bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic segmentation of dentate nuclei for microstructure assessment: example of application to temporal lobe epilepsy patients
Authors: Gaviraghi Marta , Savini Giovanni , Castellazzi Gloria , Palesi Fulvia , Rolandi Nicolò , Sacco Simone , Pichiecchio Anna , Mariani Valeria , Tartara Elena , Tassi Laura , Vitali Paolo , D’Angelo Egidio , Gandini Wheeler-Kingshott Claudia A.M.
Published: July 2020

Dentate nuclei (DNs) segmentation is helpful for assessing their potential involvement in neurological diseases. Once DNs have been segmented, it becomes possible to investigate whether DNs they are microstructurally affected, through analysis of quantitative MRI parameters, such as the ones derived from diffusion weighted imaging (DWI). This study, therefore, aimed to develop a fully automated segmentation method using the non-DWI (b0) images from a DWI dataset to obtain DN masks inherently registered with parameter maps.

Three different automatic methods were applied to healthy subjects in order to segment the DNs: registration to SUIT (a spatially unbiased atlas template of the cerebellum and brainstem), OPAL (Optimized Patch Match for Label fusion) and CNN (Convolutional Neural Network). DNs manual segmentation was considered the gold standard. Results show that the segmentation obtained with SUIT has an average Dice Similarity Coefficient (DSC) of 0.4907±0.0793 between the automatic SUIT masks and the gold standard. A comparison with manual masks was also performed for OPAL (DSC = 0.7624 ± 0.1786) and CNN (DSC = 0.8658 ± 0.0255), showing a better performance when using CNN.

OPAL and CNN were optimised on heathy subjects’ data with high spatial resolution from the Human Connectome Project. The three methods were further used to segment the DNs of a subset of subjects affected by Temporal Lobe Epilepsy (TLE). This subset was derived from a 3T MRI research study which included DWI data acquired with a coarser resolution. In TLE dataset, SUIT performed similarly to using the HCP dataset, with a DSC = 0.4145 ± 0.1023. Using TLE data, OPAL performed worse than using HCP data: after changing the probability threshold the DSC was 0.4522 ± 0.1178.

CNN was able to extract the DNs using the TLE data without need for retraining and with a good DSC = 0.7368 ± 0.0799. Statistical comparison of quantitative parameters derived from DWI analysis, as well as volumes of each DN, revealed altered and lateralised changes in TLE patients compared to healthy controls.

The proposed CNN is therefore a viable option for accurate extraction of DNs from b0 images of DWI data with different resolutions and acquired at different sites.
NK cells integrate signals over large areas when building immune synapses but require local stimuli for degranulation
Authors: Verron Quentin , Forslund Elin , Brandt Ludwig , Leino Mattias , Frisk Thomas W. , Olofsson Per E. , Önfelt Björn
Published: July 2020

Immune synapses are large-scale, transient molecular assemblies that serve as platforms for antigen presentation to B and T cells, and target recognition by cytotoxic T cells and natural killer (NK) cells. The formation of an immune synapse is a tightly regulated, stepwise process where the cytoskeleton, cell-surface receptors and signaling proteins rearrange into supramolecular activation clusters (SMACs). Here we use a reductionist system of microcontact-printed artificial immune synapses (AIS) shaped as hallmark SMAC structures to show that the spatial distribution of activating ligands influences the formation, stability and outcome of NK cell synapses. Organizing ligands into donut-shaped AIS resulted in fewer long-lasting, symmetrical synapses compared to dot-shaped AIS. NK cells spreading evenly over either AIS exhibited similar arrangement of the lytic machinery, however degranulation was only possible in regions allowing local signaling. Our results demonstrate that the macroscopic organization of ligands in the synapse can affect its outcome, which could be exploited by target cells as an escape mechanism.
Systems and classical biology approaches unraveled role of olfactory receptors in progression of kidney fibrosis
Authors: Motahharynia Ali , Moein Shiva , Kiyanpour Farnoush , Moradzadeh Kobra , Gheisari Yousof
Published: July 2020

The olfactory receptors (ORs) which are mainly known as odor-sensors in the olfactory epithelium are distributed in several non-sensory tissues. Despite the specified role of some of these receptors in normal physiology of the kidney, little is known about their potential effect in renal disorders. In this study, using the holistic view of systems biology, it was determined that ORs are significantly changed during the progression of kidney fibrosis. For further validation, common differentially expressed ORs resulted from reanalysis of two time-course microarray datasets were selected for experimental evaluation in a validated murine model of unilateral ureteral obstruction. Transcriptional analysis demonstrated considerable changes in the expression pattern ofOlfr433, Olfr129, Olfr1393, and Olfr161during the progression of kidney fibrosis. In conclusion, our results highlight the impact of systems biology in determination of the underlying mechanisms of chronic diseases and indicate the importance of time-course approaches to unravel the patterns of gene expression. The novel ORs proposed in this study could be the subject of further functional investigations in the kidney.
Virtual Screening and Elucidation of Putative Binding Mode for Small Molecule Antagonist of BCL2 BH4 Domain
Authors: Joel Ireoluwa Yinka , Adigun Temidayo Olamide , Ajibola Ahmeedah Ololade , Bankole Olukayode Olusola , Ozojiofor Ugochukwu Okechukwu , Remi-Esan Ifelolu Adeseye , Sulaimon Lateef Adegboyega
Published: July 2020

