bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering waste bound nitrogen by employing psychrophillic Aporrectodea caliginosa and priming of coprolites by associated heterotrophic nitrifiers under high altitude Himalayas
Authors: Sheikh Tahir , Baba Zahoor , Yatoo Ali Mohd , Hamid Basharat , Iqbal Sadaf , Wani Fehim , Fatima Sabah , Alfarraj Saleh , Javed Ansari Mohammad
Published: June 2022

Himalayan ecosystem is characterized by its fragile climate with rich repositories of biodiversity. Waste collection and disposal are becoming increasingly difficult due to topographical variations.Aporrectodea caligenosa, a versatile psychrophillic soil dweller, is a useful biocatalyst with potent bio-augmented capability for waste treatment at low temperatures. Microcosm experiments were conducted to elucidate the comprehensive nature of biogenic nitrogen transformation to NH4+and NO3−produced by coupling of earthworm-microbes. Higher biogenic recovery of NH4+-N from coprolites of garden soil (47.73 ± 1.16%) and Himalayan goat manure (86.32 ± 0.92%) with an increment of 14.12 and 47.21% respectively over their respective control (without earthworms) with a linear decline beyond 4th week of incubation was reported. NO3–-N recovery progressively sustained in garden soil and goat manure coprolites during entire incubation with highest 81.81 ± 0.45 and 87.20 ± 1.08 µg-N g−1dry weight recorded in 6th and 5th week of incubation respectively and peak increments as 38.58 and 53.71% relative to respective control (without earthworms). Declined NH4+–N in coprolites at low temperature (15.0 ± 2.0 °C) evidenced increased nitrification rates by taking over the process by abundant nitrifying microbes. Steady de-nitrification with progressive incubation on an average was 16.95 ± 0.46 ng-N g−1per week and 21.08 ± 0.87 ng-N g−1per week compared to 14.03 ± 0.58 ng-N g−1per week and 4.50 ± 0.31 ng-N g−1per week in respective control treatments. Simultaneous heterotrophic nitrification and aerobic denitrification (SHNAD) was found to be a prominent bioprocess at low temperature that resulted in high and stable total nitrogen and nitrate accumulation from garden soil and goat manure with relative recovery efficiency of 11.12%, 14.97% and 14.20%; 19.34%.A. caligenosashows promising prospects for mass applicability in biogenic N removal from manure of Himalayan goat.
“Long COVID” results after hospitalization for SARS-CoV-2 infection
Authors: Rigoni Marta , Torri Emanuele , Nollo Giandomenico , Donne Livia Delle , Rizzardo Sebastiano , Lenzi Lorenza , Falzone Andrea , Cozzio Susanna
Published: June 2022

Long-term sequelae of symptomatic infection caused by SARS-CoV-2 are largely undiscovered. We performed a prospective cohort study on consecutively hospitalized Sars-CoV-2 patients (March–May 2020) for evaluating COVID-19 outcomes at 6 and 12 months. After hospital discharge, patients were addressed to two follow-up pathways based on respiratory support needed during hospitalization. Outcomes were assessed by telephone consultation or ambulatory visit. Among 471 patients, 80.9% received no respiratory support during hospitalization; 19.1% received non-invasive ventilation (NIV) or invasive mechanical ventilation (IMV). 58 patients died during hospitalization, therefore 413 were enrolled for follow-up. At 6 months, among 355 patients, the 30.3% had any symptoms, 18.0% dyspnea, 6.2% neurological symptoms. Fifty-two out of 105 had major damages in interstitial computed tomography images. NIV/IMV patients had higher probability to suffer of symptoms (aOR = 4.00, 95%CI:1.99–8.05), dyspnea (aOR = 2.80, 95%CI:1.28–6.16), neurological symptoms (aOR = 9.72, 95%CI:2.78–34.00). At 12 months, among 344, the 25.3% suffered on any symptoms, 12.2% dyspnea, 10.1% neurological symptoms. Severe interstitial lesions were present in 37 out of 47 investigated patients. NIV/IMV patients in respect to no respiratory support, had higher probability of experiencing symptoms (aOR = 3.66, 95%CI:1.73–7.74), neurological symptoms (aOR = 8.96, 95%CI:3.22–24.90). COVID-19 patients showed prolonged sequelae up to 12 months, highlighting the need of follow-up pathways for post-COVID-19 syndrome.
Design of typical genes for heterologous gene expression
Authors: Simm Dominic , Popova Blagovesta , Braus Gerhard H. , Waack Stephan , Kollmar Martin
Published: June 2022

Heterologous protein expression is an important method for analysing cellular functions of proteins, in genetic circuit engineering and in overexpressing proteins for biopharmaceutical applications and structural biology research. The degeneracy of the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, plays an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the influence of a profiled codon usage adaptation approach on protein expression levels in the eukaryotic model organism Saccharomyces cerevisiae. We selected green fluorescent protein (GFP) and human α-synuclein (αSyn) as representatives for stable and intrinsically disordered proteins and representing a benchmark and a challenging test case. A new approach was implemented to design typical genes resembling the codon usage of any subset of endogenous genes. Using this approach, synthetic genes for GFP and αSyn were generated, heterologously expressed and evaluated in yeast. We demonstrate that GFP is expressed at high levels, and that the toxic αSyn can be adapted to endogenous, low-level expression. The new software is publicly available as a web-application for performing host-specific protein adaptations to a set of the most commonly used model organisms (https://odysseus.motorprotein.de).
Short periods of bipolar anodal TDCS induce no instantaneous dose-dependent increase in cerebral blood flow in the targeted human motor cortex
Authors: Liu Marie Louise , Karabanov Anke Ninija , Piek Marjolein , Petersen Esben Thade , Thielscher Axel , Siebner Hartwig Roman
Published: June 2022

