bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptomic response of brain tissue to focused ultrasound‐mediated blood–brain barrier disruption depends strongly on anesthesia
Authors: Mathew Alexander S. , Gorick Catherine M. , Thim E. Andrew , Garrison William J. , Klibanov Alexander L. , Miller G. Wilson , Sheybani Natasha D. , Price Richard J.
Published: November 2020

Focused ultrasound (FUS) mediated blood–brain barrier disruption (BBBD) targets the delivery of systemically‐administered therapeutics to the central nervous system. Preclinical investigations of BBBD have been performed on different anesthetic backgrounds; however, the influence of the choice of anesthetic on the molecular response to BBBD is unknown, despite its potential to critically affect interpretation of experimental therapeutic outcomes. Here, using bulk RNA sequencing, we comprehensively examined the transcriptomic response of both normal brain tissue and brain tissue exposed to FUS‐induced BBBD in mice anesthetized with either isoflurane with medical air (Iso) or ketamine/dexmedetomidine (KD). In normal murine brain tissue, Iso alone elicited minimal differential gene expression (DGE) and repressed pathways associated with neuronal signaling. KD alone, however, led to massive DGE and enrichment of pathways associated with protein synthesis. In brain tissue exposed to BBBD (1 MHz, 0.5 Hz pulse repetition frequency, 0.4 MPa peak‐negative pressure), we systematically evaluated the relative effects of anesthesia, microbubbles, and FUS on the transcriptome. Of particular interest, we observed that gene sets associated with sterile inflammatory responses and cell–cell junctional activity were induced by BBBD, regardless of the choice of anesthesia. Meanwhile, gene sets associated with metabolism, platelet activity, tissue repair, and signaling pathways, were differentially affected by BBBD, with a strong dependence on the anesthetic. We conclude that the underlying transcriptomic response to FUS‐mediated BBBD may be powerfully influenced by anesthesia. These findings raise considerations for the translation of FUS‐BBBD delivery approaches that impact, in particular, metabolism, tissue repair, and intracellular signaling.
Histopathological characterization of intimal lesions and arterial wall calcification in the arteries of the leg of elderly cadavers
Authors: Vos Annelotte , de Jong Pim A. , Verdoorn Daphne , Mali Willem P. T. M. , Bleys Ronald L. A. W. , Vink Aryan
Published: November 2020

Introduction

Although arteries of the leg have been studied in extensively diseased amputation specimens, little is known about the composition of vascular lesions present in the general population. The aim of this study was to describe the natural development of adaptive intimal thickening, atherosclerotic lesion development and vascular calcification in the leg of a general elderly population.

Materials and Methods

Two hundred and seventy postmortem samples from the popliteal and posterior tibial arteries of 14 elderly cadavers were studied histologically.

Results

Atherosclerotic lesions were more frequently observed in the popliteal (60%) than in the posterior tibial artery (34%; p < .0005). These atherosclerotic plaques were most often nonatheromatous (80% and 83% for popliteal and posterior tibial plaques, respectively). The atheroma's that were present were small (most <25% of plaque area). Atherosclerotic plaque calcification was observed more often in the popliteal (39%) than in the posterior tibial samples (17%; p < .0005). Medial arterial calcification was observed more often in the posterior tibial (62%) than in the popliteal samples (46%; p = .008). Plaque calcification and medial arterial calcification were not associated with lumen stenosis.

Conclusions

In the leg of elderly cadavers, the presence of atherosclerotic plaque and intimal calcification decreases from the proximal popliteal artery to the more distal posterior tibial artery and most atherosclerotic lesions are of the fibrous nonatheromatous type. In contrast, the presence and severity of medial calcification increases from proximal to distal.
Unleashing the Power of Biocatalysts
Authors: Chen Mengbin
Published: November 2020

Biocatalysis is a continuously expanding subfield in chemical biology. Herein, I describe two categories of biocatalysts, the LEGO‐brick‐like and game‐console‐like type, both of which can streamline the synthetic routes to therapeutics. A multi‐disciplinary approach to expand the biocatalytic toolkit will open up opportunities to develop new therapeutics.
Computational Hot‐Spot Analysis of the SARS‐CoV‐2 Receptor Binding Domain/ACE2 Complex**
Authors: Rosario Pedro A. , McNaughton Brian R.
Published: November 2020

Infection and replication of SARS CoV‐2 (the virus that causes COVID‐19) requires entry to the interior of host cells. In humans, a protein–protein interaction (PPI) between the SARS CoV‐2 receptor‐binding domain (RBD) and the extracellular peptidase domain of ACE2 on the surface of cells in the lower respiratory tract is an initial step in the entry pathway. Inhibition of the SARS CoV‐2 RBD/ACE2 PPI is currently being evaluated as a target for therapeutic and/or prophylactic intervention. However, relatively little is known about the molecular underpinnings of this complex. Employing multiple computational platforms, we predicted “hot‐spot” residues in a positive‐control PPI (PMI/MDM2) and the CoV‐2 RBD/ACE2 complex. Computational alanine scanning mutagenesis was performed to predict changes in Gibbs’ free energy that are associated with mutating residues at the positive control (PMI/MDM2) or SARS RBD/ACE2 binding interface to alanine. Additionally, we used the Adaptive Poisson‐Boltzmann Solver to calculate macromolecular electrostatic surfaces at the interface of the positive‐control PPI and SARS CoV‐2/ACE2 PPI. Finally, a comparative analysis of hot‐spot residues for SARS‐CoV and SARS‐CoV‐2, in complex with ACE2, is provided. Collectively, this study illuminates predicted hot‐spot residues, and clusters, at the SARS CoV‐2 RBD/ACE2 binding interface, potentially guiding the development of reagents capable of disrupting this complex and halting COVID‐19.
Electrochemical Quantification of Neurotransmitters in Single Live Cell Vesicles Shows Exocytosis is Predominantly Partial
Authors: Wang Ying , Ewing Andrew
Published: November 2020