Evading apoptosis is a hallmark of cancer cells, therefore therapeutic strategies have been developed to induce cell death. BCL2 family protein governs the intrinsic pathway of cell death. Targeting the BH4 domain to modulate the anti-apoptosis activities of BCL2 protein has been established however, BDA366 is the only BH4 binding molecule to be reported. Virtually screening ~ 1,000,000 compounds 11 putative BH4 binding small molecules with binding affinity ~ −84kcal/mol to - 64kcal/mol resulted. Using QM-polarized docking, Induced-fit docking, and QM-MM optimization, a putative binding mode for the top 3 compounds is proposed: compound 139068 interactions with GLU13, MET16, LYS17, ASP31, and GLU42; compound 138967 interactions with ASP10, ARG12, GLU13, HIS20, MET16, and GLU42; compound 38831 interactions with ASP10, ARG12, GLU13, LYS17, and GLU42. MD simulations (NMA) data showed the binding of the three compounds to be stable with low eigenvalues. Electronic properties derived via DFT calculations suggest chemical reaction of the compounds be via electrophilic reactions.
Genetic Algorithms as a method to study adaptive walks in biological landscapes
Authors: Invernizzi Edith , Ruxton Graeme D
Published: July 2020

The metaphor of fitness landscapes is common in evolutionary biology, as a way to visualise the change in allele or phenotypic frequencies of a population under selection. Understanding how different factors in the evolutionary process affect the trajectory of the population across the landscape is of interest to both theoretical and empirical evolutionary biologists. However, fitness landscape studies often have to rely heavily on mathematical methods that are not easy to access by biologically trained researchers. Here, we used a method borrowed from engineering - genetic algorithms - to simulate the evolutionary process and study how different components affect the path taken through a phenotypic fitness landscape. In a simple study, we compare five selection models that reflect different degrees of dependency of fitness on trait quality: this includes strengths of selection, trait-quality dependent reproductive hierarchy and the amount of stochasticity in the reproductive process. We include an analysis of other evolutionary variables such as population size and mutation rate. We analyse a game theory problem, as a test landscape, that lends itself to analysis through a deterministic mathematical simulation, which we use for comparison. Our results show that there are differences in the speed with which different models of selection lead to the fitness optimum.

Author summary

Evolution and adaptation in biology occurs infitness landscapes, multidimensional spaces representing all possible genotypic or phenotypic combinations, where population adapt by following the cline of the fitness dimension. The study of adaptation on complex fitness landscapes has so far been limited by the need for mathematically heavy methods. Here, we present a simulation modelling framework, genetic algorithms, that can be used for evolutionary simulations of a population on a fitness landscape of chosen features and with custom evolutionary parameters.
Regulatory T cell activation triggers specific changes in glycosylation associated with Siglec-1-dependent inflammatory responses
Authors: Wu Gang , Murugesan Gavuthami , Nagala Manjula , McCraw Alex , Haslam Stuart M. , Dell Anne , Crocker Paul R.
Published: July 2020

Siglec-1 is a macrophage lectin-like receptor that mediates sialic acid-dependent cellular interactions. It was shown previously to promote inflammation in autoimmune disease through suppressing the expansion of regulatory T cells (Tregs). We have investigated the molecular basis for Siglec-1 binding to these cells usingin vitro-induced Tregs. Siglec-1 binding was strongly upregulated on activated cells, but lost under resting conditions. Glycosylation changes that affect Siglec-1 binding were studied by comparing activated and resting Tregs using RNA-Seq, glycomics, proteomics and binding of selected antibodies and lectins. A proximity labelling and proteomics strategy identified 49 glycoproteins expressed by activated Tregs that may function as Siglec-1 counter-receptors. These represent ∼5% of the total membrane protein pool and were mainly related to T cell activation and proliferation. We demonstrate that several of these counter-receptors are upregulated following activation of Tregs and provide initial evidence that their altered glycosylation may also be important for Siglec-1 binding.
Repression ofPdzrn3is required for heart maturation and protects against heart failure
Authors: Pernot Mathieu , Jaspard-vinassa Béatrice , Abelanet Alice , Rubin Sebastien , Forfar Isabelle , Jeanningros Sylvie , Cetran Laura , Yu Murielle Han-Yee , Balse Elise , Hatem Stéphane , Dufourcq Pascale , Couffinhal Thierry , Duplàa Cécile
Published: July 2020