Anodal transcranial direct current stimulation (aTDCS) of primary motor hand area (M1-HAND) can enhance corticomotor excitability, but it is still unknown which current intensity produces the strongest effect on intrinsic neural firing rates and synaptic activity. Magnetic resonance imaging (MRI) combined with pseudo-continuous Arterial Spin Labeling (pcASL MRI) can map regional cortical blood flow (rCBF). The measured rCBF signal is sensitive to regional changes in neuronal activity due to neurovascular coupling. Therefore, concurrent TDCS and pcASL MRI may reveal the relationship between current intensity and TDCS-induced changes in overall firing rates and synaptic activity in the cortical target. Here we employed pcASL MRI to map acute rCBF changes during short-duration aTDCS of left M1-HAND. Using the rCBF response as a proxy for regional neuronal activity, we investigated if short-duration aTDCS produces an instantaneous dose-dependent rCBF increase in the targeted M1-HAND that may be useful for individual dosing. Nine healthy right-handed participants received 30 s of aTDCS at 0.5, 1.0, 1.5, and 2.0 mA with the anode placed over left M1-HAND and cathode over the right supraorbital region. Concurrent pcASL MRI at 3 T probed TDCS-related rCBF changes in the targeted M1-HAND. Movement-induced rCBF changes were also assessed. Apart from a subtle increase in rCBF at 0.5 mA, short-duration aTDCS did not modulate rCBF in the M1-HAND relative to no-stimulation periods. None of the participants showed a dose-dependent increase in rCBF during aTDCS, even after accounting for individual differences in TDCS-induced electrical field strength. In contrast, finger movements led to robust activation of left M1-HAND before and after aTDCS. Short-duration bipolar aTDCS does not produce consistant instantaneous dose-dependent rCBF increases in the targeted M1-HAND at conventional intensity ranges. Therefore, the regional hemodynamic response profile to short-duration aTDCS may not be suited to inform individual dosing of TDCS intensity.
Exploring hot spots of short birth intervals and associated factors using a nationally representative survey in Bangladesh
Authors: Islam Mohammad Zahidul , Islam M. Mofizul , Rahman Md. Mostafizur , Khan Md. Nuruzzaman
Published: June 2022

Short Birth Interval (SBI, defined as < 33 months interval between the two most recent births or < 24 months between one live birth to the next pregnancy) is a public health problem in most low- and lower-middle-income countries. Understanding geographic variations in SBI, particularly SBI hot spots and associated factors, may help intervene with tailored programs. This study identified the geographical hot spots of SBI in Bangladesh and the factors associated with them. We analyzed women’s data extracted from the 2017/18 Bangladesh Demographic and Health Survey and the healthcare facility data extracted from the 2017 Service Provision Assessment. SBI was the outcome variable, and it was defined as an interval between consecutive births of 33 months or less, as recommended by the World Health Organization. The characteristics of mothers and their partners were the explanatory variables. Moran’s I was used to examine the spatial variation of SBI in Bangladesh whereas the Getis-Ord $${G}_{i}^{*}$$

G

i

∗

(d) was used to determine the hot spots of SBI. The Geographical Weighted Regression (GWR) was used to assess the predictors of SBI at the enumeration areas’ level. The variables included in the GWR were selected using the exploratory regression and ordinary least square regression model. Data of 5941 women were included in the analyses. Around 26% of the total births in Bangladesh had occurred in short intervals. A majority of the SBI hot spots were found in the Sylhet division, and almost all SBI cold spots were in the Rajshahi and Khulna divisions. No engagement with formal income-generating activities, high maternal parity, and history of experiencing the death of a child were significantly associated with SBI in the Sylhet division. Women’s age of 34 years or less at the first birth was a protective factor of SBI in the Rajshahi and Khulna divisions. The prevalence of SBI in Bangladesh is highly clustered in the Sylhet division. We recommend introducing tailored reproductive health care services in the hot spots instead of the existing uniform approach across the country.
Assessing sequence-based protein–protein interaction predictors for use in therapeutic peptide engineering
Authors: Charih François , Biggar Kyle K. , Green James R.
Published: June 2022

Engineering peptides to achieve a desired therapeutic effect through the inhibition of a specific target activity or protein interaction is a non-trivial task. Few of the existing in silico peptide design algorithms generate target-specific peptides. Instead, many methods produce peptides that achieve a desired effect through an unknown mechanism. In contrast with resource-intensive high-throughput experiments, in silico screening is a cost-effective alternative that can prune the space of candidates when engineering target-specific peptides. Using a set of FDA-approved peptides we curated specifically for this task, we assess the applicability of several sequence-based protein–protein interaction predictors as a screening tool within the context of peptide therapeutic engineering. We show that similarity-based protein–protein interaction predictors are more suitable for this purpose than the state-of-the-art deep learning methods publicly available at the time of writing. We also show that this approach is mostly useful when designing new peptides against targets for which naturally-occurring interactors are already known, and that deploying it for de novo peptide engineering tasks may require gathering additional target-specific training data. Taken together, this work offers evidence that supports the use of similarity-based protein–protein interaction predictors for peptide therapeutic engineering, especially peptide analogs.
A deep learning approach for detecting drill bit failures from a small sound dataset
Authors: Tran Thanh , Pham Nhat Truong , Lundgren Jan
Published: June 2022