Exocytosis plays an essential role in the communication between cells in the nervous system. Understanding the regulation of neurotransmitter release during exocytosis and the amount of neurotransmitter content that is stored in vesicles is of importance, as it provides fundamental insights to understand how the brain works and how neurons elicit a certain behavior. In this minireview, we summarize recent progress in amperometric measurements for monitoring exocytosis in single cells and electrochemical cytometry measurements of vesicular neurotransmitter content in individual vesicles. Important steps have increased our understanding of the different mechanisms of exocytosis. Increasing evidence is firmly establishing that partial release is the primary mechanism of release in multiple cell types.
Superior Proton‐Transfer Catalytic Promiscuity of Cytochrome c in Self‐Organized Media
Authors: Rani Sheetal , Dasgupta Basundhara , Bhati Gaurav Kumar , Tomar Kalpana , Rakshit Sabyasachi , Maiti Subhabrata
Published: November 2020

Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton‐transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750‐fold on self‐organized systems like micelles and vesicles. The self‐organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid–base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6–7.4. Interestingly, we found almost 750‐fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.
Initial clinical experience with VersaCross transseptal system for transcatheter mitral valve repair
Authors: Sayah Neila , Simon Francois , Garceau Patrick , Ducharme Anique , Basmadjian Arsene , Bouchard Denis , Pellerin Michel , Bonan Raoul , Asgar Anita W.
Published: November 2020

Objectives

The aim of this study is to describe the initial experience with versacross transseptal (TS) system for transseptal puncture for the transcatheter mitral valve repair using the MitraClip device.

Background

Transeptal puncture is a key step in transcatheter mitral valve repair (MVR) and the use of the VersaCross system comprised of a sheath, a dilator and a radiofrequency wire has not been previously described.

Methods

Prospective single center study of consecutive patients undergoing transcatheter mitral valve repair with the MitraClip device were included. Targeted TS puncture was performed under transesophageal echocardiographic (TEE) guidance. Baseline demographics, procedural characteristics, and major adverse procedural events were collected.

Results

Twenty‐five consecutive patients underwent transseptal puncture using the VersaCross TS system. Transseptal puncture was successful in 100% of patients. The mean time for TS puncture was 3 3 ± 1.6 min with no major adverse procedural events. The mean time from insertion of the VersaCross system to insertion of the MitraClip guide catheter was 3.8 ± 3.0 minutes.

Conclusion

The VersaCross TS system was successful in all patients for MitraClip procedure with no adverse procedural events and may be associated with increased procedural efficiency.
Transcatheter mitral valve thrombosis: A case report and literature review
Authors: Alarfaj Mohammad , Jain Tushina , Krepp Joseph
Published: November 2020

Transcatheter mitral valve replacement (TMVR) is an exciting alternative therapy for complex patients with mitral valve disease. Experience with TMVR is new and there is a lot yet to discover about their durability, long‐term outcomes, and complications including mitral transcatheter heart valve (THV) thrombosis. Many factors have been speculated to increased risk of THV thrombosis. Here, we report a case of a 72‐year‐old woman who developed mitral THV thrombosis after undergoing TMVR for severe mitral regurgitation with mitral annular calcification. We reviewed 42 TMVR papers with 1,484 patients, including 60 with mitral THV thrombosis. We discussed the most common strategies used for mitral THV thromboprophylaxis and treatment.
Thyroid angiosarcoma (TAS) — A rare diagnosis not to be missed
Authors: Kehagias Dimitrios , Kostopoulou Eirini , Ravazoula Panagiota , Panagopoulos Konstantinos
Published: November 2020

Raising awareness about primary TAS, a rare and aggressive mesenchymal tumor, is important so that early diagnosis and undelayed radical surgery along with complementary radiation are possible. Extending the existing knowledge on the course and final outcome of the disease may help identify the best treatment approach to improve survival.
Succinic semialdehyde dehydrogenase deficiency presenting with central hypothyroidism
Authors: Alghamdi Malak Ali , Alkhamis Waleed H. , Jamjoom Dima Z. , Al Khalifah Reem , Alshammari Nawaf Rahi , Alsumaili Khalid , Arold Stefan T.
Published: November 2020

Central hypothyroidism might be another clinical sign of SSADH deficiency which prompts urinary organic acid screening for GHB in central hypothyroidism patients. Studies on GABA and thyroid hormone interaction might be a concept of a new therapy.
Two Challenging Cases with COVID heart
Authors: Asadian Sanaz , Hosseini Leila , Maadani Mohsen , Jahanshahi Bahareh , Rezaeian Nahid
Published: November 2020

