bluuebunny/crossref_metadata_2025 huggingface dataset:
Short treatment of peripheral blood cells product with Fas ligand using closed automated cell processing system significantly reduces immune cell reactivity of the graft in vitro and in vivo
Authors: Rodionov Galina , Rosenzwaig Michal , Tzadok Michal Schrift , Kvint Moran , Gevir Elazar , Zorde-Khvalevsky Elina , Peled Amnon , Yarkoni Shai , Ofer Amos
Published: May 2022

Mobilized peripheral blood cells (MPBCs) graft and peripheral blood cells apheresis are used for bone marrow transplantation and for treatment of graft versus host disease (GvHD). We demonstrate that a short treatment of MPBCs with Fas ligand (FasL, CD95L) for 2 h using a closed automated cell processing system selectively induces apoptosis of specific donor T cells, B cells and antigen presenting cells, but, critically, not CD34+ hematopoietic stem cells and progenitors, all of which may contribute to an increased likelihood of graft survival and functionality and reduced GvHD. Treated cells secreted lower levels of interferon-gamma as compared with control, untreated, cells. Moreover, FasL treatment of immune cells increased signals, which led to their phagocytosis by activated macrophages. FasL treated immune cells also reduced the ability of activated macrophages to secrete pro-inflammatory cytokines. Most importantly, FasL ex vivo treated MPBCs prior to transplantation in NOD-SCID NSG mice prevented GvHD and improved stem cell transplantation in vivo. In conclusion, MPBCs, as well as other blood cell products, treated with FasL by automated manufacturing (AM), may be used as potential treatments for conditions where the immune system is over-responding to both self and non-self-antigens.
Helicobacter pylori infection activates Wnt/β-catenin pathway to promote the occurrence of gastritis by upregulating ASCL1 and AQP5
Authors: Zuo Wei , Yang Hui , Li Nianshuang , Ouyang Yaobin , Xu Xinbo , Hong Junbo
Published: May 2022

Helicobacter pylori (H. pylori)infection is a well-recognized contributing factor to gastritis, but the underlying mechanisms remain to be established. It is interesting to note that AQP5 was predicted to be highly expressed in intestinal metaplasia (IM) based onH. pyloriinfection-related microarray data, and the transcription factor ASCL1 was bioinformatically predicted to associate with AQP5. Therefore, the purpose of this study is to evaluate the mechanistic significance of ASCL1 and AQP5 inH. pyloriinfection of gastritis. Gastritis mouse models were established byH. pyloriinfection, followed by determination of AQP5 and ASCL1 in gastric mucosa. Besides, the effects of AQP5 onH. pylori-induced gastritis were explored using AQP5−/−mice. It was observed thatH. pyloriinfection elevated expression of AQP5 and ASCL1 in gastric mucosa and gastric epithelial cells (GECs).H. pyloriinduced AQP5 expression by regulating ASCL1 and activated WNT/β-catenin signaling pathway in GECs. It was also found that AQP5 knockdown suppressed inflammatory response and apoptosis inH. pylori-infected mice. Moreover,H. pyloriinfection-elevated ASCL1 and AQP5 expression promoted apoptosis and inflammation in GECs. Taken together, the key findings of the present study demonstrate thatH. pyloriinfection activated WNT/β-catenin signaling pathway by upregulating ASCL1/AQP5 to induce gastritis.
Systematic and quantitative view of the antiviral arsenal of prokaryotes
Authors: Tesson Florian , Hervé Alexandre , Mordret Ernest , Touchon Marie , d’Humières Camille , Cury Jean , Bernheim Aude
Published: May 2022

Bacteria and archaea have developed multiple antiviral mechanisms, and genomic evidence indicates that several of these antiviral systems co-occur in the same strain. Here, we introduce DefenseFinder, a tool that automatically detects known antiviral systems in prokaryotic genomes. We use DefenseFinder to analyse 21000 fully sequenced prokaryotic genomes, and find that antiviral strategies vary drastically between phyla, species and strains. Variations in composition of antiviral systems correlate with genome size, viral threat, and lifestyle traits. DefenseFinder will facilitate large-scale genomic analysis of antiviral defense systems and the study of host-virus interactions in prokaryotes.
Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals
Authors: Brizzi Andrea , Whittaker Charles , Servo Luciana M. S. , Hawryluk Iwona , Prete Carlos A. , de Souza William M. , Aguiar Renato S. , Araujo Leonardo J. T. , Bastos Leonardo S. , Blenkinsop Alexandra , Buss Lewis F. , Candido Darlan , Castro Marcia C. , Costa Silvia F. , Croda Julio , de Souza Santos Andreza Aruska , Dye Christopher , Flaxman Seth , Fonseca Paula L. C. , Geddes Victor E. V. , Gutierrez Bernardo , Lemey Philippe , Levin Anna S. , Mellan Thomas , Bonfim Diego M. , Miscouridou Xenia , Mishra Swapnil , Monod Mélodie , Moreira Filipe R. R. , Nelson Bruce , Pereira Rafael H. M. , Ranzani Otavio , Schnekenberg Ricardo P. , Semenova Elizaveta , Sonabend Raphael , Souza Renan P. , Xi Xiaoyue , Sabino Ester C. , Faria Nuno R. , Bhatt Samir , Ratmann Oliver
Published: May 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the spread of Gamma across 14 state capitals, during which typically more than half of hospitalized patients aged 70 years and older died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed before the detection of Gamma. Using a Bayesian fatality rate model, we found that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization and pandemic preparedness are critical to minimize population-wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.
Arboviral disease record data - Dengue and Chikungunya, Brazil, 2013–2020
Authors: da Silva Neto Sebastião Rogério , Tabosa de Oliveira Thomás , Teixiera Igor Vitor , Medeiros Neto Leonides , Souza Sampaio Vanderson , Lynn Theo , Endo Patricia Takako
Published: May 2022