Monitoring the conditions of machines is vital in the manufacturing industry. Early detection of faulty components in machines for stopping and repairing the failed components can minimize the downtime of the machine. In this article, we present a method for detecting failures in drill machines using drill sounds in Valmet AB, a company in Sundsvall, Sweden that supplies equipment and processes for the production of pulp, paper, and biofuels. The drill dataset includes two classes: anomalous sounds and normal sounds. Detecting drill failure effectively remains a challenge due to the following reasons. The waveform of drill sound is complex and short for detection. Furthermore, in realistic soundscapes, both sounds and noise exist simultaneously. Besides, the balanced dataset is small to apply state-of-the-art deep learning techniques. Due to these aforementioned difficulties, sound augmentation methods were applied to increase the number of sounds in the dataset. In this study, a convolutional neural network (CNN) was combined with a long-short-term memory (LSTM) to extract features from log-Mel spectrograms and to learn global representations of two classes. A leaky rectified linear unit (Leaky ReLU) was utilized as the activation function for the proposed CNN instead of the ReLU. Moreover, an attention mechanism was deployed at the frame level after the LSTM layer to pay attention to the anomaly in sounds. As a result, the proposed method reached an overall accuracy of 92.62% to classify two classes of machine sounds on Valmet’s dataset. In addition, an extensive experiment on another drilling dataset with short sounds yielded 97.47% accuracy. With multiple classes and long-duration sounds, an experiment utilizing the publicly available UrbanSound8K dataset obtains 91.45%. Extensive experiments on our dataset as well as publicly available datasets confirm the efficacy and robustness of our proposed method. For reproducing and deploying the proposed system, an open-source repository is publicly available at https://github.com/thanhtran1965/DrillFailureDetection_SciRep2022.
Intercomparison of radiosensitization induced by gold and iron oxide nanoparticles in human glioblastoma cells irradiated by 6 MV photons
Authors: Guerra Danieli B. , Oliveira Elisa M. N. , Sonntag Amanda R. , Sbaraine Patricia , Fay Andre P. , Morrone Fernanda B. , Papaléo Ricardo M.
Published: June 2022

In this work, an intercomparison of sensitization effects produced by gold (GNP) and dextran-coated iron oxide (SPION-DX) nanoparticles in M059J and U87 human glioblastoma cells was performed using 6 MV-photons. Three variables were mapped: the nanoparticle material, treatment concentration, and cell radiosensitivity. For U87, GNP treatments resulted in high sensitization enhancement ratios (SER$$_{10\%}$$

10
%

up to 2.04). More modest effects were induced by SPION-DX, but still significant reductions in survival were achieved (maximum SER$$_{10\%}=1.61$$

10
%

=
1.61

). For the radiosensitive M059J, sensitization by both NPs was poor. SER$$_{10\%}$$

10
%

increased with the degree of elemental uptake in the cells, but not necessarily with treatment concentration. For GNP, where exposure concentration and elemental uptake were found to be proportional, SER$$_{10\%}$$

10
%

increased linearly with concentration in both cell lines. For SPION-DX, saturation of sensitization enhancement and metal uptake occurred at high exposures. Fold change in the $$\alpha /\beta$$

α
/
β

ratios extracted from survival curves are reduced by the presence of SPION-DX but strongly increased by GNPs , suggesting that sensitization by GNPs occurs mainly via promotion of lethal damage, while for SPION-DX repairable damage dominates. The NPs were more effective in eliminating the radioresistant glioblastoma cells, an interesting finding, as resistant cells are key targets to improve treatment outcome.
Characterization of SARS-CoV-2 replication complex elongation and proofreading activity
Authors: Jones Alisha N. , Mourão André , Czarna Anna , Matsuda Alex , Fino Roberto , Pyrc Krzysztof , Sattler Michael , Popowicz Grzegorz M.
Published: June 2022

The replication complex (RC) of SARS-CoV-2 was recently shown to be one of the fastest RNA-dependent RNA polymerases of any known coronavirus. With this rapid elongation, the RC is more prone to incorporate mismatches during elongation, resulting in a highly variable genomic sequence. Such mutations render the design of viral protein targets difficult, as drugs optimized for a given viral protein sequence can quickly become inefficient as the genomic sequence evolves. Here, we use biochemical experiments to characterize features of RNA template recognition and elongation fidelity of the SARS-CoV-2 RdRp, and the role of the exonuclease, nsp14. Our study highlights the 2′OH group of the RNA ribose as a critical component for RdRp template recognition and elongation. We show that RdRp fidelity is reduced in the presence of the 3′ deoxy-terminator nucleotide 3′dATP, which promotes the incorporation of mismatched nucleotides (leading to U:C, U:G, U:U, C:U, and A:C base pairs). We find that the nsp10–nsp14 heterodimer is unable to degrade RNA products lacking free 2′OH or 3′OH ribose groups. Our results suggest the potential use of 3′ deoxy-terminator nucleotides in RNA-derived oligonucleotide inhibitors as antivirals against SARS-CoV-2.
Identification and preliminary characterization of Plasmodium falciparum proteins secreted upon gamete formation
Authors: Grasso Felicia , Fratini Federica , Albanese Tanino Giuseppe , Mochi Stefania , Ciardo Mariagrazia , Pace Tomasino , Ponzi Marta , Pizzi Elisabetta , Olivieri Anna
Published: June 2022