COVID‐19 affects the heart through various pathways. It can increase thrombotic complications that ultimately lead to myocardial infarction even in patients without a history of underlying heart disease.
Carbamazepine‐induced Stevens‐Johnson syndrome in a patient with history of methotrexate‐induced mast cell activation syndrome
Authors: Zaalouk Tamer Mohamed , Bitar Zouheir Ibrahim , Maadarani Ossama Sajeh , Elhabibi Mohamed Elsayed
Published: November 2020

Stevens‐Johnson syndrome (SJS) is serious conditions that happen as a result of infection, side effects to medications, or unknown etiology. Carbamazepine is one of the common medications that can cause SJS. Good history taking is crucial if treatment with carbamazepine is clinically indicated. We would like to alert all physicians that carbamazepine should be avoided in any patient with a previous history of drug reaction such as mast cell activation syndrome.
Pathophysiological aspects of posterior reversible encephalopathy syndrome in two peritoneal‐dialyzed children
Authors: Keller Tamara , Wille David‐Alexander , Laube Guido F.
Published: November 2020

Hypotension, blood pressure fluctuation, and endothelial impairment indicate possible additive pathophysiological aspects in the development of posterior reversible encephalopathy syndrome in children on peritoneal dialysis.
Four narrow dental implants and conventionally cast bar‐supported removable hybrid acrylic complete denture as a therapeutic modality for terminal dentition
Authors: Alfarsi Mohammed A. , Shaik Sharaz
Published: November 2020

The report portrays four narrow implants and cast bar‐supported removable hybrid acrylic complete dentures and other terminal dentition treatment options in the maxilla. The therapeutic module could be efficient and satisfactory to patients.
Characterization of a New Structured Packing by Computational Fluid Dynamics
Authors: Hassanvand Amin , Esmaeili-Faraj Seyyed Hamid , Moghaddam Mojtaba Saei , Moradi Rasoul
Published: November 2020

The novel wire gauze structured packing PACK‐1300Y with high specific surface area was characterized by computational fluid dynamics. The main features of PACK‐1300Y were investigated including the dry and wet pressure drop as well as the height equivalent to a theoretical plate (HETP). Moreover, the flow structure of this packing was described via numerical simulations. To evaluate the amount of HETP and dry and wet pressure drop, 3D computational fluid dynamic modeling with respect to the Eulerian‐Eulerian multiphase approach was applied. The average relative errors were determined between the findings achieved from computational fluid dynamic simulation and experimental findings for mass transfer efficiency and wet and dry pressure drop, respectively.
Plasma spectroscopy + chemometrics: An ideal approach for the spectrochemical analysis of iron phosphate glass samples
Authors: Devangad Praveen , V K Unnikrishnan , M. Yogesha , Kulkarni Suresh D. , Chidangil Santhosh
Published: November 2020

The penultimate aim of all analytical techniques is to provide best quantitative information with high sensitivity and accuracy. Such techniques then can be ideal to estimate the concentration of different species in a sample or to measure the surface concentration and so on. The preliminary step involved in quantitative analysis is evaluation of the system response for a given amount of the analyte under investigation. Different methodologies are proposed and executed for the above mentioned purpose. In this work, we have demonstrated the performance of chemometric methods to study the atomic emissions from simulated nuclear waste glasses. Five samples of iron‐phosphate glasses were synthesized by doping Cr, Sr, and Ti at various concentrations. The spectra recorded using laser‐induced breakdown spectroscopy (LIBS) system were analyzed using principal component analysis (PCA), partial least square‐discriminant analysis (PLS‐DA), and support vector machines (SVM) for the classification. As compared with the PLS‐DA, SVM provided better results for classification with accuracy of 100% on both calibration and validation sets, respectively. The quantitative analysis of glass samples is carried out using partial least square regression (PLSR) and support vector regression (SVR). The root mean squared error of prediction (RMSEP) is found to be 0.16, 0.20, and 0.08 (wt%) for Cr, Sr, and Ti using PLSR. The detailed investigation elucidates the advantages of chemometrics in handling the complex LIBS spectrum of glass samples and their significance in process control of nuclear waste, nuclear forensics, and so on.
New Luminescent Tetranuclear Lanthanide‐Based Silsesquioxane Cage‐Like Architectures
Authors: Kulakova Alena N. , Bilyachenko Alexey N. , Levitsky Mikhail M. , Khrustalev Victor N. , Shubina Elena S. , Felix Gautier , Mamontova Ekaterina , Long Jérôme , Guari Yannick , Larionova Joulia
Published: November 2020

Invited for the cover of this issue are Alexey N. Bilyachenko, Joulia Larionova and co‐workers at the Russian Academy of Sciences, the Peoples’ Friendship University of Russia, and University of Montpellier. The image depicts lanthanide‐based cage‐like silsesquioxanes exhibiting magnetic and luminescence properties that could constitute a particularly interesting new family related to multifunctional nanomaterials. Read the full text of the article at 10.1002/chem.202003351.
Large‐Amplitude Thermal Vibration‐Coupled Valence Tautomeric Transition Observed in a Conductive One‐Dimensional Rhodium–Dioxolene Complex
Authors: Mitsumi Minoru , Komatsu Yuuki , Hashimoto Masahiro , Toriumi Koshiro , Kitagawa Yasutaka , Miyazaki Yuji , Akutsu Hiroki , Akashi Haruo
Published: November 2020