Heart failure is the final common stage of most cardiopathies. Cardiomyocytes connect with others via their extremities by intercalated disk protein complexes. This planar and directional organization of myocytes is crucial for mechanical coupling and anisotropic conduction of the electric signal in the heart. One of the hallmarks of heart failure is alterations in the contact sites between cardiomyocytes. Yet no factor on its own is known to coordinate cardiomyocyte polarized organization. We report enhanced levels of an ubiquitine ligasePdzrn3in diseased hypertrophic human and mouse myocardium, which correlates with a loss of cardiomyocyte polarized elongation. We provide evidence thatPdzrn3has a causative role in heart failure. We found that cardiacPdzrn3deficiency protected against heart failure while over expression ofPdzrn3in mouse cardiomyocytes during the first weeks of life, impaired postnatal cardiomyocyte maturation leading to premature death. Our results reveal a novel signaling pathway that controls a genetic program essential for heart maturation and maintenance of overall geometry, as well as the contractile function of cardiomyocytes, and implicates PDZRN3 as a potential therapeutic target for the prevention of human heart failure.
Origins, History and Molecular Characterization of Creole Cane
Authors: Evans Dyfed Lloyd , Joshi Shailesh Vinay
Published: July 2020

Since it was first introduced to Europe in 711 CE and planted in the Americas in 1506, a single type of cane dominated sugar production for 1100 years, until it was finally ousted by Tahitian cane c. 1790. This cane became known as ‘CreoleâĂŹ and is present in the ancestry of many sugarcane hybrids, even today. Whether there was only a single variety of Creole cane or multiple varieties has been a matter of debate for decades. Creole cane remains relevant today, as a Creole cane from Jamaica is the currently chosen lecotype for Saccharum officinarum. In this study we identify 18 historical images of Creole cane, many not previously published. We employ image analyses to characterize the internodes and demonstrate evidence for only a single type of Creole in the new world. Chloroplasts and 45s ribosomal RNA sequences from the cultivar BH10/12 (known to have a Creole female parent) were determined that Java ribbon cane is the historical New World sugarcane known as Creole. We demonstrate that Creole cane is an hybrid and not a single species. ThusS. officinarumhas no type specimen. We also sequence a ribbon cane (also known as Guinguam) that appeared in the Caribbean between 1790 and 1810 and demonstrate that this cane was a Sinense type from Java that links back to the work of Rumphinus (1660s).
Viscoelastic properties of wheat gluten in a molecular dynamics study
Authors: Mioduszewski Łukasz , Cieplak Marek
Published: July 2020

Wheat(Triticum spp.) gluten consists mainly of intrinsincally disordered storage proteins (glutenins and gliadins) that can form megadalton-sized networks. These networks are responsible for the unique viscoelastic properties of wheat dough and affect the quality of bread. These properties have not yet been studied by molecular level simulations. Here, we use a newly developedα-C-based coarse-grained model to study ∼ 4000-residue systems. The corresponding time-dependent properties are studied through shear and axial deformations. We measure the response force to the deformation, the number of entanglements and cavities, the size of fluctuations, the number of the inter-chain bonds, etc. Glutenins are shown to influence the mechanics of gluten much more than gliadins. Our simulations are consistent with the existing ideas about gluten elasticity and emphasize the role of entanglements and hydrogen bonding. We also demonstrate that the storage proteins in maize and rice lead to weaker elasticity which points to the unique properties of wheat gluten.
Electrical impedance detection of sickle cell vaso-occlusion in microfluidic capillary structures
Authors: Qiang Yuhao , Liu Jia , Dieujuste Darryl , Du E
Published: July 2020

Sickle cell disease (SCD) is primarily associated with episodic vaso-occlusive events. Poorly deformable sickle cells may get stuck in small blood vessels, slow down or block blood flow, leading to local hypoxia that damages tissues and organs. In this paper, we present a novel electrical impedance sensing technique for detection of the progressive occlusion by sickle cells in microfluidic capillary structures. Changes in both resistance and reactance of the sickle blood flow were observed at multiple low frequencies (< 500 kHz), upon the deoxygenation and reoxygenation processes. In contrast, no obvious impedance changes were observed in the flow of normal blood cells and sickle blood cells treated with anti-sickling agent. Accuracy of the impedance-based detection of the vaso-occlusion process was verified by microscopic observation. The results show the distinct sensing performance of sickle cell vaso-occlusion by electrical impedance, which does not require sophisticated optical microscopy or video processing. The low frequency impedance sensing can be achieved by replacing the benchtop equipment with low-cost, high precision impedance converter system, allowing for detection of sickle cell vaso-occlusion in point-of-care settings.
Precisely-timed dopamine signals establish distinct kinematic representations of skilled movements
Authors: Bova Alexandra , Gaidica Matt , Hurst Amy , Iwai Yoshiko , Leventhal Daniel K.
Published: July 2020

Brain dopamine is critical for normal motor control, as evidenced by its importance in Parkinson Disease and related disorders. Current hypotheses are that dopamine influences motor control by “invigorating” movements and regulating motor learning. Most evidence for these aspects of dopamine function comes from simple tasks (e.g., lever pressing). Therefore, the influence of dopamine on motor skills requiring multi-joint coordination is unknown. To determine the effects of precisely-timed dopamine manipulations on the performance of a complex, finely coordinated dexterous skill, we optogenetically stimulated or inhibited midbrain dopamine neurons as rats performed a skilled reaching task. We found that reach kinematics and coordination between gross and fine movements progressively changed with repeated manipulations. However, once established, rats transitioned abruptly between aberrant and baseline reach kinematics in a dopamine-dependent manner. These results suggest that precisely-timed dopamine signals have immediate and long-term influences on motor skill performance, distinct from simply “invigorating” movement.
PdgfraandPdgfrbgenetically interact in the murine neural crest cell lineage to regulate migration and proliferation
Authors: Mo Julia , Long Robert , Fantauzzo Katherine A.
Published: July 2020