One of the main categories of Neglected Tropical Diseases (NTDs) are arboviruses, of which Dengue and Chikungunya are the most common. Arboviruses mainly affect tropical countries. Brazil has the largest absolute number of cases in Latin America. This work presents a unified data set with clinical, sociodemographic, and laboratorial data on confirmed patients of Dengue and Chikungunya, as well as patients ruled out of infection from these diseases. The data is based on case notification data submitted to the Brazilian Information System for Notifiable Diseases, from Portuguese Sistema de Informação de Agravo de Notificação (SINAN), from 2013 to 2020. The original data set comprised 13,421,230 records and 118 attributes. Following a pre-processing process, a final data set of 7,632,542 records and 56 attributes was generated. The data presented in this work will assist researchers in investigating antecedents of arbovirus emergence and transmission more generally, and Dengue and Chikungunya in particular. Furthermore, it can be used to train and test machine learning models for differential diagnosis and multi-class classification.
Decoding the protein–ligand interactions using parallel graph neural networks
Authors: Knutson Carter , Bontha Mridula , Bilbrey Jenna A. , Kumar Neeraj
Published: May 2022

Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures:$$\hbox {GNN}_{\mathrm{F}}$$GNNFis the base implementation that employs distinct featurization to enhance domain-awareness, while$$\hbox {GNN}_{\mathrm{P}}$$GNNPis a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for$$\hbox {GNN}_{\mathrm{F}}$$GNNFand 0.958 for$$\hbox {GNN}_{\mathrm{P}}$$GNNPfor predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and$$\hbox {pIC}_{\mathrm{50}}$$pIC50crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on$$\hbox {pIC}_{\mathrm{50}}$$pIC50with$$\hbox {GNN}_{\mathrm{F}}$$GNNFand$$\hbox {GNN}_{\mathrm{P}}$$GNNP, respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of$$\hbox {GNN}_{\mathrm{P}}$$GNNPon SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.
Cost-utility analysis on robot-assisted and laparoscopic prostatectomy based on long-term functional outcomes
Authors: Lindenberg Melanie A. , Retèl Valesca P. , van der Poel Henk G. , Bandstra Ferdau , Wijburg Carl , van Harten Wim H.
Published: May 2022

Robot-Assisted Radical Prostatectomy (RARP) is one of the standard treatment options for prostate cancer. However, controversy still exists on its added value. Based on a recent large-sample retrospective cluster study from the Netherlands showing significantly improved long-term urinary functioning after RARP compared to Laparoscopic RP (LRP), we evaluated the cost-effectiveness of RARP compared to LRP. A decision tree was constructed to measure the costs and effects from a Dutch societal perspective over a ~ 7 year time-horizon. The input was based on the aforementioned study, including patient-reported consumption of addition care and consumed care for ergonomic issues reported by surgeons. Intervention costs were calculated using a bottom-up costing analysis in 5 hospitals. Finally, a probabilistic-, one-way sensitivity- and scenario analyses were performed to show possible decision uncertainty. The intervention costs were €9964 for RARP and €7253 for LRP. Total trajectory costs were €12,078 for RARP and €10,049 for LRP. RARP showed higher QALYs compared to LRP (6.17 vs 6.11). The incremental cost-utility ratio (ICUR) was €34,206 per QALY gained, in favour of RARP. As a best-case scenario, when RARP is being centralized (> 150 cases/year), total trajectory costs decreased to €10,377 having a higher utilization, and a shorter procedure time and length of stay resulting in an ICUR of €3495 per QALY gained. RARP showed to be cost-effective compared to LRP based on data from a population-based, large scale study with 7 years of follow-up. This is a clear incentive to fully reimburse RARP, especially when hospitals provide RARP centralized.
The impact of metformin use on the outcomes of locally advanced breast cancer patients receiving neoadjuvant chemotherapy: an open-labelled randomized controlled trial
Authors: Barakat Hadeer Ehab , Hussein Raghda R. S. , Elberry Ahmed Abdullah , Zaki Mamdouh Ahmed , Ramadan Mamdouh Elsherbiny
Published: May 2022

Recently, several clinical trials have attempted to find evidence that supports the anticancer use of metformin in breast cancer (BC) patients. The current study evaluates the anticancer activity of metformin in addition to neoadjuvant chemotherapy (NACT) in locally advanced BC patients. Additionally, we assess the safety and tolerability of this combination and its effect on the quality of life (QoL) of BC patients. Eighty non-diabetic female patients with proven locally advanced BC were randomized into two arms. The first arm received anthracycline/taxane-based NACT plus metformin. The second arm received anthracycline/taxane-based NACT only. Overall response rate (ORR), clinical complete response (cCr), pathological complete response (pCR), and breast conservative rate (BCR) were evaluated between both groups, and correlated with serum metformin concentration. ORR, cCr, pCR, and BCR increased non-significantly in the metformin group compared to the control group; 80.6% vs 68.4%, 27.8% vs 10.5%, 22.2% vs 10.5%, and 19.4% vs 13.2%, respectively. A trend towards cCR and pCR was associated with higher serum metformin concentrations. Metformin decreased the incidence of peripheral neuropathy, bone pain, and arthralgia, although worsened the gastrointestinal adverse events. Metformin combination with NACT has no effect on the QoL of BC patients. Metformin combination with NACT is safe, tolerable, and improves non-significantly the clinical and pathological tumor response of BC patients.
Temporal patterns in the soundscape of a Norwegian gateway to the Arctic
Authors: Aniceto A. S. , Ferguson E. L. , Pedersen G. , Tarroux A. , Primicerio R.
Published: May 2022