The exploration of dynamic molecular crystals is a fascinating theme for materials scientists owing to their fundamental science and potential application to molecular devices. Herein, a one‐dimensional (1D) rhodium‐dioxolene complex is reported that exhibits drastic changes in properties with the phase transition. X‐ray photoelectron spectroscopy (XPS) revealed that the room‐temperature (RT) phase is in a mixed‐valence state, and therefore, the drastic changes originate from the mixed‐valence state appearing in the RT phase. Another notable feature is that the mean square displacements of the rhodium atoms along the 1D chain dramatically increased in the RT phase, indicating a large‐amplitude vibration of the Rh−Rh bonds. From these results, a possible mechanism for the appearance of the mixed‐valence state in the RT phase was proposed based on the thermal electron transfer from the 1D d‐band to the semiquinonato π* orbital coupled with the large‐amplitude vibration of the Rh−Rh bonds.
Investigation of Luminescent Triplet States in Tetranuclear CuI Complexes: Thermochromism and Structural Characterization
Authors: Boden Pit , Di Martino‐Fumo Patrick , Busch Jasmin M. , Rehak Florian R. , Steiger Sophie , Fuhr Olaf , Nieger Martin , Volz Daniel , Klopper Willem , Bräse Stefan , Gerhards Markus
Published: November 2020

To develop new and flexible CuI containing luminescent substances, we extend our previous investigations on two metal‐centered species to four metal‐centered complexes. These complexes could be a basis for designing new organic light‐emitting diode (OLED) relevant species. Both the synthesis and in‐depth spectroscopic analysis, combined with high‐level theoretical calculations are presented on a series of tetranuclear CuI complexes with a halide containing Cu4X4 core (X=iodide, bromide or chloride) and two 2‐(diphenylphosphino)pyridine bridging ligands with a methyl group in para (4‐Me) or ortho (6‐Me) position of the pyridine ring. The structure of the electronic ground state is characterized by X‐ray diffraction, NMR, and IR spectroscopy with the support of theoretical calculations. In contrast to the para system, the complexes with ortho‐substituted bridging ligands show a remarkable and reversible temperature‐dependent dual phosphorescence. Here, we combine for the first time the luminescence thermochromism with time‐resolved FTIR spectroscopy. Thus, we receive experimental data on the structures of the two triplet states involved in the luminescence thermochromism. The transient IR spectra of the underlying triplet metal/halide‐to‐ligand charge transfer (3M/XLCT) and cluster‐centered (3CC) states were obtained and interpreted by comparison with calculated vibrational spectra. The systematic and significant dependence of the bridging halides was analyzed.
Simultaneous NOx and SO2 removal during wet flue gas desulfurization, using copper smelter slag slurry combined with yellow phorphorus
Authors: Bao Jiacheng , Xiao Helu , Li Kai , Wang Chi , Song Xin , Sun Xin , Ning Ping , Luo Yansu
Published: November 2020

The study of copper slag has attracted the attention of scholars from both China and around the world. But few have paid attention to its applications in the simultaneous removal of SO2 and NOx in wet flue gas desulfurization (WFGD), becasue WFGD technique is inappropriate for directly treating NOx owing to the low solubility of NO. This work aims to improve NOx removal efficiency in WFGD technology using copper slag slurry associated with the oxidation of NOx by yellow phosphorus. Different operating conditions, including dispersion of P4, solid‐liquid ratio, initial pH value of copper slag slurry, reaction temperature, oxygen content, and gas flow rate, were compared regarding the efficiency of SO2 and NOx simultaneous removal. The characterizations were carried out on the liquid and solid part of fresh and spent copper slag slurry after filtration. The results indicated that a great amount of metals ions, such as Fe3+ and Zn2+, were leached by reacting with produced acids (H2SO4, HNO3, and H3PO4), which had a liquid‐phase catalytic oxidation on SIV species (SO32−/HSO3−), leading to promotion in absorption for SO2. The copper slag played a significant role in dispersing the yellow phosphorus and promoting ozone generation, thus improving NOx removal efficiency. The reaction pathway can be divided into three parts: (a) ozone generation induced by yellow phosphorus, (b) the oxidation of NO by O3 and then dissolution in aqueous solution, and (c) the dissolution of SO2 and the liquid‐phase oxidation for SO2 through metal ions produced by the reaction between acid and copper slag.
Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo
Authors: Croci Matteo , Vinje Vegard , Rognes Marie E.
Published: November 2020

Efficient uncertainty quantification algorithms are key to understand the propagation of uncertainty—from uncertain input parameters to uncertain output quantities—in high resolution mathematical models of brain physiology. Advanced Monte Carlo methods such as quasi Monte Carlo (QMC) and multilevel Monte Carlo (MLMC) have the potential to dramatically improve upon standard Monte Carlo (MC) methods, but their applicability and performance in biomedical applications is underexplored. In this paper, we design and apply QMC and MLMC methods to quantify uncertainty in a convection‐diffusion model of tracer transport within the brain. We show that QMC outperforms standard MC simulations when the number of random inputs is small. MLMC considerably outperforms both QMC and standard MC methods and should therefore be preferred for brain transport models.
Recommender‐as‐a‐service with chatbot guided domain‐science knowledge discovery in a science gateway
Authors: Vekaria Komal , Calyam Prasad , Sivarathri Sai Swathi , Wang Songjie , Zhang Yuanxun , Pandey Ashish , Chen Cong , Xu Dong , Joshi Trupti , Nair Satish
Published: November 2020

