bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of influencing factors of phenanthrene adsorption by different soils in Guanzhong basin based on response surface method
Authors: Tian Hua , Zhang Qing , Tian Xue , Xie Zu-feng , Pu Fang , Wang Qian-ji 
Published: December 2022

AbstractAdsorption desorption is an important behavior affecting the migration of phenanthrene in soil. In this study, three typical soils of loess, silts and silty sand in Guanzhong Basin, Shaanxi Province, China were used as adsorbents. Batch equilibrium experiments were carried out to study the adsorption desorption kinetics and isotherm of phenanthrene in different soils. Response surface method (RSM) was used to study the effects of temperature, pH, phenanthrene concentration and organic matter content on soil adsorption of phenanthrene. The results showed that after adsorption, the outline of soil particles became more blurred and the degree of cementation increased. The kinetic adsorption of phenanthrene by soil conforms to the quasi second-order kinetic model, and the adsorption desorption isotherm is nonlinear and conforms to the Freundlich model. Due to the difference of soil properties, the adsorption amount of phenanthrene by soil is loess > silty sand > silts. The thermodynamic results show that the adsorption of phenanthrene by soil is spontaneous and endothermic, and the desorption is spontaneous and exothermic. Through RSM, the interaction between phenanthrene concentration and soil organic matter in Loess and silts is significant, and the interaction between temperature and soil organic matter in silty sand is significant. Among the four factors affecting the adsorption rate of loess, silts and silty sand, soil organic matter is the most significant. The theoretical optimum adsorption rates of loess, silts and silty sand are 98.89%, 96.59% and 93.37% respectively.
Optimization of Bacillus subtilis NRC1 growth conditions using response surface methodology for sustainable biosynthesis of gold nanoparticles
Authors: El-Bendary Magda A. , Afifi Salwa S. , Moharam Maysa E. , Elsoud Mostafa M. Abo , Gawdat Noha A. 
Published: December 2022

AbstractGold nanoparticles (AuNPs) have different unique properties and a wide range of applications in different fields. Thereby, there is a growing urgency for the production of AuNPs using a safe and an economic method. In this study, optimization of fermentation conditions by Bacillus subtilis NRC1 for extracellular AuNPs synthesis using response surface methodology was achieved. The data obtained from Plackett–Burman design followed by Box–Behnken design indicated the accuracy and reliability of the model and it could be used to navigate the design space with a reasonable accuracy. Numerical optimization of Bacillus subtilis NRC1 active extracellular filtrate production, showed the optimum conditions of 0.74% (w/v) casein hydrolysate, 3.99% (w/v) dextrin, 47 × 106 CFU/ml inoculum size at pH 7.76 and 25 $$^\circ$$

∘

C to give the maximum AuNPs biosynthesis. The model was highly valid and the obtained data had a confidence factor of 98.48%. Statistical optimization resulted in a 2.6-fold increase in AuNPs production compared with that of the non-optimized medium.
The effects of daily autobiographical memory training on memory bias, mood and stress resilience in dysphoric individuals
Authors: Bovy Leonore , Ikani Nessa , van de Kraats Livia N. M. , Dresler Martin , Tendolkar Indira , Vrijsen Janna N. 
Published: December 2022

AbstractNegative memory bias refers to the enhanced recall of negative memories and is a prominent cognitive factor causing and maintaining depression. Surprisingly few studies modify this negative recall. The current study used a smartphone-based autobiographical memory training to increase positive memory recall and thereby alter negative memory bias. A total of 96 dysphoric (≥ 13 BDI-II) participants were randomly allocated to a positive, sham or no-training condition, conducted over a period of 6 days. Positive memory bias (i.e., recalled event evaluation) significantly increased from pre- to post-training after positive and sham intervention, suggesting an unspecific training effect. No transfer to memory specificity, implicit memory bias or depressive symptoms was found, nor was the training effect modulated by pre-existing level of positive memory bias. A post-hoc follow-up measurement during the initial COVID-19 crisis revealed that subjects who benefitted most from either of the trainings maintained their stress levels better during a natural stressful period, compared to those who responded least to the training. Future studies should carefully consider the impact of sham training design. Moreover, it is important to examine transfer effects of bias training as practice in daily life.
4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists
Authors: Wang Ke , Bleasdale Madeleine , Le Moyne Charles , Freund Cacilia , Krause Johannes , Boivin Nicole , Schiffels Stephan 
Published: December 2022

AbstractPetrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.
Optical transparency and label-free vessel imaging of zebrafish larvae in shortwave infrared range as a tool for prolonged studying of cardiovascular system development
Authors: Volkov Mikhail , Machikhin Alexander , Bukova Valeriya , Khokhlov Demid , Burlakov Alexander , Krylov Viacheslav 
Published: December 2022

AbstractOptical techniques are utilized for the non-invasive analysis of the zebrafish cardiovascular system at early developmental stages. Being based mainly on conventional optical microscopy components and image sensors, the wavelength range of the collected and analyzed light is not out of the scope of 400–900 nm. In this paper, we compared the non-invasive optical approaches utilizing visible and near infrared range (VISNIR) 400–1000 and the shortwave infrared range (SWIR) 900–1700 nm. The transmittance spectra of zebrafish tissues were measured in these wavelength ranges, then vessel maps, heart rates, and blood flow velocities were calculated from data in VISNIR and SWIR. An increased pigment pattern transparency was registered in SWIR, while the heart and vessel detection quality in this range is not inferior to VISNIR. Obtained results indicate an increased efficiency of SWIR imaging for monitoring heart function and hemodynamic analysis of zebrafish embryos and larvae and suggest a prolonged registration period in this range compared to other optical techniques that are limited by pigment pattern development.
Three-dimensional close-to-substrate trajectories of magnetic microparticles in dynamically changing magnetic field landscapes
Authors: Huhnstock Rico , Reginka Meike , Sonntag Claudius , Merkel Maximilian , Dingel Kristina , Sick Bernhard , Vogel Michael , Ehresmann Arno 
Published: December 2022

AbstractThe transport of magnetic particles (MPs) by dynamic magnetic field landscapes (MFLs) using magnetically patterned substrates is promising for the development of Lab-on-a-chip (LOC) systems. The inherent close-to-substrate MP motion is sensitive to changing particle–substrate interactions. Thus, the detection of a modified particle–substrate separation distance caused by surface binding of an analyte is expected to be a promising probe in analytics and diagnostics. Here, we present an essential prerequisite for such an application, namely the label-free quantitative experimental determination of the three-dimensional trajectories of superparamagnetic particles (SPPs) transported by a dynamically changing MFL. The evaluation of defocused SPP images from optical bright-field microscopy revealed a “hopping”-like motion of the magnetic particles, previously predicted by theory, additionally allowing a quantification of maximum jump heights. As our findings pave the way towards precise determination of particle–substrate separations, they bear deep implications for future LOC detection schemes using only optical microscopy.
Tree species composition mapping with dimension reduction and post-classification using very high-resolution hyperspectral imaging
Authors: Likó Szilárd Balázs , Bekő László , Burai Péter , Holb Imre J. , Szabó Szilárd 
Published: December 2022

AbstractTree species’ composition of forests is essential in forest management and nature conservation. We aimed to identify the tree species structure of a floodplain forest area using a hyperspectral image. We proposed an efficient novel strategy including the testing of three dimension reduction (DR) methods: Principal Component Analysis, Minimum Noise Fraction (MNF) and Indipendent Component Analysis with five machine learning (ML) algorithms (Maximum Likelihood Classifier, Support Vector Classification, Support Vector Machine, Random Forest and Artificial Neural Network) to find the most accurate outcome; altogether 300 models were calculated. Post-classification was applied by combining the multiresolution segmentation and filtering. MNF was the most efficient DR technique, and at least 7 components were needed to gain an overall accuracy (OA) of > 75%. Forty-five models had > 80% OAs; MNF was 43, and the Maximum Likelihood was 19 times among these models. Best classification belonged to MNF with 10 components and Maximum Likelihood classifier with the OA of 83.3%. Post-classification increased the OA to 86.1%. We quantified the differences among the possible DR and ML methods, and found that even > 10% worse model can be found using popular standard procedures related to the best results. Our workflow calls the attention of careful model selection to gain accurate maps.
Abstractness emerges progressively over the second year of life
Authors: Bellagamba Francesca , Borghi Anna M. , Mazzuca Claudia , Pecora Giulia , Ferrara Fabiana , Fogel Alan 
Published: December 2022