As an Arctic gateway, the Norwegian Sea sustains a rich diversity of seasonal and resident species of soniferous animals, vulnerable to the effects of climate change and anthropogenic activities. We show the occurrence of seasonal patterns of acoustic signals in a small canyon off Northern Norway, and investigate cetacean vocal behavior, human-made noise, and climatic contributions to underwater sound between January and May 2018. Mostly median sound levels ranged between 68.3 and 96.31 dB re 1 μPa2 across 1/3 octave bands (13 Hz–16 kHz), with peaks in February and March. Frequencies under 2 kHz were dominated by sounds from baleen whales with highest rates of occurrence during winter and early spring. During late-spring non-biological sounds were predominant at higher frequencies that were linked mainly to ship traffic. Seismic pulses were also recorded during spring. We observed a significant effect of wind speed and ship sailing time on received sound levels across multiple distance ranges. Our results provide a new assessment of high-latitude continental soundscapes in the East Atlantic Ocean, useful for management strategies in areas where anthropogenic pressure is increasing. Based on the current status of the local soundscape, we propose considerations for acoustic monitoring to be included in future management plans.
Curvature dependence of BAR protein membrane association and dissociation kinetics
Authors: Jin Rui , Cao Rui , Baumgart Tobias
Published: May 2022

BAR (Bin/Amphiphysin/Rvs) domain containing proteins function as lipid bilayer benders and curvature sensors, and they contribute to membrane shaping involved in cell signaling and metabolism. The mechanism for their membrane shape sensing has been investigated by both equilibrium binding and kinetic studies. In prior research, stopped-flow spectroscopy has been used to deduce a positive dependence on membrane curvature for the binding rate constant, kon, of a BAR protein called endophilin. However, the impact of bulk diffusion of endophilin, on the kinetic binding parameters has not been thoroughly considered. Employing similar methods, and using lipid vesicles of multiple sizes, we obtained a linear dependence of kon on vesicle curvature. However, we found that the observed relation can be explained without considering the local curvature sensing ability of endophilin in the membrane association process. In contrast, the diffusion-independent unbinding rate constant (koff) obtained from stopped-flow measurements shows a negative dependence on membrane curvature, which is controlled/mediated by endophilin-membrane interactions. This latter dependency, in addition to protein–protein interactions on the membrane, explains the selective binding of BAR proteins to highly curved membranes in equilibrium binding experiments.
Maximizing citizen scientists’ contribution to automated species recognition
Authors: Koch Wouter , Hogeweg Laurens , Nilsen Erlend B. , Finstad Anders G.
Published: May 2022

Technological advances and data availability have enabled artificial intelligence-driven tools that can increasingly successfully assist in identifying species from images. Especially within citizen science, an emerging source of information filling the knowledge gaps needed to solve the biodiversity crisis, such tools can allow participants to recognize and report more poorly known species. This can be an important tool in addressing the substantial taxonomic bias in biodiversity data, where broadly recognized, charismatic species are highly over-represented. Meanwhile, the recognition models are trained using the same biased data, so it is important to consider what additional images are needed to improve recognition models. In this study, we investigated how the amount of training data influenced the performance of species recognition models for various taxa. We utilized a large citizen science dataset collected in Norway, where images are added independently from identification. We demonstrate that while adding images of currently under-represented taxa will generally improve recognition models more, there are important deviations from this general pattern. Thus, a more focused prioritization of data collection beyond the basic paradigm that “more is better” is likely to significantly improve species recognition models and advance the representativeness of biodiversity data.
Research on permeable pores in collapse column fillings with different gradation structures
Authors: Song Shuang , Zhang Tianjun , Pan Hongyu , Pang Mingkun , Zhang Xiufeng , Zhang Lei , Bao Ruoyu
Published: May 2022

Particle loss is an important cause of water inrush catastrophes in collapsed columns. In order to study the relationship between the lost particles of different graded rock samples and the pore structure of the subsidence column filling, experiments were designed and the changes of the seepage parameters of graded rock samples during the particle migration process under different permeable water pressures P and axial loads F were determined. The results show that: (1) There will be obvious collapse, silting and particle loss behaviors in the sample during different loading processes, and the rock samples with gradation values of n = 0.3 and n = 0.5 are dominant; (2) The relationship between porosity φ and bearing pressure The exponential function can be used to fit the loads F well, and the porosity decreases with the increase of the bearing load. The water surging characteristics before and after 1.2 MPa are mainly in the turbulent water gushing stage, accompanied by instantaneous slurry. Possibility of splashing and indenter sliding; (3) After infiltration, the condition of the remaining skeleton rock samples in the cylinder generally shows a trend of first decreasing rapidly, then increasing slowly, and then decreasing; (4) The gradation value n of the sample and the bottom There is a good correlation between the damaged area and the mean value S of the maximum area of the top water inrush channel. The maximum area increase of the damaged area and the maximum area increase of the water inrush channel show an opposite trend. The permeable pores of the graded samples can be divided into There are three situations of digging and collapse, water inrush gap and scouring hole, and the pore seepage process can be divided into 4 stages of inoculation of water seepage, rapid adjustment, rapid scour and steady flow.
Spatial–temporal variability and health impact of particulate matter during a 2019–2020 biomass burning event in Southeast Asia
Authors: Othman Murnira , Latif Mohd Talib , Hamid Haris Hafizal Abd , Uning Royston , Khumsaeng Thipsukon , Phairuang Worradorn , Daud Zawawi , Idris Juferi , Sofwan Nurzawani Md , Lung Shih-Chun Candice
Published: May 2022