Scientists in disciplines such as neuroscience and bioinformatics are increasingly relying on science gateways for experimentation on voluminous data, as well as analysis and visualization in multiple perspectives. Though current science gateways provide easy access to computing resources, data sets and tools specific to the disciplines, scientists often use slow and tedious manual efforts to perform knowledge discovery to accomplish their research/education tasks. Recommender systems can provide expert guidance and can help them to navigate and discover relevant publications, tools, data sets, or even automate cloud resource configurations suitable for a given scientific task. To realize the potential of integration of recommenders in science gateways in order to spur research productivity, we present a novel “OnTimeRecommend” recommender system. The OnTimeRecommend comprises of several integrated recommender modules implemented as microservices that can be augmented to a science gateway in the form of a recommender‐as‐a‐service. The guidance for use of the recommender modules in a science gateway is aided by a chatbot plug‐in viz., Vidura Advisor. To validate our OnTimeRecommend, we integrate and show benefits for both novice and expert users in domain‐specific knowledge discovery within two exemplar science gateways, one in neuroscience (CyNeuro) and the other in bioinformatics (KBCommons).
Impact of Ion‐Pairing Effects on Linear and Nonlinear Photophysical Properties of Polymethine Dyes**
Authors: Pascal Simon , Chi San‐Hui , Perry Joseph W. , Andraud Chantal , Maury Olivier
Published: November 2020

The two‐photon absorption (2PA) and photophysics of heptamethine dyes featuring cyanine or dipolar electronic structures have been compared for the first time. The perfectly delocalized cyanine system is classically characterized by a two‐photon transition matching the vibronic component of its lower energy absorption band. The dipolar species is generated by ion‐pairing with a hard counterion in a non‐dissociating solvent and displays significant modifications oft he optical properties, including a significant hypochromic shift of absorption, weaker emission and 2PA matching the lower energy transition, thus revealing symmetry breaking within the polymethine electronic structure.
Culture of Intestinal Epithelial Cell Monolayers and Their Use in Multiplex Macromolecular Permeability Assays for In Vitro Analysis of Tight Junction Size Selectivity
Authors: Pongkorpsakol Pawin , Turner Jerrold R. , Zuo Li
Published: November 2020

Tight junctions form a selectively permeable barrier that limits paracellular flux across epithelial‐lined surfaces. Small molecules (less than ∼8 Å diameter) can traverse the junction via the size‐ and charge‐selective, high‐conductance pore pathway. In contrast, the low‐conductance leak pathway accommodates larger macromolecules (up to ∼100 Å diameter) and is not charge‐selective. Flux across the tight junction–independent, high‐conductance, non‐selective, unrestricted pathway occurs at sites of epithelial damage. Cytokines can regulate each of these pathways, but commonly used measures of barrier function cannot discriminate between tight junction regulation and epithelial damage. This article describes methods for culturing intestinal epithelial cell monolayers and assessing the impact of cytokine treatment on leak and unrestricted pathway permeabilities. © 2020 Wiley Periodicals LLC.

Basic Protocol 1: Generation and culture of cell monolayers in Transwells

Basic Protocol 2: Assessment of cytokine (IFNγ and TNF) treatment effects on barrier function

Support Protocol: Immunofluorescent staining of monolayers

Basic Protocol 3: Multiplex flux assay
Dissecting the Biology of the Fungal Wheat Pathogen Zymoseptoria tritici: A Laboratory Workflow
Authors: Fagundes Wagner C. , Haueisen Janine , Stukenbrock Eva H.
Published: November 2020

The fungus Zymoseptoria tritici is one of the most devastating pathogens of wheat. Aside from its importance as a disease‐causing agent, this species has emerged as a powerful model system for evolutionary genetic studies of crop‐infecting fungal pathogens. Z. tritici exhibits exceptionally high levels of genetic and phenotypic diversity as well as morphological plasticity, which can make experimental studies and comparability of results obtained in different laboratories, e.g., from infection assays, challenging. Therefore, standardized experimental methods are crucial for research on Z. tritici biology and the interaction of this fungus with its wheat host. Here, we describe a suite of well‐tested and optimized protocols ranging from isolation of Z. tritici field specimens to analyses of virulence assays under controlled conditions. Several biological and technical aspects of working with Z. tritici under laboratory conditions are considered and carefully described in each protocol. © 2020 The Authors.

