bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of typical genes for heterologous gene expression
Authors: Simm Dominic , Popova Blagovesta , Braus Gerhard H. , Waack Stephan , Kollmar Martin 
Published: June 2022

AbstractHeterologous 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

AbstractAnodal 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

AbstractShort 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

AbstractEngineering 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

AbstractMonitoring 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

AbstractIn 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

AbstractThe 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

AbstractMalaria 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

AbstractThe 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

AbstractSingle-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

AbstractThere 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

AbstractA 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.