AbstractAbstract words, terms not referring to here and now, are acquired slowly in infancy. They are difficult to acquire as they are more detached from sensory modalities than concrete words. Recent theories propose that, because of their complexity, other people are pivotal for abstract concepts’ acquisition and use. Eight children (4 girls) and their mothers were observed longitudinally and extensively from 12 to 24 months of age. Video recordings of mother-infant free play with toys were done every two weeks in a laboratory setting with families in the USA. Children progressively use a range of words referring to abstract concepts, with a major shift from 12 to 15 months and again from 22 to 24 months, but the qualitative data testify an incremental growth of abstract concepts. We identified a progression in the acquisition of words denoting abstract concepts in relation to the overall productive vocabulary, suggesting that having more abstract terms in one’s vocabulary promotes faster language acquisition.
Risk factors associated with cytomegalovirus reactivation in patients receiving immunosuppressive therapy for rheumatic diseases: a retrospective study
Authors: Shimada Tatsuya , Higashida-Konishi Misako , Izumi Keisuke , Hama Satoshi , Oshige Tatsuhiro , Oshima Hisaji , Okano Yutaka 
Published: December 2022

AbstractImmunosuppressive treatment is a common cause of cytomegalovirus (CMV) reactivation. However, there is no consensus regarding the risk factors for CMV reactivation in rheumatic diseases. Therefore, this study aimed to elucidate the risk factors associated with CMV reactivation. We retrospectively collected the data of 472 patients with rheumatic diseases whose CMV pp65 antigen (C7-HRP) titer was measured. We divided the patients into those with and those without C7-HRP. We retrospectively collected data on age, sex, primary condition and organ involvement, and blood test results. We also investigated the use of immunosuppressants and the maximum and cumulative doses of prednisolone (PSL). We performed univariate and multivariate analyses to identify risk factors for CMV reactivation. Multivariate analysis showed that higher age (71.2 vs. 64.4 years, p = 0.0022), hypoalbuminemia (2.9 vs. 3.4 g/dL, p = 0.0104), higher creatinine level (1.2 vs. 0.9 mg/dL, p = 0.0026), cyclosporine use (8.2 vs. 3.6%, p = 0.0101), and higher maximum (552.4 vs. 243.3 mg, p < 0.0001) and cumulative (2785.9 vs. 1330.5 mg, p < 0.0001) doses of PSL were associated with CMV reactivation. Older age, hypoalbuminemia, higher creatinine level, cyclosporine use, and higher maximum and cumulative doses of PSL were significant risk factors for CMV reactivation in rheumatic diseases.
A probabilistic computational framework for the prediction of corrosion-induced cracking in large structures
Authors: Qian Guofeng , Tantratian Karnpiwat , Chen Lei , Hu Zhen , Todd Michael D. 
Published: December 2022