Basic Protocol 1: Purification of Z. tritici field isolates from leaf material

Basic Protocol 2: Molecular identification of Z. tritici isolates

Support Protocol 1: Rapid extraction of Z. tritici genomic DNA

Support Protocol 2: Extraction of high‐quality Z. tritici genomic DNA

Basic Protocol 3: In vitro culture and long‐term storage of Z. tritici isolates

Basic Protocol 4: Analysis of Z. tritici virulence in wheat

Support Protocol 3: Preparation of Z. tritici inoculum
Depolymerization of Technical‐Grade Polyamide 66 and Polyurethane Materials through Hydrogenation
Authors: Zhou Wei , Neumann Paul , Al Batal Mona , Rominger Frank , Hashmi A. Stephen K. , Schaub Thomas
Published: November 2020

Chemical recycling provides a promising solution to utilize plastic waste. Here, a catalytic hydrogenative depolymerization of polyamide 66 (PA 66) and polyurethane (PU) was developed. The system employed Ru pincer complexes at high temperature (200 °C) in THF solution, and even technical‐grade polymers could be hydrogenated with satisfactory yields under these conditions. A comparison of the system with some known heterogeneous catalysts as well as catalyst poisoning tests supported the homogeneity of the system. These results demonstrate the potential of chemical recycling to regain building blocks for polymers and will be interesting for the further development of polymer hydrogenation.
Natural history of model organisms: The secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology
Authors: Morimoto Juliano , Pietras Zuzanna
Published: November 2020

Model organisms such as Drosophila melanogaster have been key tools for advancing our fundamental and applied knowledge in biological and biomedical sciences. However, model organisms have become intertwined with the idea of controlled and stable laboratory environments, and their natural history has been overlooked.

In holometabolous insects, lack of natural history information on larval ecology has precluded major advances in the field of developmental ecology, especially in terms of manipulations of population density early in life (i.e., larval density). This is because of relativistic and to some extent, arbitrary methodologies employed to manipulate larval densities in laboratory studies. As a result, these methodologies render comparisons between species impossible, precluding our understanding of macroevolutionary responses to population densities during development that can be derived from comparative studies.

We recently proposed a new conceptual framework to address this issue, and here, we provide the first natural history investigation of Drosophila melanogaster larval density under such framework. First, we characterized the distribution of larval densities in a wild population of D. melanogaster using rotting apples as breeding substrate in a suburban area in Sweden.

Next, we compiled the commonly used methodologies for manipulating larval densities in laboratory studies from the literature and found that the majority of laboratory studies identified did not manipulate larval densities below or above the densities observed in nature, suggesting that we have yet to study true life history and physiological responses to low and high population densities during D. melanogaster development.

This is, to our knowledge, the first direct natural history account of larval density in nature for this model organism. Our study paves the way for a more integrated view of organismal biology which re‐incorporates natural history of model organisms into hypothesis‐driven research in developmental ecology.
Voltammetric Detection of Aqueous Glyphosate on a Copper and Poly(Pyrrole)‐electromodified Activated Carbon Fiber
Authors: Shrivastava Surabhi , Kumar Arun , Verma Nishith , Chen Bor‐Yann , Chang Chang‐Tang
Published: November 2020

Aqueous glyphosate (GLYP) was voltammetrically detected using a Cu‐(poly)pyrrole composite electrochemically deposited on activated carbon fiber for the first time in a single‐step method. Differential pulse voltammetry indicated good linearity (R2= 0.9902) in the response over 0.02–12 mg L−1range, with a low limit of detection (0.01 mg L−1). The sensor exhibited reproducibility for soil and fruit samples (RSD values = 2.41 and 3.87%, respectively). The response showed repeatability over 100 consecutive measurements. The response was also unaffected by the interfering substances containing the same functional groups as in GLYP and its metabolite. The method described in this study is facile.
Characterization and electrocatalytic properties of electrospun Pt‐IrO2 nanofiber catalysts for oxygen evolution reaction
Authors: Wang Zhi Ming , Liu Peng , Cao Yan Peng , Ye Feng , Xu Chao , Du Xiao Ze
Published: November 2020

In this study, novel Pt‐IrO2 nanofiber catalysts for oxygen evolution reaction (OER) were successfully prepared using the electrospinning method with a high‐concentration precursor solution. The composition and structure of catalysts were characterized, and the electrocatalytic performance of the nanofiber catalysts in water electrolysis was investigated from various aspects such as overpotential, charge transfer resistance, and exchange current density. Special attention was paid on the effect of Pt/Ir ratio on the electrocatalytic activity of the electrospun nanofibers. The results showed that the Pt‐IrO2 nanofiber catalysts with average fiber diameters ranging from 10 to 100 nm can be successfully obtained by the electrospinning method, and the average diameter decreased with the increase of Pt content. Since a bigger amount of IrO2 content and a thinner fiber structure are all beneficial to the electrocatalytic performance, the Pt‐IrO2 catalysts with Pt:Ir = 1:9 and Pt:Ir = 9:1 both showed better catalytic performance for OER than the commercial IrO2, which was also demonstrated by the lower charge transfer resistance and higher exchange current density. As a result, the overpotentials of Pt‐IrO2 catalysts with Pt:Ir = 1:9 and Pt:Ir = 9:1 are 50 mV and 32 mV lower than the overpotential of the commercial IrO2 at 30 mA cm−2 in 0.5 M H2SO4, respectively. The electrospun Pt‐IrO2 nanofiber catalyst with proper Pt content seems to be very promising since it can not only improve the catalytic performance and the safety of PEM electrolysis cells, but also reduce the amount of more expensive Ir in catalysts.
Effects of kiwi’s pectin methylesterase inhibitor, nanomilling and pasteurization on orange juice quality
Authors: Bazaraa Wael A. , Ammar Abdalla S. , Aqlan Abdulghani M.
Published: November 2020