To understand the characteristics of particulate matter (PM) in the Southeast Asia region, the spatial–temporal concentrations of PM10, PM2.5 and PM1 in Malaysia (Putrajaya, Bukit Fraser and Kota Samarahan) and Thailand (Chiang Mai) were determined using the AS-LUNG V.2 Outdoor sensor. The period of measurement was over a year from 2019 to 2020. The highest concentrations of all sizes of PM in Putrajaya, Bukit Fraser and Kota Samarahan were observed in September 2019 while the highest PM10, PM2.5 and PM1 concentrations in Chiang Mai were observed between March and early April 2020 with 24 h average concentrations during haze days in ranges 83.7–216 µg m−3, 78.3–209 µg m−3 and 57.2–140 µg m−3, respectively. The average PM2.5/PM10 ratio during haze days was 0.93 ± 0.05, which was higher than the average for normal days (0.89 ± 0.13) for all sites, indicating higher PM2.5 concentrations during haze days compared to normal days. An analysis of particle deposition in the human respiratory tract showed a higher total deposition fraction value during haze days than on non-haze days. The result from this study indicated that Malaysia and Thailand are highly affected by biomass burning activity during the dry seasons and the Southwest monsoon.
Darcy resistance flow of Sutterby nanofluid with microorganisms with applications of nano-biofuel cells
Authors: Aldabesh Abdulmajeed , Haredy A. , Al-Khaled Kamel , Khan Sami Ullah , Tlili Iskander
Published: May 2022

The objective of current research is to endorse the thermal aspect of Sutterby nanofluid containing the microorganisms due the stretched cylinder. The features of nonlinear thermal radiation, Darcy resistance and activation energy are also incorporated to inspect the thermal prospective. The problem is further extended with implementation of modified Fourier and Fick’s theories. The results are presented for the stretched cylinder and also for stationary plate. The numerical formulation for the problem is presented by following the shooting technique. The comparative numerical is performed to verify the computed simulations. The results convey that the presence of Darcy resistance parameter enhanced the velocity more effectively for stretched cylinder. A reduction in velocity due to Sutterby fluid parameter and buoyancy ratio parameter has been observed. Moreover, the temperature profile enhanced with larger sponginess parameter more effectively for stretching cylinder.
LincRNA#1 knockout alone does not affect polled phenotype in cattle heterozygous for the celtic POLLED allele
Authors: Hennig Sadie L. , McNabb Bret R. , Trott Josephine F. , Van Eenennaam Alison L. , Murray James D.
Published: May 2022

A long intergenic non-coding RNA (lincRNA#1) is overexpressed in the horn bud region of polled (hornless) bovine fetuses, suggesting a potential role in horn bud suppression. Genome editing was used to test whether the absence of this sequence was associated with the horned phenotype. Two gRNAs with high mutation efficiencies targeting the 5′ and the 3′ regions flanking the lincRNA#1 sequence were co-injected with Cas9 as ribonucleoprotein complexes into bovine zygotes (n = 121) 6 h post insemination. Of the resulting blastocysts (n = 31), 84% had the expected 3.7 kb deletion; of these embryos with the 3.7 kb deletions, 88% were biallelic knockouts. Thirty-nine presumptive edited 7-day blastocysts were transferred to 13 synchronized recipient cows resulting in ten pregnancies, five with embryos heterozygous for the dominant PCPOLLED allele at the POLLED locus, and five with the recessive pp genotype. Eight (80%) of the resulting fetuses were biallelic lincRNA#1 knockouts, with the remaining two being mosaic. RT-qPCR analysis was used to confirm the absence of lincRNA#1 expression in knockout fetuses. Phenotypic and histological analysis of the genotypically (PCp) POLLED, lincRNA#1 knockout fetuses revealed similar morphology to non-edited, control polled fetuses, indicating the absence of lincRNA#1 alone does not result in a horned phenotype.
Automatic radar-based 2-D localization exploiting vital signs signatures
Authors: Mercuri Marco , Russo Pietro , Glassee Miguel , Castro Ivan Dario , De Greef Eddy , Rykunov Maxim , Bauduin Marc , Bourdoux André , Ocket Ilja , Crupi Felice , Torfs Tom
Published: May 2022

In light of the continuously and rapidly growing senior and geriatric population, the research of new technologies enabling long-term remote patient monitoring plays an important role. For this purpose, we propose a single-input-multiple-output (SIMO) frequency-modulated continuous wave (FMCW) radar system and a signal processing technique to automatically detect the number and the 2-D position (azimuth and range information) of stationary people (seated/lying down). This is achieved by extracting the vital signs signatures of each single individual, separating the Doppler shifts caused by the cardiopulmonary activities from the unwanted reflected signals from static reflectors and multipaths. We then determine the number of human subjects present in the monitored environment by counting the number of extracted vital signs signatures while the 2-D localization is performed by measuring the distance from the radar where the vital signs information is sensed (i.e., locating the thoracic region). We reported maximum mean absolute errors (MAEs) of 0.1 m and 2.29$$^{\circ }$$