Cranial neural crest cells (cNCCs) are migratory, multipotent cells that originate from the forebrain to the hindbrain and eventually give rise to the bone and cartilage of the frontonasal skeleton, among other derivatives. Signaling through the two members of the platelet-derived growth factor receptor (PDGFR) family of receptor tyrosine kinases, alpha and beta, plays critical roles in the cNCC lineage to regulate craniofacial development during murine embryogenesis. Further, the PDGFRs have been shown to genetically interact during murine craniofacial development at mid-to-late gestation. Here, we examined the effect of ablating bothPdgfraandPdgfrbin the murine NCC lineage on earlier craniofacial development and determined the cellular mechanisms by which the observed phenotypes arose. Our results confirm a genetic interaction between the two receptors in this lineage, as phenotypes observed in an allelic series of mutant embryos often worsened with the addition of conditional alleles. The defects observed here were shown to stem from reduced cNCC stream size and aberrant cNCC directional migration, as well as decreased proliferation of the facial mesenchyme upon combined decreases in PDGFRα and PDGFRβ signaling. Importantly, we found that PDGFRα plays a predominant role in cNCC migration whereas PDGFRβ primarily contributes to proliferation of the facial mesenchyme. Our findings provide insight into the distinct mechanisms by which PDGFRα and PDGFRβ signaling regulate cNCC activity and subsequent craniofacial development in the mouse embryo.
Single-nuclei transcriptomics of schizophrenia prefrontal cortex primarily implicates neuronal subtypes
Authors: Reiner Benjamin C. , Crist Richard C. , Stein Lauren M. , Weller Andrew E. , Doyle Glenn A. , Arauco-Shapiro Gabriella , Turecki Gustavo , Ferraro Thomas N. , Hayes Matthew R. , Berrettini Wade H.
Published: July 2020

Transcriptomic studies of bulk neural tissue homogenates from persons with schizophrenia and controls have identified differentially expressed genes in multiple brain regions. However, the brain’s heterogeneous nature prevents identification of relevant cell types. This study analyzed single-nuclei transcriptomics of ~275,000 nuclei from frozen human postmortem dorsolateral prefrontal cortex samples from males with schizophrenia (n = 12) and controls (n = 14). 4,766 differential expression events were identified in 2,994 unique genes in 16 of 20 transcriptomically-distinct cell populations. ~96% of differentially expressed genes occurred in five neuronal cell types, and differentially expressed genes were enriched for genes associated with schizophrenia and bipolar GWAS loci. Downstream analyses identified cluster-specific enriched gene ontologies, KEGG pathways, and canonical pathways. Additionally, microRNAs and transcription factors with overrepresented neuronal cell type-specific targets were identified. These results expand our knowledge of disrupted gene expression in specific cell types and permit new insight into the pathophysiology of schizophrenia.
Genomic insights into the host specific adaptation of thePneumocystisgenus and emergence of the human pathogenPneumocystis jirovecii
Authors: Cissé Ousmane H. , Ma Liang , Dekker John P. , Khil Pavel P. , Youn Jung-Ho , Brenchley Jason M. , Blair Robert , Pahar Bapi , Chabé Magali , Van Rompay Koen K.A. , Keesler Rebekah , Sukura Antti , Hirsch Vanessa , Kutty Geetha , Liu Yueqin , Li Peng , Chen Jie , Song Jun , Weissenbacher-Lang Christiane , Xu Jie , Upham Nathan S. , Stajich Jason E. , Cuomo Christina A. , Cushion Melanie T. , Kovacs Joseph A.
Published: July 2020

Pneumocystis jirovecii, the fungal agent of humanPneumocystispneumonia, is closely related to macaquePneumocystis. Little is known about otherPneumocystisspecies in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity inPneumocystisremains unknown as experiments are limited due to an inability to culture any speciesin vitro. To explorePneumocystisevolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals novel insights into the evolution ofP. jirovecii, the sole member of the genus able to infect humans.
Polygenic Scores Predict the Development of Alcohol and Nicotine Use Problems from Adolescence through Young Adulthood
Authors: Deak Joseph D. , Clark D. Angus , Liu Mengzhen , Durbin C. Emily , Iacono William G. , McGue Matt , Vrieze Scott I. , Hicks Brian M.
Published: July 2020

Objective

Molecular genetic studies of alcohol and nicotine have identified many genome-wide loci. We examined the predictive utility of drinking and smoking polygenic scores (PGS) for alcohol and nicotine use from late childhood to early adulthood, substance-specific versus broader-liability PGS effects, and if PGS performance varied between consumption versus pathological use.

Methods

Latent growth curve models with structured residuals were used to assess the predictive utility of drinks per week and regular smoking PGS for measures of alcohol and nicotine consumption and problematic use from age 14 to 34. PGSs were generated from the largest discovery sample for alcohol and nicotine use to date (i.e., GSCAN), and examined for associations with alcohol and nicotine use in the Minnesota Twin Family Study (N=3225).