Malaria long-term elimination depends on parasite transmission control. Plasmodium sexual stage maturation in the mosquito, including egress from the host erythrocyte, is one of the prime targets for transmission-blocking interventions. This work aims to identify candidate molecules potentially involved in gamete emergence from the host erythrocyte, as novel transmission blocking targets. We analyzed by quantitative mass spectrometry the proteins released/secreted by purified Plasmodium falciparum gametocytes upon induction of gametogenesis. The proteome obtained showed a good overlap (74%) with the one previously characterized in similar conditions from gametocytes of the rodent malaria parasite P. berghei. Four candidates were selected based on comparative analysis of their abundance values in released vs total gametocyte proteome. We also characterized the P. falciparum orthologue of the microgamete surface protein (MiGS), a marker of male gametocyte secretory vesicles in murine models of malaria. The findings of this study reveal that all the selected candidate proteins are expressed in both genders and localize to vesicle-like structures that respond to gametogenesis stimuli. This result, together with the fact that the selected proteins are released during gamete emergence in both Plasmodium species, makes them interesting candidates for future functional studies to investigate their potential role in the gametogenesis process.
Analysis of the competition among viral strains using a temporal interaction-driven contagion model
Authors: Abbey Alex , Shahar Yuval , Mokryn Osnat
Published: June 2022

The temporal dynamics of social interactions were shown to influence the spread of disease. Here, we model the conditions of progression and competition for several viral strains, exploring various levels of cross-immunity over temporal networks. We use our interaction-driven contagion model and characterize, using it, several viral variants. Our results, obtained on temporal random networks and on real-world interaction data, demonstrate that temporal dynamics are crucial to determining the competition results. We consider two and three competing pathogens and show the conditions under which a slower pathogen will remain active and create a second wave infecting most of the population. We then show that when the duration of the encounters is considered, the spreading dynamics change significantly. Our results indicate that when considering airborne diseases, it might be crucial to consider the duration of temporal meetings to model the spread of pathogens in a population.
Classification-based motion analysis of single-molecule trajectories using DiffusionLab
Authors: Maris J. J. Erik , Rabouw Freddy T. , Weckhuysen Bert M. , Meirer Florian
Published: June 2022

Single-particle tracking is a powerful approach to study the motion of individual molecules and particles. It can uncover heterogeneities that are invisible to ensemble techniques, which places it uniquely among techniques to study mass transport. Analysis of the trajectories obtained with single-particle tracking in inorganic porous hosts is often challenging, because trajectories are short and/or motion is heterogeneous. We present the DiffusionLab software package for motion analysis of such challenging data sets. Trajectories are first classified into populations with similar characteristics to which the motion analysis is tailored in a second step. DiffusionLab provides tools to classify trajectories based on the motion type either with machine learning or manually. It also offers quantitative mean squared displacement analysis of the trajectories. The software can compute the diffusion constant for an individual trajectory if it is sufficiently long, or the average diffusion constant for multiple shorter trajectories. We demonstrate the DiffusionLab approach via the analysis of a simulated data set with motion types frequently observed in inorganic porous hosts, such as zeolites. The software package with graphical user interface and its documentation are freely available.
Pre-marital sex and its association with peer pressure and watching pornography among young individuals in Ethiopia: a systematic review and meta-analysis
Authors: Damtie Yitayish , Cherie Nigus , Fentaw Habtamu , Kefale Bereket , Addisu Elsabeth , Yalew Melaku , Arefaynie Mastewal , Adane Metadel , Adane Bezawit , Kassa Assefa Andargie , Abebayehu Aregash , Ayele Fanos Yeshanew
Published: June 2022

There is no national representative estimate on pre-marital sex and its association with peer pressure and watching pornography among young individuals in Ethiopia. So, this study aimed to estimate the pooled prevalence of pre-marital sex and its association with peer pressure and watching pornography among young individuals in Ethiopia. A comprehensive search of international databases including CINAHL, Google Scholar, Cochrane Library, PubMed, HINARI, and Global Health was carried out to estimate the pooled prevalence of pre-marital sex and its association with peer pressure and watching pornography among young individuals in Ethiopia. The data were analyzed using STATA/SE version-14. The random-effect model was used to estimate the effect size and I-squared statistics and Egger's test were used to assess the heterogeneity publication bias respectively. A total of thirty-two studies with 18,354 study subjects were included in this meta-analysis. The pooled prevalence of premarital sex among young in Ethiopia was 33.59% [95% CI (29.09, 38.09)]. There was significant heterogeneity among the included articles (I2 = 97.9,p = 0.000). Young individuals who experienced peer pressure were three times more likely to practice premarital sex compared to their counterparts [OR = 2.90, 95%, CI (1.01, 8.31)]. As the crude analysis result indicated, there was a significant association between watching pornography (sex movies) and premarital sexual practice [OR = 3.41, 95% CI (1.99, 5.84)]. However, after doing trim-and-fill analysis, the publication-bias adjusted OR indicates the absence of significant association between watching pornography and premarital sex [OR = 1.23, 95% CI (0.69, 1.76)]. The proportion of premarital sex among young individuals in Ethiopia remains high. Peer pressure had a statistically significant association with premarital sexual practice. However, the publication-bias adjusted OR indicates the absence of a significant association between watching pornography and premarital sex. Peer counseling services, sex education, and behavioral change communications should be strengthened to address factors associated with pre-marital sexual practices.
Study on sand liquefaction induced by Songyuan earthquake with a magnitude of M5.7 in China
Authors: Li Ping , Tian Zhaoyang , Bo Jingshan , Zhu Sheng , Li Yuying
Published: June 2022

