### Recent Submissions

• #### A zero liquid discharge system integrating multi-effect distillation and evaporative crystallization for desalination brine treatment

(Desalination, Elsevier BV, 2021-01-13) [Article]
• #### Generation of iPSC lines (KAUSTi011-A, KAUSTi011-B) from a Saudi patient with epileptic encephalopathy carrying homozygous mutation in the GLP1R gene.

(Stem cell research, Elsevier BV, 2021-01-09) [Article]
Glucagon-like peptide-1 receptor (GLP1R) is a seven-transmembrane-spanning helices membrane protein expressed in multiple human tissues including pancreatic islets, lung, brain, heart and central nervous system (CNS). GLP1R agonists are commonly used as antidiabetic drugs, but a neuroprotective function in neurodegenerative disorders is emerging. Here, we established two iPSC lines from a patient harboring a rare homozygous splice site variant in GLP1R (NM_002062.3; c.402 + 3delG). This patient displays severe developmental delay and epileptic encephalopathy. Therefore, the derivation of these iPSC lines constitutes a primary model to study the molecular pathology of GLP1R dysfunction and develop novel therapeutic targets.
• #### Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

(Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
• #### Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites.

(Journal of translational medicine, Springer Science and Business Media LLC, 2021-01-08) [Article]
BackgroundMetastasis is the most devastating stage of cancer progression and often shows a preference for specific organs.MethodsTo reveal the mechanisms underlying organ-specific metastasis, we systematically analyzed gene expression profiles for three common metastasis sites across all available primary origins. A rank-based method was used to detect differentially expressed genes between metastatic tumor tissues and corresponding control tissues. For each metastasis site, the common differentially expressed genes across all primary origins were identified as organ-specific metastasis genes.ResultsPathways enriched by these genes reveal an interplay between the molecular characteristics of the cancer cells and those of the target organ. Specifically, the neuroactive ligand-receptor interaction pathway and HIF-1 signaling pathway were found to have prominent roles in adapting to the target organ environment in brain and liver metastases, respectively. Finally, the identified organ-specific metastasis genes and pathways were validated using a primary breast tumor dataset. Survival and cluster analysis showed that organ-specific metastasis genes and pathways tended to be expressed uniquely by a subgroup of patients having metastasis to the target organ, and were associated with the clinical outcome.ConclusionsElucidating the genes and pathways underlying organ-specific metastasis may help to identify drug targets and develop treatment strategies to benefit patients.
• #### Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection

(Frontiers in bioengineering and biotechnology, Frontiers Media SA, 2021-01-08) [Article]
Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the nonpathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.
• #### Strong enhancement of Penning ionisation in cold Rydberg gases II: Tom and Jerry pairs for alkali-metal atoms

(Journal of Physics B: Atomic, Molecular and Optical Physics, IOP Publishing, 2021-01-08) [Article]
Penning ionisation (PI) processes involving pairs of Rydberg alkali-metal atoms, excited to different quantum states and experiencing dipole-dipole interactions, have a wide range of important properties in atomic physics. Within the framework of the semi-classical approximation, we have used both numerical and analytical approaches to examine the Penning autoionisation width dependence on the state quantum numbers in a quasi-molecule formed by the interacting partner atoms. We described the characteristics of optimal quantum numbers that lead to enhanced PI widths for the interacting Rydberg atom pairs of all alkali-metal atoms. The excited states of atoms in these pairs are asymmetric, resulting in a large atomic shell size difference: inspired by [1], we call such pair "Tom" and "Jerry" (for "big" and "small"). Compared to symmetric pairs, the optimal asymmetric pairs display a significant (by several orders of magnitude) increase in the PI rate. This property makes PI a relevant source for producing charged particles in cold Rydberg systems that spontaneously evolve into cold plasma. Contrary to hydrogen atoms examined in [1], the difference of quantum defects in alkali-metal atoms results in a strong Penning width dependence on the orbital quantum numbers l of the quasi-molecule. In particular, alkali-metal atoms exhibit two PI channels associated with bound-bound optical transitions showing ∆l = ±1 - individual and closely spaced (doublet-like) configurations of optimal pairs. Furthermore, we demonstrate that the presence of Förster resonances can lead to a notable (up to 5 times) increase of the PI efficiency.
• #### Molecular basis for the adaptive evolution of environment sensing by H-NS proteins

(eLife, eLife Sciences Publications, Ltd, 2021-01-07) [Article]
The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less NMR spectroscopy and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS–mediated environmental sensing and suggests that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
• #### Chain Conformation Control of Fluorene-Benzothiadiazole Copolymer Light-Emitting Diode Efficiency and Lifetime

(ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2021-01-07) [Article]
The β-phase, in which the intermonomer torsion angle of a fraction of chain segments approaches ∼180°, is an intriguing conformational microstructure of the widely studied light-emitting polymer poly(9,9-dioctylfluorene) (PFO). Its generation can in turn be used to significantly improve the performance of PFO emission-layer-based light-emitting diodes (LEDs). Here, we report the generation of β-phase chain segments in a copolymer, 90F8:10BT, containing 90% 9,9-dioctylfluorene (F8) and 10% 2,1,3-benzothiadiazole (BT) units and show that significant improvements in performance also ensue for LEDs with β-phase 90F8:10BT emission layers, generalizing the earlier PFO results. The β-phase was induced by both solvent vapor annealing and dipping copolymer thin films into a solvent/nonsolvent mixture. Subsequent absorption spectra show the characteristic fluorene β-phase peak at ∼435 nm, but luminescence spectra (∼530 nm peak) and quantum yields barely change, with the emission arising following efficient energy transfer to the lowest-lying excited states localized in the vicinity of the BT units. For ∼5% β-phase chain segment fraction relative to 0% β-phase, the LED luminance at 10 V increased by ∼25% to 5940 cd m<sup>-2</sup>, the maximum external quantum efficiency by ∼61 to 1.91%, and the operational stability from 64% luminance retention after 20 h of operation to 90%. Detailed studies addressing the underlying device physics identify a reduced hole injection barrier, higher hole mobility, correspondingly more balanced electron and hole charge transport, and decreased carrier trapping as the dominant factors. These results confirm the effectiveness of chain conformation control for fluorene-based homo- and copolymer device optimization.
• #### Dark Self-Healing Mediated Negative Photoconductivity of Lead-Free Cs3Bi2Cl9 Perovskite Single Crystal

(arXiv, 2021-01-07) [Preprint]
Halide perovskites are recently emerged as one of the frontline optoelectronic materials for device applications and have been extensively studied in past few years. Among these while, lead-based materials were most widely explored, investigation of optical properties of lead-free perovskites is limited. Being optically active, these materials were expected to show light-induced enhanced photoconductivity and the same was reported for lead halide perovskite single crystals. However, on contrary, herein, light-induced degradation of bismuth halide perovskite Cs3Bi2Cl9 single crystals is reported which was evidenced by negative photoconductivity with slow recovery. The femtosecond transient reflectance (fs-TR) spectroscopy studies further revealed these electronic transport properties were due to the formation of light-activated metastable trap states within the perovskite crystal. The figure of merits of Cs3Bi2Cl9 single-crystal detectors such as responsivity (17 mA/W), detectivity (6.23 X 10power 11 Jones) and the ratio of current in dark to light (~7160) was calculated and it is found that they are comparable or higher to reported perovskite single crystals based positive photodetectors. This observation for lead-free perovskite single crystals which were optically active but showed retroactive photocurrent on irradiation remained unique for such materials.
• #### Landslide size matters: a new spatial predictive paradigm

(California Digital Library (CDL), 2021-01-07) [Preprint]
The standard definition of landslide hazard requires the estimation of where, when (or how frequently) and how large a given landslide event may be. The geomorphological community involved in statistical models has addressed the component pertaining to how large a landslide event may be by introducing the concept of landslide-event magnitude scale. This scale, which depends on the planimetric area of the given population of landslides, in analogy to the earthquake magnitude, has been expressed with a single value per landslide event. As a result, the geographic or spatially-distributed estimation of how large a population of landslide may be when considered at the slope scale, has been disregarded in statistically-based landslide hazard studies. Conversely, the estimation of the landslide extent has been commonly part of physically-based applications, though their implementation is often limited to very small regions.
• #### Tractable Bayes of Skew-Elliptical Link Models for Correlated Binary Data

(arXiv, 2021-01-06) [Preprint]
Correlated binary response data with covariates are ubiquitous in longitudinal or spatial studies. Among the existing statistical models the most well-known one for this type of data is the multivariate probit model, which uses a Gaussian link to model dependence at the latent level. However, a symmetric link may not be appropriate if the data are highly imbalanced. Here, we propose a multivariate skew-elliptical link model for correlated binary responses, which includes the multivariate probit model as a special case. Furthermore, we perform Bayesian inference for this new model and prove that the regression coefficients have a closed-form unified skew-elliptical posterior. The new methodology is illustrated by application to COVID-19 pandemic data from three different counties of the state of California, USA. By jointly modeling extreme spikes in weekly new cases, our results show that the spatial dependence cannot be neglected. Furthermore, the results also show that the skewed latent structure of our proposed model improves the flexibility of the multivariate probit model and provides better fit to our highly imbalanced dataset.
• #### Ion-exchange doped polymers at the degenerate limit: what limits conductivity at 100% doping efficiency?

(arXiv, 2021-01-05) [Preprint]
Doping of semiconducting polymers has seen a surge in research interest driven by emerging applications in sensing, bioelectronics and thermoelectrics. A recent breakthrough was a doping technique based on ion-exchange, which separates the redox and charge compensation steps of the doping process. The improved microstructural control this process allows enables us for the first time to systematically address a longstanding but still poorly understood question: what limits the electrical conductivity at high doping levels? Is it the formation of charge carrier traps in the Coulomb potentials of the counterions, or is it the structural disorder in the polymer lattice? Here, we apply ion-exchange doping to several classes of high mobility conjugated polymers and identify experimental conditions that achieve near 100% doping efficiency under degenerate conditions with nearly 1 charge per monomer. We demonstrate very high conductivities up to 1200 S/cm in semicrystalline polymer systems, and show that in this regime conductivity is poorly correlated with ionic size, but strongly correlated with paracrystalline disorder. This observation, backed by a detailed electronic structure model that incorporates ion-hole and hole-hole interactions and a carefully parameterized model of disorder, indicates that trapping by dopant ions is negligible, and that maximizing crystalline order is critical to improving conductivity.