Results

The drinking PGS was a significant predictor of age 14 problematic alcohol use and increases in problematic use during young adulthood. The smoking PGS was a significant predictor for all nicotine use outcomes. After adjusting for the effects of both PGSs, the smoking PGS demonstrated incremental predictive utility for most alcohol use outcomes and remained a significant predictor of nicotine use trajectories.

Conclusions

Higher PGS for drinking and smoking were associated with more problematic levels of substance use longitudinally. The smoking PGS seems to capture both nicotine-specific and non-specific genetic liability for substance use, and may index genetic risk for broader externalizing behavior. Validation of PGS within longitudinal designs may have important clinical implications should future studies support the clinical utility of PGS for substance use disorders.
Analysis of site and structure specific core fucosylation in liver disease progression using exoglycosidase-assisted data-independent LC-MS/MS
Authors: Sanda Miloslav , Ahn Jaeil , Kozlik Petr , Goldman Radoslav
Published: July 2020

Carbohydrates form one of the major groups of biological macromolecules in living organisms. Many biological processes including protein folding, stability, immune response, and receptor activation are regulated by glycosylation. Fucosylation of proteins regulates such processes and is associated with various diseases including autoimmunity and cancer. Mass spectrometry efficiently identifies structures of fucosylated glycans or sites of core fucosylated N-glycopeptides but quantification of the glycopeptides remains less explored. We performed experiments that facilitate quantitative analysis of the core fucosylation of proteins with partial structural resolution of the glycans and we present results of the mass spectrometric SWATH-type DIA analysis of relative abundances of the core fucosylated glycoforms of 45 glycopeptides derived from 18 serum proteins in liver disease of different etiologies. Our results show that a combination of soft fragmentation with exoglycosidases is efficient at the assignment and quantification of the core fucosylated N-glycoforms at specific sites of protein attachment. In addition, our results show that disease-associated changes in core fucosylation are peptide-dependent and further differ by branching of the core fucosylated glycans. Further studies are needed to verify whether tri- and tetra-antennary core fucosylated glycopeptides could be used as markers of liver disease progression.
Resistance to tembotrione, a 4- Hydroxyphenylpyruvate Dioxygenase-Inhibitor inSorghum bicolor
Authors: Pandian Balaji Aravindhan , Varanasi Aruna , Vennapusa Amaranatha R. , Sathishraj Rajendran , Lin Guifang , Zhao Mingxia , Tunnell Madison , Tesso Tesfaye , Liu Sanzhen , Prasad P.V. Vara , Jugulam Mithila
Published: July 2020

Postemergence grass weed control continues to be a big challenge in grain sorghum (Sorghum bicolorL. Moench), primarily due to a lack of herbicide options registered for use in this crop. The development of herbicide-resistant sorghum technology to facilitate broad-spectrum postemergence weed control is an economical and viable solution. The 4-hydroxyphenylpyruvate dioxygenase-inhibitor herbicides (e.g. mesotrione or tembotrione) can control broad-spectrum of weeds including grasses, which, however, is not registered for postemergence application in sorghum due to crop injury. In this study we identified two tembotrione-resistant sorghum genotypes (G-200, G-350) and one highly susceptible genotype (S-1) through screening 317 sorghum lines from the sorghum association panel (SAP). Compared to S-1, G-200 and G-350 exhibited 10- and 7-fold more resistance to tembotrione, respectively. Genetic analyses of the F1and F2progeny generated from a cross between tembotrione-resistant and -susceptible genotypes demonstrated that the resistance is a semi-dominant polygenic trait. Furthermore, cytochrome P450 (CYP)-inhibitor assay using malathion and piperonyl butoxide suggested possible CYP-mediated metabolism of tembotrione in G-200 and G-350. Genotype-by-sequencing based quantitative trait loci (QTL) mapping revealed eight QTLs associated with tembotrione resistance in grain sorghum. Sorghum genotypes G-200 and G-350 confer a high level of metabolic resistance to tembotrione and controlled by a polygenic trait. There is an enormous potential to introgress the tembotrione resistance into breeding lines to develop agronomically desirable sorghum hybrids.

One-sentence summary

This research focuses on characterization, genetic analyses, identification of QTLs-linked to metabolic resistance to tembotrione in Sorghum bicolor, for improved weed control and increased yield
Biofabrication using maize protein: 3D printing using zein formulations
Authors: Tavares-Negrete Jorge Alfonso , Aceves-Colin Alberto Emanuel , Rivera-Flores Delia Cristal , Díaz-Armas Gladys Guadalupe , Mertgen Anne-Sophie , Trinidad-Calderón Plinio Alejando , Olmos-Cordero Jorge Miguel , Gómez-López Elda Graciela , Pérez-Carrillo Esther , Escobedo-Avellaneda Zamantha Judith , Tamayol Ali , Moisés Alvarez Mario , Trujillo-de Santiago Grissel
Published: July 2020