A large-scale sand liquefaction producing typical and novel surface phenomena was found at the epicenter of Songyuan M5.7 earthquake occurring on May 28, 2018. Field survey and experimental test encompassing boring sampling, standard penetration test (SPT), cone penetration test (CPT), scanning electron microscopy (SEM), X-ray diffraction (XRD), and X-ray fluorescence (XRF) were performed to ascertain the liquefaction damage and site characteristic. Cone penetration test is an excellent assay for the identification of liquefied sand layer and acquisition of physio-mechanical parameter. Moreover, the assay is applicable for in-situ post-earthquake investigation. Factors promoting the formation and controlling the distribution of the sand liquefaction were analyzed. The liquefaction impacted an 80 km2 area, and was primarily embodied as sand boil and water sprout on rice field, despite producing no significant structural damage. Due to the simple profile of local soil layer, ground motion, geomorphic condition, and groundwater level were the main factors governing the distribution of the liquefaction. Majority of the liquefied sand layer was discovered at the depth less than 10 m. However, deep layer liquefaction at the depth greater than 18 m was also discovered, which was demonstrated by the upward movement of liquefied sand towards the upper silty clay layer at the depth of 17 m. Most importantly, we have identified loess liquefaction, a phenomenon which had not been reported previously in Northeast China. Lastly, it is important to highlight the risk of significant liquefaction damage at Songyuan. Hence, investigating the liquefaction risk is potentially beneficial for augmenting planning on earthquake mitigation, engineering reconnaissance, and design project.
Genome-wide transcriptome profiling of human trabecular meshwork cells treated with TGF-β2
Authors: Callaghan Breedge , Lester Karen , Lane Brian , Fan Xiaochen , Goljanek-Whysall Katarzyna , Simpson David A. , Sheridan Carl , Willoughby Colin E.
Published: June 2022

Glaucoma is a complex neurodegenerative disease resulting in progressive optic neuropathy and is a leading cause of irreversible blindness worldwide. Primary open angle glaucoma (POAG) is the predominant form affecting 65.5 million people globally. Despite the prevalence of POAG and the identification of over 120 glaucoma related genetic loci, the underlaying molecular mechanisms are still poorly understood. The transforming growth factor beta (TGF-β) signalling pathway is implicated in the molecular pathology of POAG. To gain a better understanding of the role TGF-β2 plays in the glaucomatous changes to the molecular pathology in the trabecular meshwork, we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM). We identified a significant number of differentially expressed genes and associated pathways that contribute to the pathogenesis of POAG. The differentially expressed genes were predominantly enriched in ECM regulation, TGF-β signalling, proliferation/apoptosis, inflammation/wound healing, MAPK signalling, oxidative stress and RHO signalling. Canonical pathway analysis confirmed the enrichment of RhoA signalling, inflammatory-related processes, ECM and cytoskeletal organisation in HTM cells in response to TGF-β2. We also identified novel genes and pathways that were affected after TGF-β2 treatment in the HTM, suggesting additional pathways are activated, including Nrf2, PI3K-Akt, MAPK and HIPPO signalling pathways. The identification and characterisation of TGF-β2 dependent differentially expressed genes and pathways in HTM cells is essential to understand the patho-physiology of glaucoma and to develop new therapeutic agents.
TACSTD2 upregulation is an early reaction to lung infection
Authors: Lenárt Sára , Lenárt Peter , Knopfová Lucia , Kotasová Hana , Pelková Vendula , Sedláková Veronika , Vacek Ondřej , Pokludová Jana , Čan Vladimír , Šmarda Jan , Souček Karel , Hampl Aleš , Beneš Petr
Published: June 2022

TACSTD2encodes a transmembrane glycoprotein Trop2 commonly overexpressed in carcinomas. While the Trop2 protein was discovered already in 1981 and first antibody–drug conjugate targeting Trop2 were recently approved for cancer therapy, the physiological role of Trop2 is still not fully understood. In this article, we show thatTACSTD2/Trop2 expression is evolutionarily conserved in lungs of various vertebrates. By analysis of publicly available transcriptomic data we demonstrate thatTACSTD2level consistently increases in lungs infected with miscellaneous, but mainly viral pathogens. Single cell and subpopulation based transcriptomic data revealed that the major source ofTACSTD2transcript are lung epithelial cells and their progenitors and thatTACSTD2is induced directly in lung epithelial cells following infection. Increase inTACSTD2expression may represent a mechanism to maintain/restore epithelial barrier function and contribute to regeneration process in infected/damaged lungs.
Telomere-to-telomere human DNA replication timing profiles
Authors: Massey Dashiell J. , Koren Amnon
Published: June 2022

The spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first nearly-gapless telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.
HideRNAs protect against CRISPR-Cas9 re-cutting after successful single base-pair gene editing
Authors: Harmsen Tim J. W. , Pritchard Colin E. J. , Riepsaame Joey , van de Vrugt Henri J. , Huijbers Ivo J. , te Riele Hein
Published: June 2022

Promiscuous activity of the Streptococcus pyogenes DNA nuclease CRISPR-Cas9 can result in destruction of a successfully modified sequence obtained by templated repair of a Cas9-induced DNA double-strand break. To avoid re-cutting, additional target-site-disruptions (TSDs) are often introduced on top of the desired base-pair alteration in order to suppress target recognition. These TSDs may lower the efficiency of introducing the intended mutation and can cause unexpected phenotypes. Alternatively, successfully edited sites can be protected against Cas9 re-cutting activity. This method exploits the finding that Cas9 complexed to trimmed guideRNAs can still tightly bind specific genomic sequences but lacks nuclease activity. We show here that the presence of a guideRNA plus a trimmed guideRNA that matches the successfully mutated sequence, which we call hideRNA, can enhance the recovery of precise single base-pair substitution events tenfold. The benefit of hideRNAs in generating a single point mutation was demonstrated in cell lines using plasmid-based delivery of CRISPR-Cas9 components and in mouse zygotes injected with Cas9/guideRNA plus Cas9/hideRNA ribonucleoprotein complexes. However, hRNA protection sometimes failed, which likely reflects an unfavorable affinity of hRNA/Cas9 versus gRNA/Cas9 for the DNA target site. HideRNAs can easily be implemented into current gene editing protocols and facilitate the recovery of single base-pair substitution. As such, hideRNAs are of great value in gene editing experiments demanding high accuracy.
A method for the controllable fabrication of optical fiber-based localized surface plasmon resonance sensors
Authors: Calatayud-Sanchez Alba , Ortega-Gomez Angel , Barroso Javier , Zubia Joseba , Benito-Lopez Fernando , Villatoro Joel , Basabe-Desmonts Lourdes
Published: June 2022

Optical fiber-based Localized Surface Plasmon Resonance (OF-LSPR) biosensors have emerged as an ultra-sensitive miniaturized tool for a great variety of applications. Their fabrication by the chemical immobilization of gold nanoparticles (AuNPs) on the optic fiber end face is a simple and versatile method. However, it can render poor reproducibility given the number of parameters that influence the binding of the AuNPs. In order to develop a method to obtain OF-LSPR sensors with high reproducibility, we studied the effect that factors such as temperature, AuNPs concentration, fiber core size and time of immersion had on the number and aggregation of AuNPs on the surface of the fibers and their resonance signal. Our method consisted in controlling the deposition of a determined AuNPs density on the tip of the fiber by measuring its LSPR signal (or plasmonic signal, Sp) in real-time. Sensors created thus were used to measure changes in the refractive index of their surroundings and the results showed that, as the number of AuNPs on the probes increased, the changes in the Sp maximum values were ever lower but the wavelength shifts were higher. These results highlighted the relevance of controlling the relationship between the sensor composition and its performance.
Use and subjective experience of the impact of motor-assisted movement exercisers in people with amyotrophic lateral sclerosis: a multicenter observational study
Authors: Maier André , Gaudlitz Marcel , Grehl Torsten , Weyen Ute , Steinbach Robert , Grosskreutz Julian , Rödiger Annekathrin , Koch Jan Christoph , Lengenfeld Teresa , Weydt Patrick , Günther René , Wolf Joachim , Baum Petra , Metelmann Moritz , Dorst Johannes , Ludolph Albert C. , Kettemann Dagmar , Norden Jenny , Koc Ruhan Yasemin , Walter Bertram , Hildebrandt Barbara , Münch Christoph , Meyer Thomas , Spittel Susanne
Published: June 2022

Motor-assisted movement exercisers (MME) are devices that assist with physical therapy in domestic settings for people living with ALS. This observational cross-sectional study assesses the subjective experience of the therapy and analyzes users' likelihood of recommending treatment with MME. The study was implemented in ten ALS centers between February 2019 and October 2020, and was coordinated by the research platform Ambulanzpartner. Participants assessed symptom severity, documented frequency of MME use and rated the subjective benefits of therapy on a numerical scale (NRS, 0 to 10 points, with 10 being the highest). The Net Promotor Score (NPS) determined the likelihood of a participant recommending MME. Data for 144 participants were analyzed. Weekly MME use ranged from 1 to 4 times for 41% of participants, 5 to 7 times for 42%, and over 7 times for 17%. Particularly positive results were recorded in the following domains: amplification of a sense of achievement (67%), diminution of the feeling of having rigid limbs (63%), diminution of the feeling of being immobile (61%), improvement of general wellbeing (55%) and reduction of muscle stiffness (52%). Participants with more pronounced self-reported muscle weakness were more likely to note a beneficial effect on the preservation and improvement of muscle strength during MME treatment (p < 0.05). Overall, the NPS for MME was high (+ 61). High-frequency MME-assisted treatment (defined as a minimum of five sessions a week) was administered in the majority of participants (59%) in addition to physical therapy. Most patients reported having achieved their individual therapeutic objectives, as evidenced by a high level of satisfaction with MME therapy. The results bolster the justification for extended MME treatment as part of a holistic approach to ALS care.
A mechano-sensing mechanism for waving in plant roots
Authors: Zhang Zhenwei , van Ophem Danie , Chelakkot Raghunath , Lazarovitch Naftali , Regev Ido
Published: June 2022