Endogenous pectin methylesterase (PME) is the enzyme responsible for phase separation and cloud loss in orange juice (OJ) manufacturing. The effect of kiwi's PME inhibitor (PMEI), nanomilling, and pasteurization on OJ quality was evaluated. The microbial quality, PME activity, OJ separation, pH, ascorbic acid content and the sensory characteristics of the juice were followed during 5 weeks storage (4°C). PMEI as freeze‐dried kiwi powder (0.3%, w/w) succeeded in inhibiting 89.3% of the OJ PME without affecting the microbial and the sensory quality. Nanomilling of OJ pulp, to prepare nano‐particles OJ (NPOJ), reduced the initial microbial load by 1.65 and 1.83 log for psychrotrophs and yeasts and molds, respectively; significantly (p < .05) inactivated 40.9% of the residual PME activity and the juice separation was significantly reduced by 48.3% (after 14 days of storage). Nanomilling exhibited no effect on OJ pH, but slight (p < .05) decrease in ascorbic acid content was noted. The combination of PMEI with NPOJ resulted in improved OJ stability with reduced separation to 36.4% of that of control. Such combination also allowed to use a lower pasteurization temperature at lower exposure time (60°C/5 min) needed to obtain new NPOJ with comparable high quality as fresh OJ and which has a shelf life of 3 weeks (4°C).
Hepatic Predictors of Mortality in Severe Acute Respiratory Syndrome Coronavirus 2: Role of Initial Aspartate Aminotransferase/Alanine Aminotransferase and Preexisting Cirrhosis
Authors: Frager Shalom Z. , Szymanski James , Schwartz Jonathan M. , Massoumi Hatef S. , Kinkhabwala Milan , Wolkoff Allan W.
Published: November 2020

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS‐CoV2) is the causative agent of coronavirus disease 2019 (COVID‐19). The presenting symptoms of this virus are variable, and there is an increasing body of literature on risk factors for mortality. The aim of this study was to evaluate the effect of initial aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels and preexisting liver disease, including cirrhosis, in a cohort of patients admitted with COVID‐19 infection at a tertiary care hospital network in the Bronx, New York. We reviewed 3,352 patients who had a positive SARS‐CoV2 nasal swab, were over 18 years of age, and had an associated inpatient admission and discharge (or death) to the Montefiore Medical Center from February 28, 2020, to May 22, 2020. Of these, 39/86 (45%) patients died when the initial ALT was >5 times the upper limit of normal (ULN); 115/230 (50%) patients died when the initial AST was >3 times the ULN. The mortality of patients without preexisting liver disease was 26.6% compared to a mortality rate of 29.5% in patients with liver disease. Subgroup analysis showed a mortality of 36.1% in the patients with cirrhosis. Cirrhosis conferred a hazard ratio for mortality of 1.67 (95% confidence interval, 1.09, 2.55; P = 0.019). The baseline Model for End‐Stage Liver Disease score was not prognostic in the cirrhosis cohort. There was no statistical difference between mortality in patients with a history of compensated or decompensated cirrhosis. The most common cause of death in the cirrhosis cohort was respiratory failure. Conclusion: COVID‐19 hepatitis may lead to poor outcomes in patients who are hospitalized for the disease. Patients with cirrhosis are at a higher risk of COVID‐19‐related mortality.
Conjunctive representation of what and when in monkey hippocampus and lateral prefrontal cortex during an associative memory task
Authors: Cruzado Nathanael A. , Tiganj Zoran , Brincat Scott L. , Miller Earl K. , Howard Marc W.
Published: November 2020

Adaptive memory requires the organism to form associations that bridge between events separated in time. Many studies show interactions between hippocampus (HPC) and prefrontal cortex (PFC) during formation of such associations. We analyze neural recording from monkey HPC and PFC during a memory task that requires the monkey to associate stimuli separated by about a second in time. After the first stimulus was presented, large numbers of units in both HPC and PFC fired in sequence. Many units fired only when a particular stimulus was presented at a particular time in the past. These results indicate that both HPC and PFC maintain a temporal record of events that could be used to form associations across time. This temporal record of the past is a key component of the temporal coding hypothesis, a hypothesis in psychology that memory not only encodes what happened, but when it happened.
Factors affecting in‐hospital cost and mortality of patients with stroke: Evidence from a case study in a tertiary hospital in China
Authors: Liu Chuang , Luo Li , Duan Lijuan , Hou Shangyan , Zhang Baoyue , Jiang Yan
Published: November 2020

Objective

The study aims to investigate the factors causing the difference of stroke patients' in‐hospital cost and study these factors on health outcome in terms of mortality.

Methods

Eight hundred and sixty‐two in‐patients with stroke in a tertiary hospital in China from 2017 to 2019 were included in the database. Descriptive statistics indexes were used to describe patients' in‐hospital cost and mortality. Based on Elixhauser coding algorithms, multiple linear regression and logistic regressions (LRs) were used to evaluate the impact of factors identified from univariate analysis on in‐hospital cost and mortality, respectively. In addition to LRs, a comparison study was then carried out with random forest, gradient boosting decision tree and artificial neural network.

Results

Factors affecting both cost and mortality are age, discharged day‐of‐week, length of stay, stroke subtype, other neurological disorders, renal failure, fluid and electrolyte disorders and total number of comorbidities.