The use of three-dimensional (3D) printing for biomedical applications has expanded exponentially in recent years. However, the current portfolio of 3D printable inks is still limited. For instance, only a few protein matrices have been explored as printing/bioprinting materials. Here, we introduce the use of zein, the primary constitutive protein in maize seeds, as a 3D-printable material. Zein-based inks were prepared by dissolving commercial zein powder in ethanol with or without polyethylene glycol (PEG400) as a plasticizer. The rheological characteristics of our materials, studied during 21 days of aging/maturation, showed an increase in the apparent viscosity as a function of time in all formulations. The addition of PEG 400 decreased the apparent viscosity. Inks with and without PEG400 and at different maturation times were tested for printability in a BioX bioprinter. We optimized the 3D printing parameters for each ink formulation in terms of extrusion pressure and linear printing velocity. Higher fidelity structures were obtained with inks that had maturation times of 10 to 14 days. We present different proof-of-concept experiments to demonstrate the versatility of the engineered zein inks for diverse biomedical applications. These include printing of complex and/or free-standing 3D structures, materials for controlled drug release, and scaffolds for cell culture.
High-throughput identification of nuclear envelope protein interactions inSchizosaccharomyces pombeusing an arrayed membrane yeast-two hybrid library
Authors: Varberg Joseph M. , Gardner Jennifer M. , McCroskey Scott , Saravanan Snehabala , Bradford William D. , Jaspersen Sue L.
Published: July 2020

The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins in the fission yeastSchizosaccharomyces pombefor high-throughput screening using the split-ubiquitin based membrane yeast two hybrid sys-tem. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nu-clear membrane: Cut11/Ndc1, Lem2, and Ima1/Samp1/NET5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitivecut11mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.
Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials
Authors: Rufa Dominic A. , Bruce Macdonald Hannah E. , Fass Josh , Wieder Marcus , Grinaway Patrick B. , Roitberg Adrian E. , Isayev Olexandr , Chodera John D.
Published: July 2020

Alchemical free energy methods with molecular mechanics (MM) force fields are now widely used in the prioritization of small molecules for synthesis in structure-enabled drug discovery projects because of their ability to deliver 1–2 kcal mol−1accuracy in well-behaved protein-ligand systems. Surpassing this accuracy limit would significantly reduce the number of compounds that must be synthesized to achieve desired potencies and selectivities in drug design campaigns. However, MM force fields pose a challenge to achieving higher accuracy due to their inability to capture the intricate atomic interactions of the physical systems they model. A major limitation is the accuracy with which ligand intramolecular energetics—especially torsions—can be modeled, as poor modeling of torsional profiles and coupling with other valence degrees of freedom can have a significant impact on binding free energies. Here, we demonstrate how a new generation of hybrid machine learning / molecular mechanics (ML/MM) potentials can deliver significant accuracy improvements in modeling protein-ligand binding affinities. Using a nonequilibrium perturbation approach, we can correct a standard, GPU-accelerated MM alchemical free energy calculation in a simple post-processing step to efficiently recover ML/MM free energies and deliver a significant accuracy improvement with small additional computational effort. To demonstrate the utility of ML/MM free energy calculations, we apply this approach to a benchmark system for predicting kinase:inhibitor binding affinities—a congeneric ligand series for non-receptor tyrosine kinase TYK2 (Tyk2)—wherein state-of-the-art MM free energy calculations (with OPLS2.1) achieve inaccuracies of 0.93±0.12 kcal mol−1in predicting absolute binding free energies. Applying an ML/MM hybrid potential based on the ANI2x ML model and AMBER14SB/TIP3P with the OpenFF 1.0.0 (“Parsley”) small molecule force field as an MM model, we show that it is possible to significantly reduce the error in absolute binding free energies from 0.97 [95% CI: 0.68, 1.21] kcal mol−1(MM) to 0.47 [95% CI: 0.31, 0.63] kcal mol−1(ML/MM).
In vitroreduction ofPlasmodium falciparumgametocytes byArtemisia spp.tea infusions
Authors: Snider Danielle , Weathers Pamela J.
Published: July 2020

In this study, we showedin vitroevidence that supports the efficacy ofA. annuaandA. afratea infusions used in a 2015 clinical trial not only for clearing asexualPlasmodium falciparumparasites, but also for eliminating sexual gametocytes.P. falciparumNF54 was grownin vitro,synchronized, and induced to form gametocytes using N-acetylglucosamine. Cultures during asexual, early, and late stage gametogenesis were treated with artemisinin, methylene blue, andArtemisia annuaandA. afratea infusions (5g DW/L) using cultivars that contained 0-283 μM artemisinin. Asexual parasitemia and gametocytemia were analyzed microscopically. Gametocyte morphology was also scored. Markers of early(PfGEXP5)and late stage(Pfs25)gametocyte gene expression were also measured using RT-qPCR. BothA. annuaandA. afratea infusions reduced gametocytemiain vitro, and the effect was mainly artemisinin dependent. Expression levels of both marker genes were reduced with the effect mainly attributed to artemisinin content of the our testedArtemisiacultivars. Tea infusions of both species also inhibited asexual parasitemia and although mainly artemisinin dependent, there was a weak antiparasitic effect from artemisinin-deficientA. afra. These results showed thatA. annuaand to a lesser extent,A. afra,inhibited parasitemia and gametogenesisin vitro,and results are consistent with earlier observed clinical results.
Bringing the pancreas patient back to the bench:Ex vivoculture of intact human patient derived pancreatic tumour tissue
Authors: Kokkinos John , Sharbeen George , Haghighi Koroush S. , Ignacio Rosa Mistica C. , Kopecky Chantal , Gonzales-Aloy Estrella , Youkhana Janet , Pandzic Elvis , Boyer Cyrille , Davis Thomas P. , Butler Lisa M. , Goldstein David , McCarroll Joshua A. , Phillips Phoebe A.
Published: July 2020