∘

and maximum root-mean-square errors (RMSEs) of 0.12 m and 3.04$$^{\circ }$$

∘

in measuring respectively the ranges and azimuth angles. The experimental validation demonstrated the ability of the proposed approach in monitoring paired human subjects in a typical office environment.
Apical-out airway organoids as a platform for studying viral infections and screening for antiviral drugs
Authors: Stroulios Georgios , Brown Tyler , Moreni Giulia , Kondro Douglas , Dei Alessandro , Eaves Allen , Louis Sharon , Hou Juan , Chang Wing , Pajkrt Dasja , Wolthers Katja C. , Sridhar Adithya , Simmini Salvatore
Published: May 2022

Airway organoids are polarized 3D epithelial structures that recapitulate the organization and many of the key functions of the in vivo tissue. They present an attractive model that can overcome some of the limitations of traditional 2D and Air–Liquid Interface (ALI) models, yet the limited accessibility of the organoids’ apical side has hindered their applications in studies focusing on host–pathogen interactions. Here, we describe a scalable, fast and efficient way to generate airway organoids with the apical side externally exposed. These apical-out airway organoids are generated in an Extracellular Matrix (ECM)-free environment from 2D-expanded bronchial epithelial cells and differentiated in suspension to develop uniformly-sized organoid cultures with robust ciliogenesis. Differentiated apical-out airway organoids are susceptible to infection with common respiratory viruses and show varying responses upon treatment with antivirals. In addition to the ease of apical accessibility, these apical-out airway organoids offer an alternative in vitro model to study host–pathogen interactions in higher throughput than the traditional air–liquid interface model.
Identification of functional features underlying heat stress response in Sprague–Dawley rats using mixed linear models
Authors: Kotlarz Krzysztof , Mielczarek Magda , Wang Yachun , Dou Jinhuan , Suchocki Tomasz , Szyda Joanna
Published: May 2022

Since global temperature is expected to rise by 2 °C in 2050 heat stress may become the most severe environmental factor. In the study, we illustrate the application of mixed linear models for the analysis of whole transcriptome expression in livers and adrenal tissues of Sprague–Dawley rats obtained by a heat stress experiment. By applying those models, we considered four sources of variation in transcript expression, comprising transcripts (1), genes (2), Gene Ontology terms (3), and Reactome pathways (4) and focussed on accounting for the similarity within each source, which was expressed as a covariance matrix. Models based on transcripts or genes levels explained a larger proportion of log2 fold change than models fitting the functional components of Gene Ontology terms or Reactome pathways. In the liver, among the most significant genes were PNKD and TRIP12. In the adrenal tissue, one transcript of the SUCO gene was expressed more strongly in the control group than in the heat-stress group. PLEC had two transcripts, which were significantly overexpressed in the heat-stress group. PER3 was significant only on gene level. Moving to the functional scale, five Gene Ontologies and one Reactome pathway were significant in the liver. They can be grouped into ontologies related to DNA repair, histone ubiquitination, the regulation of embryonic development and cytoplasmic translation. Linear mixed models are valuable tools for the analysis of high-throughput biological data. Their main advantages are the possibility to incorporate information on covariance between observations and circumventing the problem of multiple testing.
On implementation of a semi-analytic strategy to develop an analytical solution of a steady-state isothermal tube drawing model
Authors: Butt Azhar Iqbal Kashif , Shah Nehad Ali , Ahmad Waheed , Botmart Thongchai , Ahmad Naeed
Published: May 2022

In this paper, we consider an isothermal glass tube drawing model consisting of three coupled nonlinear partial differential equations. The steady-state solution of this model is required in order to investigate its stability. With the given initial and boundary conditions, it is not possible to determine an analytical solution of this model. The difficulty lies in determining the constants of integrations while solving the second order ordinary differential equation analytically appearing in the steady-state model. To overcome this difficulty, we present a numerical based approach for the first time to develop an analytical solution of the steady-state isothermal tube drawing model. We use a numerical technique called shooting method to convert the boundary value problem into a set of initial value problems. Once the model has been converted into a system of differential equations with initial values, an integrating technique is implemented to develop the analytical solution. The computed analytical solution is then compared with the numerical solution to better understand the accuracy of obtained solution with necessary discussions.
One-pot synthesis of Au-M@SiO2 (M = Rh, Pd, Ir, Pt) core–shell nanoparticles as highly efficient catalysts for the reduction of 4-nitrophenol
Authors: Hao Junfang , Liu Bin , Maenosono Shinya , Yang Jianhui
Published: May 2022

The conversion of p-nitrophenol (4-NP) to p-aminophenol (4-AP) is of great significance for pharmaceutical and material manufacturing. In this work, Au-M@SiO2 (M = Rh, Pd, Ir, Pt) nanoparticles (NPs) with core–shell structures, which are expected to be excellent catalysts for the transformation of 4-NP to 4-AP, were synthesized by a facile one-pot one-step method. The structure and composition of the NPs were characterized through transmission electron microscopy, X-ray powder diffraction and X-ray photoelectron spectroscopy. Au-M@SiO2 (M = Rh, Pd, Ir, Pt) core–shell NPs showed excellent catalytic activity in the reduction of 4-NP, which is superior to most catalysts reported in the previous literature. The enhanced catalytic activity of Au-M@SiO2 core–shell NPs is presumably related to the bimetallic synergistic effect. This study provides a simple strategy to synthesize core–shell bimetallic NPs for catalytic applications.
Acetylome analysis of acetylation providing new insight into sclerotial generation in medicinal fungus Polyporus umbellatus
Authors: Li Bing , Liu Liu , Shan Tingting , Xing Yongmei , Guo Shunxing
Published: May 2022