AbstractCorrosion can initiate cracking that leads to structural integrity reduction. Quantitative corrosion assessment is challenging, and the modeling of corrosion-induced crack initiation is essential for model-based corrosion reliability analysis of various structures. This paper proposes a probabilistic computational analysis framework for corrosion-to-crack transitions by integrating a phase-field model with machine learning and uncertainty quantification. An electro-chemo-mechanical phase-field model is modified to predict pitting corrosion evolution, in which stress is properly coupled into the electrode chemical potential. A crack initiation criterion based on morphology is proposed to quantify the pit-to-cracking transition. A spatiotemporal surrogate modeling method is developed to facilitate this, consisting of a Convolution Neural Network (CNN) to map corrosion morphology to latent spaces, and a Gaussian Process regression model with a nonlinear autoregressive exogenous model (NARX) architecture for prediction of corrosion dynamics in the latent space over time. It enables the real-time prediction of corrosion morphology and crack initiation behaviors (whether, when, and where the corrosion damage triggers the crack initiation), and thus makes it possible for probabilistic analysis, with uncertainty quantified. Examples at various stress and corrosion conditions are presented to demonstrate the proposed computational framework.
Probing photoprotection properties of lipophilic chain conjugated thiourea-aryl group molecules to attenuate ultraviolet-A induced cellular and DNA damages
Authors: Rana Sobia , Fatima Noor , Yaqoob Sana , Hameed Abdul , Mirza Munazza Raza , Jabeen Almas , Iqbal Jamshed 
Published: December 2022

AbstractUltraviolet-A (UVA) radiation is a major contributor to reactive oxygen species (ROS), reactive nitrite species (RNS), inflammation, and DNA damage, which causes photoaging and photocarcinogenesis. This study aimed to evaluate the UVA protective potential of lipophilic chain conjugated thiourea-substituted aryl group molecules against UVA-induced cellular damages in human dermal fibroblasts (BJ cell line). We tested a series of nineteen (19) molecules for UVA photoprotection, from which 2′,5′-dichlorophenyl-substituted molecule DD-04 showed remarkable UVA protection properties compared to the reference (benzophenone). The results indicate that DD-04 significantly reduced intracellular ROS and nitric oxide (NO) as compared to the UVA-irradiated control (p < 0.001). Moreover, the compound DD-04 showed anti-inflammatory activity as it significantly reduced the levels of tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) pro-inflammatory cytokines produced by THP-1 (human monocytic) cells (p < 0.05). DNA damage was also prevented by DD-04 treatment in the presence of UVA. It was observed that DD-04 significantly reduced the number of cyclobutane pyrimidine dimers (CPDs) when compared to the UVA-irradiated control (p < 0.001). Finally, the DNA strand breaks were checked and a single intact DNA band was seen upon treatment with DD-04 in the presence of UVA. In conclusion, DD-04 can be considered a potential candidate UVA filter due to its photoprotective potential.
Meiotic transmission patterns of additional genomic elements in Brachionus asplanchnoidis, a rotifer with intraspecific genome size variation
Authors: Blommaert Julie , Stelzer Claus-Peter 
Published: December 2022

AbstractIntraspecific genome size (GS) variation in Eukaryotes is often mediated by additional, nonessential genomic elements. Physically, such additional elements may be represented by supernumerary (B-)chromosomes or by large heterozygous insertions into the regular chromosome set. Here we analyze meiotic transmission patterns of Megabase-sized, independently segregating genomic elements (ISEs) in Brachionus asplanchnoidis, a planktonic rotifer that displays an up to two-fold intraspecific GS variation due to variation in size and number of these elements. To gain insights into the meiotic transmission patterns of ISEs, we measured GS distributions of haploid males produced by individual mother clones using flow cytometry and compared these distributions to theoretical distributions expected under a range of scenarios. These scenarios considered transmission biases resembling (meiotic) drive, or cosegregation biases, e.g., if pairs of ISEs preferentially migrated towards the same pole during meiosis. We found that the inferred transmission patterns were diverse and ranged from positive biases (suggesting drive) to negative biases (suggesting drag), depending on rotifer clone and its ISE composition. Additionally, we obtained evidence for a negative cosegregation bias in some of the rotifer clones, i.e., pairs of ISEs exhibited an increased probability of migrating towards opposite poles during meiosis. Strikingly, these transmission and segregation patterns were more similar among members of a genetically homogeneous inbred line than among outbred members of the population. Comparisons between early and late stages of haploid male embryonic development (e.g., young synchronized male eggs vs. hatched males) showed very similar GS distributions, suggesting that transmission biases occur very early in male development, or even during meiosis. Very large genome size was associated with reduced male embryonic survival, suggesting that excessive amounts of ISEs might be detrimental to male fitness. Altogether, our results indicate considerable functional diversity of ISEs in B. asplanchnoidis, with consequences on meiotic transmission and embryonic survival.
Expression analysis of NF-ƙB-related long non-coding RNAs in bipolar disorder
Authors: Teshnizi Sara Ahmadi , Shahani Pariya , Taheri Mohammad , Hussen Bashdar Mahmud , Eslami Solat , Sadeghzadeh Zahra , Ghafouri-Fard Soudeh , Sayad Arezou 
Published: December 2022