Arabidopsis roots grown on inclined agar surfaces exhibit unusual sinusoidal patterns known as root-waving. The origin of these patterns has been ascribed to both genetic and environmental factors. Here we propose a mechano-sensing model for root-waving, based on a combination of friction induced by gravitropism, the elasticity of the root and the anchoring of the root to the agar by thin hairs, and demonstrate its relevance to previously obtained experimental results. We further test the applicability of this model by performing experiments in which we measure the effect of gradually changing the inclination angles of the agar surfaces on the wavelength and other properties of the growing roots. We find that the observed dynamics is different than the dynamics reported in previous works, but that it can still be explained using the same mechano-sensing considerations. This is supported by the fact that a scaling relation derived from the model describes the observed dependence of the wavelength on the tilt angle for a large range of angles. We also compare the prevalence of waving in different plant species and show that it depends on root thickness as predicted by the model. The results indicate that waving can be explained using mechanics and gravitropism alone and that mechanics may play a greater role in root growth and form than was previously considered.
Inter-donor variability of extracellular matrix production in long-term cultures of human fibroblasts
Authors: Kawecki Fabien , Gluais Maude , Claverol Stéphane , Dusserre Nathalie , McAllister Todd , L'Heureux Nicolas
Published: June 2022

Several tissue engineering approaches are based on the ability of mesenchymal cells to endogenously synthesize an extracellular matrix (ECM)in vitro, which can be seen as a form of biomaterial.
Bioreducible polymer-mediated delivery of oncolytic adenovirus can attenuate antiviral immune response and concurrently enhance the induction of antitumor immune response to effectively prevent metastasis
Authors: Kasala Dayananda , Lee Soo-Hwan , Hong JinWoo , Oh Eonju , Yoon A-Rum , Yun Chae-Ok
Published: June 2022

Bioreducible polymer modified oAd can overcome CAR-dependent entry and lead to enhance expression of therapeutic genes, viral replication, and infiltration of T cells into the tumor tissues, ultimately resulting in improved therapeutic index of oAd.
Uptake and depuration of Ag nanoparticles versus Ag ions by zebrafish through dietary exposure: characterization of Ag nanoparticle formation and dissolution in vivo and toxicokinetic modeling
Authors: Yang Jung , Hou Wen-Che
Published: June 2022

The dynamic biological fate of silver nanoparticles as dissolution and neo-formation in zebrafish influences the number concentration-based versus mass concentration-based toxicokinetics.
Protein binding on acutely toxic and non-toxic polystyrene nanoparticles during filtration by Daphnia magna
Authors: Kelpsiene Egle , Brandts Irene , Bernfur Katja , Ekvall Mikael T. , Lundqvist Martin , Teles Mariana , Cedervall Tommy
Published: June 2022

Toxic and non-toxic polystyrene particles bind different proteins during filtration by zooplankton.
Visualizing optically-induced strains by five-dimensional ultrafast electron microscopy
Authors: Nakamura A. , Shimojima T. , Ishizaka K.
Published: June 2022

Optically-induced nanoscale strain dynamics in nano-fabricated Si thin films are quantitatively visualized on the picosecond scale. A newly developed ultrafast five-dimensional convergent beam electron diffraction method is introduced.
Electro-mechanochemical approach towards the chloro sulfoximidations of allenes under solvent-free conditions in a ball mill
Authors: Amer Mostafa M. , Hommelsheim Renè , Schumacher Christian , Kong Deshen , Bolm Carsten
Published: June 2022

Under mechanochemical conditions, BaTiO3 nanoparticles activate a Cu(ii)/ligand combination, allowing the catalytic addition of sulfoximidoyl chlorides to allenes.
Tracking the gastrointestinal digestive and metabolic behaviour of Dendrobium officinale polysaccharides by fluorescent labelling
Authors: Wu Zhijing , Zhang Yu , Nie Gang , Liu Junxi , Mei Hao , He Zihao , Dou Pengfei , Wang Kaiping
Published: June 2022

After oral administration, DOP was metabolized to stable oligosaccharide-like substances in the distal intestine by the gut microbiota represented by Bacteroides.
Wearable anti-temperature interference strain sensor with metal nanoparticle thin film and hybrid ligand exchange
Authors: Choi Young Kyun , Park Taesung , Lee Dong Hyun David , Ahn Junhyuk , Kim Yong Hwan , Jeon Sanghyun , Han Myung Joon , Oh Soong Ju
Published: June 2022

Anti-interference characteristics, whereby undesirable signal interference is minimized, are required for multifunctional sensor platforms. We fabricate the anti-temperature interference strain sensor by hybrid ligand exchange method with metal nanoparticles thin films.
Formal total synthesis of dankasterone B
Authors: Deng Shengzhen , Xu Hongjin , Jiang Huanfeng , Ma Zhiqiang
Published: June 2022

A formal total synthesis of dankasterone B was achieved in 15 steps.
A mechanistic study on electro-Fenton system cooperating with phangerochate chrysosporium to degrade lignin
Authors: Qin Yingjian , Wang Na , Ma Zhongmin , Li Jinsheng , Wang Yaozong , Zang Lihua
Published: June 2022