Sclerotium-forming fungi are ecologically diverse and possess notable pathogenic or medicinal properties. The sclerotial generation mechanism is still elusive though Polyporus umbellatus sclerotia are typical Traditional Chinese Medicine with diuretic and antitumor effects. Protein acetylation displays a crucial role in several biological processes, but the functions of acetylation in this valuable fungus are unknown at present. In this study, acetylome of P. umbellatus was studied using nano LC-Triple TOF mass spectrometry system following immune-affinity-based enrichment. Totally, 648 acetylated sites in 342 proteins were identified and nine motifs were found to be conserved in P. umbellatus including KacY, KacA, KacL, KacG, MacS, MacA, RacA, RacL, and RacG. Acetylated proteins taken part in types of biological processes, particularly to those in biological processes associated with reactive oxygen species (ROS) metabolism. Inhibitors complement tests were carried out to verify the role of ROS in acetylation modification. It was concluded that oxidative stress regulated sclerotial generation via proteins acetylation in P. umbellatus. The present study presents new insight into the essential roles of acetylation in sclerotial formation, which may also be applicable for other sclerotium-forming fungi.
Effect of smoking on the development and outcomes of inflammatory bowel disease in Taiwan: a hospital-based cohort study
Authors: Chen Bor-Cheng , Weng Meng-Tzu , Chang Chin-Hao , Huang Ling-Yun , Wei Shu-Chen
Published: May 2022

Smoking influences the risks of inflammatory bowel disease (IBD). A hospital-based cohort was conducted to evaluate the effect of smoking on the development and outcomes of IBD, with age, sex and comorbidities matched non-IBD controls from the National Health Interview Survey database of Taiwan. 700 IBD patients (360 ulcerative colitis (UC), 340 Crohn’s disease (CD)) were analyzed for outcomes; and 575 patients (297 UC, 278 CD) were analyzed for prevalence. Smoking prevalence was significantly lower in UC patients than controls (20.9% vs. 30.4%, p < 0.01), but no difference between CD patients and controls (19.8% vs. 22.1%, p = 0.60). UC smokers had fewer admissions (1.6 vs. 2.5, p < 0.05) but higher rates of new cancer development (16% vs. 6.7%, p < 0.05) and mortality (16% vs. 4.9%, p < 0.01) than nonsmokers. CD smokers tended to have higher rates of stricturing and penetrating diseases (p < 0.05), and higher surgery risk (60.3% vs. 38.3%, p < 0.01) than nonsmokers. Smoking prevents UC occurrence and is associated with fewer hospitalization but increases risks of cancer and mortality. By contrast, smoking does not affect CD occurrence but is related to more aggressive behavior which results in a higher surgical rate.
A QR code-based user-friendly visual cryptography scheme
Authors: Ren Lijing , Zhang Denghui
Published: May 2022

Benefiting from the development of the Internet and smart devices, it is now convenient to transmit images anywhere and anytime, which poses a new challenge for image security. The Visual Cryptography Scheme (VCS) is a secret sharing method for protecting an image without a key, the merit of VCS is the human visual system (HVS) can restore the secret image by simply superimposing qualified shares, without any computation. To eliminate noise-like shares in traditional VCS, this paper presents a novel QR code-based expansion-free and meaningful visual cryptography scheme (QEVCS), which generates visually appealing QR codes for transmitting meaningful shares. When distributing on public networks, this scheme does not attract the attention of potential attackers. By limiting the gray-level of a halftoned image, QEVCS both keep the computation-free of visual cryptography and the size of recovery image same as the secret images. The experimental results show the effectiveness of QEVCS when preserving the privacy of images.
Molecular investigation of the multi-phase photochemistry of Fe(iii)–citrate in aqueous solution
Authors: West Christopher P. , Morales Ana C. , Ryan Jackson , Misovich Maria V. , Hettiyadura Anusha P. S. , Rivera-Adorno Felipe , Tomlin Jay M. , Darmody Andrew , Linn Brittany N. , Lin Peng , Laskin Alexander
Published: May 2022

The comprehensive reaction mechanism of FeIII–citrate multiphase photochemistry and formation of unexplored colloidal reaction products that contribute to terrestrial light-absorbing materials.
Niobium grafted mesoporous silica for the production of biorenewable p-xylene from concentrated 2,5-dimethylfuran
Authors: Zhao Yi , Wang Kai-Zhi , Sun Ze-Hui , Zhang Qi , Wang Zi-Jian , Liu Yong-Mei , He He-Yong , Cao Yong
Published: May 2022

The Diels–Alder cycloaddition of bio-based 2,5-dimethylfuran (DMF) and ethylene and the subsequent dehydration of the cycloadduct intermediate hold promise to produce renewable p-xylene (PX) from biofeedstocks.
Droplet motion on a wrinkled PDMS surface with a gradient structural length scale shorter than the droplet diameter
Authors: Yamada Yutaka , Isobe Kazuma , Horibe Akihiko
Published: May 2022

Gradient wrinkled PDMS surfaces were fabricated through metal film deposition with installation of a mask and the motion of impinged droplets on the surfaces followed the structural gradient.
Boosting the oxygen evolution stability and activity of a heterogeneous IrRu bimetallic coating on a WO3 nano-array electrode for PEM water electrolysis
Authors: Jiang Guang , Yu Hongmei , Yao Dewei , Li Yonghuan , Chi Jun , Zhang Hongjie , Shao Zhigang
Published: May 2022