The poor prognosis of pancreatic ductal adenocarcinoma (PDAC) is attributed to the highly fibrotic stroma and complex multi-cellular microenvironment that is difficult to fully recapitulate in pre-clinical human models. To fast-track translation of therapies and to inform personalised medicine, we aimed to develop a whole-tissueex vivoexplant model that maintains viability, 3D multicellular architecture, and microenvironmental cues present in human pancreatic tumours. Patient-derived surgically-resected PDAC tissue was cut into 2 mm explants, cultured on gelatin sponges, and grown for 12 days. Immunohistochemistry revealed that human PDAC tissue explants were viable for 12 days and maintained their original tumour, stromal and extracellular matrix architecture. As proof-of-principle, human PDAC tissue explants responded to Abraxane®treatment with a 3.7-fold increase in cell-death (p=0.0007). PDAC explants were also transfected with polymeric nanoparticles+Cy5-siRNA and we observed abundant cytoplasmic distribution of nanoparticle+Cy5-siRNA throughout the PDAC explant tissue. Our novel model retains the 3D architecture of human pancreatic tumours and has several advantages over standard organoids: presence of functional multi-cellular stroma and fibrosis and no tissue manipulation, digestion, or artificial propagation of organoids. This provides an unprecedented opportunity to study PDAC biology, tumour-stromal interactions and rapidly assess therapeutic response that could drive personalised treatment for PDAC.
STIL-a novel link in Shh and Wnt signaling, endowing oncogenic and stem like attributes to colorectal cancer
Authors: Pradhan Tapas , Kumar Vikas , Evangeline Surya H , Krishna R , John Samu , Jissa VT , Anjana S , Chandramohan K , Nair S Asha
Published: July 2020

Discovery of potent gene regulating tumorigenesis and drug resistance is of high clinical importance. STIL is an oncogene, however its molecular insights and role in colorectal oncogenesis are unknown. In this study we have explored role of STIL in tumorigenesis and studied its molecular targets in colorectal cancer (CRC). STIL silencing reduced proliferation and tumor growth in CRC. Further, STIL was found to regulate stemness markers CD133 & CD44 and drug resistant markers Thymidylate synthase, ABCB1 & ABCG2 both in in-vitro and in-vivo CRC models. In addition, over expression of STIL mRNA was found to be associated with reduced disease free survival in CRC cases. To our surprise we observed an Shh independent regulation of stemness and drug resistant genes mediated by STIL. Interestingly, we found an Shh independent regulation of β-catenin mediated by STIL via p-AKT, which partially answers Shh independent regulatory mechanism of CSC markers by STIL. Our study suggest an instrumental role of STIL in molecular manifestation of CRC and progression.
Diffraction gratings with two-orders-of-magnitude-enhanced dispersion rates for sub-meV resolution soft X-ray spectroscopy
Authors: Shvyd'ko Yuri
Published: July 2020

Diffraction gratings with large angular dispersion rates are central to obtaining high spectral resolution in grating spectrometers operating over a broad spectral range from infrared to soft X-ray domains. The greatest challenge is of course to achieve large dispersion rates in the short-wavelength X-ray domain. Here it is shown that crystals in non-coplanar asymmetric X-ray Bragg diffraction can function as high-reflectance broadband soft X-ray diffraction gratings with dispersion rates that are at least two orders of magnitude larger than those that are possible with state-of-the-art man-made gratings. This opens new opportunities to design and implement soft X-ray resonant inelastic scattering (RIXS) spectrometers with spectral resolutions that are up to two orders of magnitude higher than what is currently possible, to further advance a very dynamic field of RIXS spectroscopy, and to make it competitive with inelastic neutron scattering. Examples of large-dispersion-rate crystal diffraction gratings operating near the 930 eV L
3 absorption edge in Cu and of the 2.838 keV L
3-edge in Ru are presented.
Evolution of conformal antenna design with the aid of probability improved crow search algorithm
Authors: Nagendra Nama Ajay , Pappula Lakshman
Published: July 2020

Purpose

The issues of radiating sources in the existence of smooth convex matters by such objects are of huge significance in the modeling of antennas on structures. Conformal antenna arrays are necessary when an antenna has to match to certain platforms. A fundamental problem in the design is that the possible surfaces for a conformal antenna are infinite in number. Furthermore, if there is no symmetry, each element will see a different environment, and this complicates the mathematics. As a consequence, the element factor cannot be factored out from the array factor.

