to achieve denoised dimension-reduction features. Subsequently, the extracted features and sample labels are put into DBN for supervised learning. Thus, the semisupervised fault diagnosis of aeroengine can be achieved by the combination of unsupervised learning and supervised learning.

Findings

The JT9D aeroengine data set and simulated aeroengine data set are applied to test the effectiveness of the proposed method. The result shows that the semisupervised fault diagnosis method of aeroengine based on DAE and DBN has great robustness and can maintain high accuracy of fault diagnosis under noise interference. Compared with other traditional models and separate deep learning model, the proposed method also has lower error and higher accuracy of fault diagnosis.

Originality/value

Multiple state parameters with long time series are processed to form high-dimensional fault samples. As a typical unsupervised learning, DAE is used to denoise the fault samples and extract dimension-reduction features for future deep learning. Based on supervised learning, DBN is applied to process the extracted features and fault diagnosis of aeroengine with multiple state parameters can be achieved through the pretraining and reverse fine-tuning of restricted Boltzmann machines.
Sustainable entrepreneurship practices in women-owned micro enterprises using evidence from Owino market, Kampala, Uganda
Authors: Kimuli Saadat Nakyejwe Lubowa , Sendawula Kasimu , Nagujja Shakilah
Published: May 2022

Purpose

This study aims to explore the sustainable entrepreneurship practices undertaken in women-owned businesses, challenges and strategies that women business owners intend to adopt to implement more sustainable entrepreneurship practices using evidence from Uganda.

Design/methodology/approach

This study is cross-sectional and qualitative in nature. It involved conducting in-depth interviews with women business owners operating in Owino market and study results were analyzed using ATLAS. ti 8.

Findings

The results indicate that women business owners undertake social, environmental and economic practices in their businesses. However, participants are constrained by fire outbreaks, riskiness of their businesses and breakdown of machinery. Therefore, indicated plans of using energy-saving stoves and electronic tailoring machines digitizing their businesses and hiring skilled workers in order to improve sustainable entrepreneurship practices in their businesses.

Originality/value

This study offers maiden evidence on the sustainable entrepreneurship practices undertaken by women business owners, challenges faced and strategies undertaken to support uptake of more sustainable entrepreneurship practices in their businesses using evidence from Uganda.
Distinctive phenolic accumulation response to temperature-induced by row orientation of two field-grown Vitis vinifera cultivars
Authors: Yin Haining , Zhang Hui , Xi Zhumei
Published: May 2022

Purpose

Phenolic compounds play a critical role in grape quality, and their content is strongly influenced by bunch zone temperature during the ripening period. The mechanism of responding to temperature was found to highly depend on cultivars. The present study aimed to evaluate the effects of row orientation and canopy side on phenolic content in grape berries.

Design/methodology/approach

The authors analyzed the accumulation of phenolic compounds in mature berries of Cabernet Sauvignon and Cabernet Gernischt. They were harvested from various canopy sides of north-south and east-west row orientations, which were NS–E and NS–W, EW–S and EW–N.

Findings

During the ripening period, mean temperatures of the bunch zones, NS–W and EW–N were respectively higher than NS–E and EW–S. At harvest, the total phenolic, total anthocyanin, tannin and reducing sugar contents were higher in NS–E and EW–S, than in NS–W and EW–N, respectively, indicating a negative relationship with temperature. For both varieties, EW–S had the highest proportion of malvidins anthocyanins. Peonidins, delphinidins, and cyanidins anthocyanins of EW–N showed a higher ratio in Cabernet Sauvignon, while NS–E showed a higher ratio in Cabernet Gernischt.

Originality/value

To improve grape monomeric anthocyanin content, the results indicate that Cabernet Sauvignon of NS–W and Cabernet Gernischt of NS–E can be utilized for an effective strategy. Moreover, the optimal combination planting choices with cultivars would improve wine quality by increasing pigment concentrations linked to the color and antioxidant potential.
Privacy-preserving techniques in recommender systems: state-of-the-art review and future research agenda
Authors: Pramod Dhanya
Published: May 2022

Purpose

This study explores privacy challenges in recommender systems (RSs) and how they have leveraged privacy-preserving technology for risk mitigation. The study also elucidates the extent of adopting privacy-preserving RSs and postulates the future direction of research in RS security.

Design/methodology/approach

The study gathered articles from well-known databases such as SCOPUS, Web of Science and Google scholar. A systematic literature review using PRISMA was carried out on the 41 papers that are shortlisted for study. Two research questions were framed to carry out the review.

Findings

It is evident from this study that privacy issues in the RS have been addressed with various techniques. However, many more challenges are expected while leveraging technology advancements for fine-tuning recommenders, and a research agenda has been devised by postulating future directions.

Originality/value

The study unveils a new comprehensive perspective regarding privacy preservation in recommenders. There is no promising study found that gathers techniques used for privacy protection. The study summarizes the research agenda, and it will be a good reference article for those who develop privacy-preserving RSs.
Hierarchical structure and transfer mechanism to assess the scheduling-related risk in construction of prefabricated buildings: an integrated ISM–MICMAC approach
Authors: Fan Cheng , Binchao Deng , Yin Yilin
Published: May 2022

Purpose

Under the background that engineering, procurement and construction (EPC) contracting model is introduced to adapt to the highly fragmented characteristics of prefabricated construction, the schedule management of general contractor is faced with the challenge of dynamic transmission and interaction of construction scheduling-related risk. The purpose of this paper is to develop the hierarchy of prefabricated construction scheduling-related risks from the perspective of the general contractor, and to analyze the transmission mechanism between risks. The paper also aims to further distinguish the difference of the impact degree of scheduling-related risks, and provide reference for formulating the strategy to alleviate the construction delay.

Design/methodology/approach

Based on a review of the literature on prefabricated buildings, this paper identifies 22 scheduling-related risks in construction from the perspective of the general contractor. Semi-structured interviews were then conducted to obtain experts' views on the interrelationships among these risks. Following this, their overall structure was determined by using a hierarchical structure established by using interpretive structural modeling (ISM), and Matrice d'Impacts Croisés Multiplication Appliqués à un Classement (MICMAC) technique was applied to classify them into four groups according to their driving and dependence powers.

Findings

The results indicate that the 22 scheduling-related risks in construction followed the inherent path of step-by-step transmission, and all of them could cause different degrees of delays in prefabricated construction. Among them, general experience in contracting projects, the use of emerging technologies and the completeness of the relevant standards and specifications were strong drivers of scheduling delays in construction, and should be prioritized by the general contractor in schedule management. The transitive link between scheduling risks can guide them in developing prevention strategies.

Research limitations/implications

Data quality and reliability risks are the major drawbacks of semi-structured interviews. These were minimized by engaging experts with rich theoretical and hands-on experience in prefabricated construction projects. The hierarchical model only reflects static influence relationships, and so dynamic interactions among scheduling-related risks should be studied in future.

Originality/value

The primary value of this study is in its development of a hierarchical model by using the integrated ISM–MICMAC approach that reflects the interaction between scheduling risks in the construction of prefabricated buildings. The hierarchy of these risks and the results of a “driving-dependence power” analysis can guide the general contractor in taking targeted preventive measures to avoid scheduling delays in the construction of prefabricated buildings.