Conclusion

With the increase of age, the mortality rate of in‐patients (except for the juvenile) with stroke increases and the cost of hospitalization decreases. Intracerebral haemorrhage is the most devastating stroke for its highest mortality in short length of stay. Medical services should focus on these specific comorbidities.
MEG3 aggravates hypoxia/reoxygenation induced apoptosis of renal tubular epithelial cells via the miR‐129‐5p/HMGB1 axis
Authors: Mao Huihui , Huang Qiao , Liu Ying
Published: November 2020

The apoptosis of renal tubular epithelial cells (TECs) during ischemia/reperfusion (I/R) facilitates the progression of acute kidney injury (AKI). This study aimed to probe the role of long noncoding RNA maternally expressed 3 (MEG3) in I/R‐induced apoptosis of TECs. In this study, with CoCl2 and hypoxia/reoxygenation treatments, cell models were established to mimic I/R using the human kidney tubular cell line HK‐2. In HK‐2 cells, expression of MEG3 detected using quantitative real‐time polymerase chain reaction (qRT‐PCR), was significantly upregulated after CoCl2 treatment and hypoxia/reoxygenation treatment. The results of cell counting kit‐8 assay and flow cytometry suggested that knockdown of MEG3 significantly increased the viability of HK‐2 cells but inhibited its apoptosis, while overexpression of MEG3 exerted the reverse effects. Additionally, expression levels of interleukin 6 and tumor necrosis factor‐α in the medium were elevated after MEG3 was overexpressed in HK‐2 cells. Together with qRT‐PCR and Western blot analysis, a dual‐luciferase reporter gene assay was used to verify the interactions among MEG3, miR‐129‐5p, and HMGB1. The results demonstrated that in HK‐2 cells, miR‐129‐5p was a target of MEG3, and HMGB1 served as a target gene of miR‐129‐5p. Besides this, compared with the control group, the expression levels of MEG3 and HMGB1 in samples derived from AKI patients were remarkably upregulated, and the expression of miR‐129‐5p was downregulated. Therefore, taken together, we conclude that the overexpression of MEG3 induced by I/R promotes apoptosis of TECs via regulating the miR‐129‐5p/HMGB1 axis.
Insights into the regulatory role and clinical relevance of mediator subunit, MED12, in human diseases
Authors: Srivastava Srishti , Kulshreshtha Ritu
Published: November 2020

Transcriptional dysregulation is central to many diseases including cancer. Mutation or deregulated expression of proteins involved in transcriptional machinery leads to aberrant gene expression that disturbs intricate cellular processes of division and differentiation. The subunits of the mediator complex are master regulators of stimuli‐derived transcription and are essential for transcription by RNA polymerase II. MED12 is a part of the CDK8 kinase module of the mediator complex and is essential for kinase assembly and function. Other than its function in activation of the kinase activity of CDK8 mediator, it also brings about transcription repression or activation, in response to several signalling pathways, a function that is independent of its role as a part of kinase assembly. Accumulating evidence suggests that MED12 controls complex transcription programs that are defining in cell fate determination, differentiation, and carcinogenesis. Mutations or differential expression of MED12 manifest in several human disorders and diseases. For instance, MED12 mutations are the gold standard for the diagnosis of several X‐linked intellectual disability syndromes. Further, certain MED12 mutations are categorised as driver mutations in carcinogenesis as well. This is a timely review that provides for the first time a wholesome view on the critical roles and pathways regulated by MED12, its interactions along with the implications of MED12 alterations/mutations in various cancers and nonneoplastic disorders. Based on the preclinical studies, MED12 indeed emerges as an attractive novel therapeutic target for various diseases and intellectual disorders.
GBE attenuates arsenite‐induced hepatotoxicity by regulating E2F1‐autophagy‐E2F7a pathway and restoring lysosomal activity
Authors: Chen Xiong , Wang Dapeng , Sun Baofei , Liu Chunyan , Zhu Kai , Zhang Aihua
Published: November 2020

Arsenic is an environmental toxicant. Its overdose can cause liver damage. Autophagy has been reported to be involved in arsenite (iAs3+) cytotoxicity and plays a dual role in cell proliferation and cell death. However, the effect and molecular regulative mechanisms of iAs3+ on autophagy in hepatocytes remains largely unknown. Here, we found that iAs3+ exposure lead to hepatotoxicity by inducing autophagosome and autolysosome accumulation. On the one hand, iAs3+ promoted autophagosome synthesis by inhibiting E2F1/mTOR pathway in L‐02 human hepatocytes. On the other, iAs3+ blocked autophagosome degradation partially via suppressing the expression of INPP5E and Rab7 as well as impairing lysosomal activity. More importantly, autophagosome and autolysosome accumulation induced by iAs3+ increased the protein level of E2F7a, which could further inhibit cell viability and induce apoptosis of L‐02 cells. The treatment of Ginkgo biloba extract (GBE) effectively reduced autophagosome and autolysosome accumulation and thus alleviated iAs3+‐induced hepatotoxicity. Moreover, GBE could also protect lysosomal activity, promote the phosphorylation level of E2F1 (Ser364 and Thr433) and Rb (Ser780) as well as suppress the protein level of E2F7a in iAs3+‐treated L‐02 cells. Taken together, our data suggested that autophagosome and autophagolysosome accumulation play a critical role for iAs3+‐induced hepatotoxicity, and GBE is a promising candidate for intervening iAs3+ induced liver damage by regulating E2F1‐autophagy‐E2F7a pathway and restoring lysosomal activity.