Design/methodology/approach

This paper intends to enhance the design of the conformal antenna. Here, the main objective of this task is to maximize the antenna gain and directivity from the first-side lobe and other side-lobes in the two way radiation pattern. Thus the adopted model is designed as a multiobjective concern. In order to attain this multiobjective function, both the element spacing and the radius of each antenna element should be optimized based on the probability of the Crow Search Algorithm (CSA). Thus the proposed method is named Probability Improved CSA (PI-CSA). Here, the First Null Beam Width (FNBW) and Side-Lobe Level (SLL) are minimized. Moreover, the adopted scheme is compared with conventional algorithms, and the results are attained.

Findings

From the analysis, the gain of the presented PI-CSA scheme in terms of best performance was 52.68% superior to ABC, 25.11% superior to PSO, 13.38% superior to FF and 3.21% superior to CS algorithms. Moreover, the mean performance of the adopted model was 62.94% better than ABC, 13.06% better than PSO, 24.34% better than FF and 10.05% better than CS algorithms. By maximizing the gain and directivity, FNBW and SLL were decreased. Thus, the optimal design of the conformal antenna has been attained by the proposed PI-CSA algorithm in an effective way.

Originality/value

This paper presents a technique for enhancing the design of the conformal antenna using the PI-CSA algorithm. This is the first work that utilizes PI-CSA-based optimization for improving the design of the conformal antenna.
Simplified analysis of cable-stayed bridges with longitudinal viscous dampers
Authors: Li Xu , Li Jun , Zhang Xiaoyi , Gao Jianfeng , Zhang Chao
Published: July 2020

Purpose

Viscous dampers are commonly used in large span cable-stayed bridges to mitigate seismic effects and have achieved great success.

Design/methodology/approach

However, the nonlinear analysis on damper parameters is usually computational intensive and nonobjective. To address these issues, this paper proposes a simplified method to determine the viscous damper parameters for double-tower cable-stayed bridges. An empirical formula of the equivalent damping ratio of viscous dampers is established through decoupling nonclassical damping structures and linearization of nonlinear viscous dampers. Shaking table tests are conducted to verify the feasibility of the proposed method. Moreover, this simplified method has been proved in long-span cable-stayed bridges.

Findings

The feasibility of this method is verified by the simplified model shaking table test. This simplified method for determining the parameters of viscous dampers is verified in cable-stayed bridges with different spans.

Originality/value

This simplified method has been validated in cable-stayed bridges with various spans.
Public investment and private sector performance in Nigeria
Authors: Adeosun Opeoluwa Adeniyi , Orisadare Monica Adele , Fagbemi Fisayo , Adedokun Sikiru Adetona
Published: July 2020

Purpose

This study explores the asymmetric linkage between public investment and private sector performance in Nigeria. This is due to the presence of nonlinear structures in the behavior of domestic investment series with evidences of structural time breaks, which fall within periods of global financial crises and oil shocks.

Design/methodology/approach

Main data on gross capital formation, gross fixed capital formation, domestic credit to private sector, domestic credit to private sector by banks are used for the study span through 1986 to 2017. Evidence of asymmetry spurs the study to adopt the nonlinear autoregressive distributed lag, asymmetric generalized impulse response and variance decomposition and asymmetric granger causality techniques.

Findings

It is shown that positive (negative) investment shocks exhibit a non-negligible and substantial stimulating (dampening) influence on the long-run performance of private sector in the economy. However, there is evidence that negative investment shocks portend a positive influence on the performance of private sector in the short run. This suggests that negative shocks to investment may not dampen the effectiveness of private sector in the short run, and this thus brings to bear the debate on the tenability of public investment as a potent counter cyclical tool in enhancing short-run private sector growth. The nonlinear granger causality also shows a unidirectional nonlinear causality from public investment to private sector performance. However, there is no evidence of bidirectional nonlinear causality.

Originality/value

This study provides quantitative evidence that Nigeria still depends exclusively on public investment, and as an oil-based rentier economy its economic diversification drive still remains bleak.
Supply chain integration and its impact on supply chain agility and organizational flexibility in manufacturing firms
Authors: Shukor Ahmad Azwan Ahmad , Newaz Md. Shah , Rahman Muhammad Khalilur , Taha Azni Zarina
Published: July 2020

Purpose

This study investigates the impact of environmental uncertainty and organizational ambidexterity on supply chain integration and its relationship between supply chain agility and organizational flexibility in the manufacturing firms.

Design/methodology/approach

The data were collected from 526 managers in services and manufacturing industry in Kuala Lumpur. The partial least square (SmartPLS 3.0) tool was applied through the use of the structural equation modeling (SEM) technique.

Findings

The results revealed that a strong relationship exist between environmental uncertainty and supply chain integrations including customer, supplier and internal integration. Organizational ambidexterity has a significant relationship with supply chain integration. Supply chain integrations were shown to have a positive impact on the firm's supply chain agility and organizational flexibility.

Originality/value

The findings may assist to establish a set of key drivers for enhancing supply chain agility and organizational flexibility as a supply chain management initiative in the manufacturing and service industry.