Designing WO3 nano-array electrode with an IrRu bimetallic coating is critical to achieve an efficient PEM water electrolysis.
A novel ratiometric fluorescent and colorimetric sensor based on a 1,8-naphthalimide derivative for nanomolar Cu2+ sensing: smartphone and food applications
Authors: Karuk Elmas Sukriye Nihan , Arslan Fatma Nur , Aydin Duygu
Published: May 2022

A novel 1,8-naphthalimide-based chemical sensor with ratiometric fluorescence behavior, as well as “naked-eye” response was developed for the sensitive and specific determination of Cu2+ at nanomolar levels.
Development and application of an LC-MS method to the determination of poly- and perfluoroalkyl substances (PFASs) in drinking, sea and surface water samples
Authors: Huerta Belinda , McHugh Brendan , Regan Fiona
Published: May 2022

New analytical method developed and validated for the analysis of 15 perfluorinated compounds in different water matrices: river water, drinking water and seawater.
A feasibility study on the use of a pocket-sized NIR spectrometer and multivariate algorithm to distinguish expired drugs from unexpired ones
Authors: Opoku-Ansah Jerry , Yahaya Ewura Seidu , Amuah Charles Lloyd Yeboah , Nyorkeh Regina , Adom-Konadu Agnes , Osei-Wusu Adueming Peter , Teye Ernest
Published: May 2022

An onsite technique for determining drug integrity in sub-Saharan Africa is needed for ensuring drug integrity and enhancing public health.
Decoupling the metal–insulator transition temperature and hysteresis of VO2 using Ge alloying and oxygen vacancies
Authors: Schofield Parker , Braham Erick J. , Zhang Baiyu , Andrews Justin L. , Drozdick Hayley K. , Zhao Dexin , Zaheer Wasif , Gurrola Rebeca M. , Xie Kelvin , Shamberger Patrick J. , Qian Xiaofeng , Banerjee Sarbajit
Published: May 2022

Ge alloying enables independent control of forward and reverse metal–insulator transitions in VO2, enabling decoupling of transformation-temperature and hysteresis.
An orbital principle to design P2-NaxMO2 cathode materials for sodium-ion batteries
Authors: Tong Lu , Ma Pengju , Shu Jiaohong , Wang Lili , Chen Guanglong , Wu Jianbao , Mi Yiming , Zhao Xinxin
Published: May 2022

We studied the influences that 3d transition metals have on the cohesive energies, structural changes and operating voltages of P2-NaxMO2 during discharge based on first-principles calculations.
Ultrafast proton transfer of the aqueous phenol radical cation
Authors: Bin Mohd Yusof Muhammad Shafiq , Song Hongwei , Debnath Tushar , Lowe Bethany , Yang Minghui , Loh Zhi-Heng
Published: May 2022

Ultrafast spectroscopy and quantum dynamics simulations elucidate the ∼0.1 ps ultrafast proton transfer of photoionized aqueous phenol.
Tracing the vibrational dynamics of sodium iodide via the spectrum of emitted photofragments
Authors: Biró László , Csehi András
Published: May 2022

Multicolor mapping of the vibrational dynamics of diatomics in bound electronic states is possible via the energy spectra of dissociating fragments. This is demonstrated for sodium iodide using ultrafast, resonant time-delayed laser pulses.
Quantum effects in photosensitization: the case of singlet oxygen generation by thiothymines
Authors: Manae Meghna A. , Hazra Anirban
Published: May 2022

Photosensitization rate constants have been calculated using two variants of Fermi’s golden rule: a classical limit which severely underestimates rates, and a quantum treatment which fares notably better, stressing the importance of quantum effects.
Depolarization of few-layer III–V and II–VI materials through symmetric rumpling
Authors: Sun An-An , Gao Shang-Peng
Published: May 2022

A stabilization mechanism is unraveled for III–V and II–VI films to remove the dipoles by adopting a symmetrically rumpled configuration.
Self-assembled hierarchical metal–polyphenol-coordinated hybrid 2D Co–CTA@g-C3N4heterostructured nanosheets for efficient electrocatalytic oxygen reduction
Authors: Xiao Gao , Lin Huiying , Lin Yiting , Chen Liyin , Jiang Xiancai , Cao Xia , Afewerki Samson , Zhang Yujuan , Zhang Weixia
Published: May 2022

We exquisitely designed thein situgrowth of Co nanoparticles coated with tannin-carbon embedded on the hierarchical ultrathin g-C3N4nanosheets for boosting electrocatalytic oxygen reduction through the MPNs strategy.
Development of an alkaline electro-Fenton process based on the synthesis of H2O2 in bicarbonate electrolytes
Authors: Liu Xiaotian , Yang Yuran , Duan Feng , Wen Jinyu , Wei Xijun , Huang Yujie , Jia Bi , Ke Gaili , He Huichao , Zhou Yong
Published: May 2022

An alkaline electro-Fenton process be proposed based on H2O2 synthesis in a bicarbonate electrolyte and H2O2 activation into ˙OH. This alkaline electro-Fenton process can achieve the degradation of organic pollutants in alkaline aqueous solution.
Nitrogen-doped nickel-molybdenum oxide as a highly efficient electrocatalyst for benzyl alcohol oxidation
Authors: Wan Jiang , Mu Xiao , Jin Yu , Zhu Jiukang , Xiong Yucong , Li Tianyu , Li Rong
Published: May 2022