The combined catalytic system of Electro-Fenton (E-Fenton) and Phanerochaete chrysosporium (P. chrysosporium) was constructed in liquid medium with additional potential to overcome the limitations of lignin degradation by white rot fungi alone.
Reversible functionalization and exfoliation of graphite by a Diels–Alder reaction with furfuryl amine
Authors: Torkaman Najmeh Filvan , Kley Marina , Bremser Wolfgang , Wilhelm René
Published: June 2022

Furfuryl amine-functionalized few-layered graphene was preparedviaa mechanochemical process by a [4 + 2] cycloaddition under solvent-free conditions.
Practical asymmetric amine nucleophilic approach for the modular construction of protected α-quaternary amino acids
Authors: Liu Teng , Ni Shaofei , Guo Wusheng
Published: June 2022

We report the first amine nucleophilic approach for the modular construction of enantioenriched protected α-quaternary amino acids.
Strength of fluid-filled soft composites across the elastofracture length
Authors: Barney Christopher W. , Valentine Megan T. , Helgeson Matthew E.
Published: June 2022

This work probes the mechanical strength of composite hydrogels as the assembly size scale of the hydrophobic secondary phase transitions across the elastofracture length.
Dendrite-free lithium deposition on conventional graphite anode by growth of defective carbon-nanotube for lithium-metal/ion hybrid batteries
Authors: Yeo Gyuchan , Sung Jaekyung , Choi Minhong , Kim Namhyung , Ko Minseong
Published: June 2022

Full cell performance of conventional graphite and double-layer electrode of dCNT-G and G (dCNT-G/G) electrode at reverse designed N/P ratio (0.8). Inset images are schemes of each electrode at lithiated state with extra lithium layer.
Experimental analysis of liquid metal galinstan for electronics actuation
Authors: Anwar M.S. , Ehlers F. , Bangert A.
Published: June 2022

The experimental interfacial tension measurements of galinstan as a function of applied DC voltages are presented. The measurements are based on a tailored, modified pendent drop setup to make it suitable for this experiment. The findings rationalise Galinstan corresponding to Marangoni flow that actuates under the influence of a change in interfacial tension, resulting from applied voltages. Galinstan is substantiated as an actuation medium to enable ON or OFF states by using a very low applied voltage (∼ 0.8V). The illustrated nature of measurements performed in this work has significance for a variety of reconfigurable RF applications, by enabling well‐controlled actuations.
FFT, DA, and Mori-Tanaka approximation to determine the elastic moduli of three-phase composites with the random inclusions
Authors: Nguyen Van-Luat
Published: June 2022

In this work, some solutions such as Mori-Tanaka approximation (MTA), Differential approximations (DA), and Fast Fourier transformation method (FFT) were applied to estimate the elastic bulk and shear modulus of three-phase composites in 2D. In which two different sizes of circular inclusions are arranged randomly non-overlapping in a continuous matrix. The numerical solutions using FFT analysis were compared with DA, MTA, and Hashin-Strikman's bounds. The MTA and DA reasonably agreeable solution with the FFT solution shows the effectiveness of the approximation methods, which makes MTA, DA useful with simplicity and ease of application.
Implémentation matérielle d’un algorithme de cryptographie légère pour objets connectés
Authors: Roussel N. , Potin O. , Rigaud J. B. , Dutertre J. M.
Published: June 2022

Le monde de la microélectronique a fait place à l’internet des objets (IoT). Ces objets étant de plus en plus connectés et nomades, ils ont d’abord été conçus avec des fortes contraintes de consommation. Cependant, de récentes attaques ont démontré leur vulnérabilité et la sécurité est devenue une contrainte majeure. Pour répondre à cette problématique, le projet ANR MISTRAL propose de réaliser une implémentation matérielle d’algorithme de cryptographie légère (LWC) en associant CMOS et MRAM. Cet article présente une implémentation pure CMOS d’ASCON, un algorithme de cryptographie légère finaliste du concours du NIST. Cette implémentation servira de référence pour une future implémentation hybride de l’algorithme.
Enseignement par la pratique de la conception conjointe Hard/Soft de systèmes numériques embarqués sur cible FPGA
Authors: Dadouche F. , Uhring W.
Published: June 2022

Ce travail a pour but de partager une expérience d’enseignement dédiée à la conception de systèmes numériques embarqués sur cibles reconfigurables de type FPGA en première année de master au sein de l’université de Strasbourg. Cette dernière introduit une méthode d’apprentissage des concepts de la conception conjointe matérielle/logicielle (Hard/Soft) par la pratique. Dans cette méthode, la proportion des enseignements théoriques en cours magistraux est réduite au strict minimum pour laisser place aux travaux pratiques durant lesquels les étudiants sont confrontés à une situation réelle qu’ils doivent réaliser de manière individuelle dans le cadre d’un mini-projet. Ce dernier définit un seuil minimum de réalisation pour valider le projet, pour aller plus loin, des pistes d’amélioration sont suggérées par l’enseignant et au-delà les étudiants peuvent proposer leurs propres améliorations. Les retours, que nous avons eus, montrent que les étudiants sont très satisfaits de ce dispositif et souvent souhaitent la généralisation de la méthode à d’autres enseignements adaptés à un apprentissage par la pratique.