AbstractBipolar disorder (BD) is a mental disorder that leads to abnormal swings in mood, energy, activity level, attention, and the capability to accomplish daily tasks. Several long non-coding RNAs (lncRNAs) are dysregulated in BD patients. We have compared expression levels of five NF-κB-associated lncRNAs, namely ANRIL, CEBPA-DT, H19, NKILA and HNF1A-AS1 in blood samples of BD patients compared with controls. While ANRIL, CEBPA-DT and HNF1-AS1 were significantly under-expressed in BD patients compared with controls, NKILA levels were higher in patients versus controls. Among differentially expressed genes, HFN1A-AS1 exhibited the best diagnostic parameters in the separation of patients from controls (AUC ± SD = 0.86 ± 0.03, sensitivity = 0.82, specificity = 0.82, P value < 0.0001). AUC values for NKILA, ANRIL and CEBPA-DT were 0.71, 0.68 and 0.65, respectively. In accordance with the previously reported participation of NF-ƙB in the pathophysiology of BD, the current study provides evidence for dysregulation of NF-κB-associated lncRNAs in BD.
Surveying lncRNA-lncRNA cooperations reveals dominant effect on tumor immunity cross cancers
Authors: Shao Tingting , Xie Yunjin , Shi Jingyi , Yang Changbo , Zou Haozhe , Li Yongsheng , Xu Juan , Li Xia 
Published: December 2022

AbstractLong non-coding RNAs (lncRNAs) can crosstalk with each other by post-transcriptionally co-regulating genes involved in the same or similar functions; however, the regulatory principles and biological insights in tumor-immune are still unclear. Here, we show a multiple-step model to identify lncRNA-lncRNA immune cooperation based on co-regulating functional modules by integrating multi-omics data across 20 cancer types. Moreover, lncRNA immune cooperative networks (LICNs) are constructed, which are likely to modulate tumor-immune microenvironment by regulating immune-related functions. We highlight conserved and rewired network hubs which can regulate interactions between immune cells and tumor cells by targeting ligands and activating or inhibitory receptors such as PDCD1, CTLA4 and CD86. Immune cooperative lncRNAs (IC-lncRNAs) playing central roles in many cancers also tend to target known anticancer drug targets. In addition, these IC-lncRNAs tend to be highly expressed in immune cell populations and are significantly correlated with immune cell infiltration. The similar immune mechanisms cross cancers are revealed by the LICNs. Finally, we identify two subtypes of skin cutaneous melanoma with different immune context and prognosis based on IC-lncRNAs. In summary, this study contributes to a comprehensive understanding of the cooperative behaviours of lncRNAs and accelerating discovery of lncRNA-based biomarkers in cancer.
An artificial neural network explains how bats might use vision for navigation
Authors: Goldshtein Aya , Akrish Shimon , Giryes Raja , Yovel Yossi 
Published: December 2022

AbstractAnimals navigate using various sensory information to guide their movement. Miniature tracking devices now allow documenting animals’ routes with high accuracy. Despite this detailed description of animal movement, how animals translate sensory information to movement is poorly understood. Recent machine learning advances now allow addressing this question with unprecedented statistical learning tools. We harnessed this power to address visual-based navigation in fruit bats. We used machine learning and trained a convolutional neural network to navigate along a bat’s route using visual information that would have been available to the real bat, which we collected using a drone. We show that a simple feed-forward network can learn to guide the agent towards a goal based on sensory input, and can generalize its learning both in time and in space. Our analysis suggests how animals could potentially use visual input for navigation and which features might be useful for this purpose.