Replacing the sluggish oxygen evolution reaction (OER) with electrocatalytic alcohol oxidation to construct hybrid water electrolysis systems is more economically attractive than conventional water splitting.
One-step assembly of barcoded planar microparticles for efficient readout of multiplexed immunoassay
Authors: Bae Sangwook , Lee Daewon , Na Hunjong , Jang Jisung , Kwon Sunghoon
Published: May 2022

A microfluidic chip design that enables pipetting-based particle packing for efficient readout of multiplexed immunoassays using barcoded microparticles.
Dual-functional 3D carbon fibers decorated with Co nanoparticles and Co-Nx sites for rechargeable aprotic Li–O2 batteries
Authors: He Lingyan , Shi Kaiyuan , Pan Yu , Wu Jinghua , Li Xing , Xin Xing
Published: May 2022

Due to the function of the Co/CNF-750 fibrous skeleton in the concurrent management of cathode optimization and dendrite inhibition, Co/CNF-750-based Li–O2 full batteries can achieve a life of 160 cycles at 200 mA g-1.
Utilising buckling modes for the determination of the anisotropic mechanical properties of As2S3 nanosheets
Authors: Dong Ming , Sun Yiwei , Dunstan David J. , Papageorgiou Dimitrios G.
Published: May 2022

The mechanical properties of As2S3 were measured by utilising buckling modes. The results make As2S3 one of the softest, polarization-dependent anisotropic 2D materials.
High-strength, high-toughness, self-healing thermosetting shape memory polyurethane enabled by dual dynamic covalent bonds
Authors: Wang Xiaoyue , Xu Jing , Zhang Yaoming , Wang Tingmei , Wang Qihua , Yang Zenghui , Zhang Xinrui
Published: May 2022

A high-strength and high-toughness thermosetting polyurethane, which has shape memory effects as well as self-healing performance to extend its service life.
Insight on the effect of Ni and Ni–N co-doping on SnO2 anode materials for lithium-ion batteries
Authors: Shi Jianjian , Chen Tao , Song Minhang , Sun Xiaoli
Published: May 2022

Energy barriers of Li, where red, green and yellow curves represent diffusion energy barriers of Li in the pure, Ni-doped, and Ni–N co-doped SnO2, respectively.
Water-soluble optical sensors: keys to detect aluminium in biological environment
Authors: Unniram Parambil Ajmal Roshan , P. Kavyashree , Silswal Akshay , Koner Apurba Lal
Published: May 2022

Aluminium ion plays a critical role in cellular health. Therefore, its detection in water is highly demanding.
Identification of a novel ene reductase from Pichia angusta with potential application in (R)-levodione production
Authors: Zhang Baoqi , Sun Jiale , Zheng Yanqiu , Mao Xinlei , Lin Jinping , Wei Dongzhi
Published: May 2022

Asymmetric reduction of electronically activated alkenes by ene reductases (ERs) is an attractive approach for the production of enantiopure chiral products.
Enhanced catalysis of radical-to-polysulfide interconversion via increased sulfur vacancies in lithium–sulfur batteries
Authors: Xu Rui , Tang Hongan , Zhou Yuanyuan , Wang Fangzheng , Wang Hongrui , Shao Minhua , Li Cunpu , Wei Zidong
Published: May 2022

Sulfur vacancies can harmonize chemisorption and generate amounts of radicals to boost the conversions of LiPSs.
Two-dimensional layered nickel-based coordination polymer for supercapacitive performance
Authors: Deka Rakesh , Kumar Viresh , Rajak Richa , Mobin Shaikh M.
Published: May 2022

A nickel based coordination polymer (Ni-CP) is synthesized by slow diffusion technique which reveals a 2D layer like structure having sql topology, further this Ni-CP was employed for high performance supercapacitor application.
MgH2/single-atom heterojunctions: effective hydrogen storage materials with facile dehydrogenation
Authors: Dong Shuai , Li Chaoqun , Lv Erfei , Wang Jinhui , Liu Hao , Gao Zhengyang , Xiong Wei , Ding Zhao , Yang Weijie , Li Hao
Published: May 2022

MgH2/single-atom heterojunction systems were designed with improved dehydrogenation performance for hydrogen storage applications.
Quasi-2D halide perovskite crystals and their optoelectronic applications
Authors: Sheng Xin , Li Yahui , Xia Ming , Shi Enzheng
Published: May 2022

The unique semiconductor properties, synthetic strategies, and corresponding optoelectronic applications of quasi-2D halide perovskite crystals are summarized and discussed in this review.
Amorphous copper iodide: a p-type semiconductor for solution processed p-channel thin-film transistors and inverters
Authors: Lee Han Ju , Lee Seonjeong , Lee Keun Hyung , Hong Kihyon
Published: May 2022

Amorphous p-type copper iodide (a-CuI) semiconductor and corresponding p-channel vertical TFTs are demonstrated. The a-CuI-TFTs exhibit excellent device performance, high current density of 1400 mA cm−2 and normalized transconductance of 6.46 S m−1.
Doping of semicrystalline conjugated polymers: dopants within alkyl chains do it better
Authors: Comin Massimiliano , Lemaur Vincent , Giunchi Andrea , Beljonne David , Blase Xavier , D’Avino Gabriele
Published: May 2022

Electronic structure calculations unveil structure-property relationships in doped polymers: dopants inserted in the alkyl chains are stronger electron acceptors than those in conjugated backbones, leading to integer charge transfer complexes.