bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study of reasonable mesh size of geogrid reinforced tailings
Authors: Du Changbo , Niu Ben , Wang Laigui , Yi Fu , Liang Lidong
Published: June 2022

Currently, the influence of geogrid mesh size on interface characteristics are disregarded in various codes and standards. To explore the reasonable mesh size of geogrid used for reinforced tailings, the direct shear test and pull-out test of geogrid reinforced tailings with different mesh sizes were done. The results show that the shear surface of geogrid reinforced tailings is characterized by the combined action of geogrid-tailings interface and tailings-tailings interface; the geogrid-tailings interface friction was separated from the comprehensive interface friction to analyze the influence of area ratio on it under different test conditions; and the mesh size of geogrid reinforced tailings, that is, the area ratio of the geogrid-tailings interface to the shear surface (α), has a greater influence on the pseudo-cohesion and less on the pseudo-friction angle. The friction strength of the geogrid-tailings interface increases slightly with increasing mesh size, then decreases sharply, and the reinforcement effect of geogrid quickly disappears. Considering the direct shear test and pull-out test, the reasonable mesh size of geogrid reinforced tailings should be the mesh size corresponding to α 0.47–0.55. With the increase α, the effect of the geogrid reinforced tailings can be divided into four stages where the third stage ($$0.4 \le \alpha < 0.6$$

0.4
≤
α
<
0.6

) is the stage with the best reinforcement effect.
Association of ideal cardiovascular health with carotid intima-media thickness (cIMT) in a young adult population
Authors: Chavoshi Vajihe , Barzin Maryam , Ebadinejad Amir , Dehghan Pooneh , Momeni Moghaddam Amin , Mahdavi Maryam , Hadaegh Farzad , Niroomand Mahtab , Valizadeh Majid , Azizi Fereidoun , Mirmiran Parvin , Hosseinpanah Farhad
Published: June 2022

Ideal cardiovascular health (CVH) is associated with a lower risk of developing cardiovascular diseases. This study aims to investigate the association of CVH metrics with carotid intima-media thickness (cIMT) as a marker of subclinical atherosclerosis in young adults. A cross-sectional study was performed on 1295 adults, average age of 29.7 ± 4.0 years, selected from the participants of the Tehran Lipid and Glucose Study. The participants were divided into three groups based on the overall CVH score: ideal, intermediate, and poor CVH. Multivariate-adjusted linear regression was used to determine the association of the CVH score with cIMT. Multivariate-adjusted odds ratios (ORs) were calculated for high cIMT (≥ 95% percentile). Also, the independent effects of each ideal CVH metric on cIMT were analyzed. The prevalence of ideal CVH was 6.4% in men and 12.4% in women, and mean cIMT was obtained 0.53 ± 0.09 mm in men and 0.57 ± 0.08 mm in women. A 1-point increase of the CVH score in men and women was associated with a cIMT decrease of 0.009 and 0.011 mm (men: Beta [SE] = − 0.009 [0.003]; women: − 0.011 [0.007], p < 0.001), rendering the ORs of 0.66 and 0.70 for having a high cIMT (≥ 95% percentile), respectively. Ideal blood pressure in both sexes and body mass index in women had significant inverse association with cIMT. There was an inverse graded association between the CVH score and cIMT among young adults, indicating that ideal CVH metrics were associated with better vascular health in this population.
High incidence of cleft palate and vomer deformities in patients with Eustachian tube dysfunction
Authors: Bae Seong Hoon , Kim Jun-Young , Jeong Mincheol , Moon In Seok , Kim Sung Huhn , Choi Jae Young , Jung Jinsei
Published: June 2022

Although the cleft palate is regarded as a contraindication for Eustachian tube ballooning, the presence of submucosal cleft palate may be overlooked while diagnosing Eustachian tube dysfunction. Therefore, we aimed to determine the incidence of the presence of a hard palate bony notch and vomer defect, which indicate the presence of submucosal cleft palate in patients with Eustachian tube dysfunction. In the Eustachian tube dysfunction group (n = 28), 4 patients (14.3%) exhibited a hard palate bony notch and a concurrent vomer defect. Three of them exhibited the presence of occult submucosal cleft palate, which had not been diagnosed previously. None of the control group (n = 39) showed any of these findings. The hard palate length of patients in the Eustachian tube dysfunction group was significantly lesser than that of those in the control group (34.2 ± 5.6 mm vs. 37.2 ± 2.1 mm, P = 0.016). Patients with Eustachian tube dysfunction have a high incidence of submucosal cleft palate and its occult variant, which are challenging to diagnose without any preexisting suspicion. Clinicians should evaluate the hard palate and vomer to exclude the presence of occult submucosal cleft palate while diagnosing Eustachian tube dysfunction.
Heterogeneity in coronary heart disease risk
Authors: Simonetto Cristoforo , Rospleszcz Susanne , Kaiser Jan Christian , Furukawa Kyoji
Published: June 2022

There is large inter-individual heterogeneity in risk of coronary heart disease (CHD). Risk factors traditionally used in primary risk assessment only partially explain this heterogeneity. Residual, unobserved heterogeneity leads to age-related attenuation of hazard rates and underestimation of hazard ratios. Its magnitude is unknown. Therefore, we aimed to estimate a lower and an approximate upper bound. Heterogeneity was parametrized by a log-normal distribution with shape parameter σ. Analysis was based on published data. From concordance indices of studies including traditional risk factors and additional diagnostic imaging data, we calculated the part of heterogeneity explained by imaging data. For traditional risk assessment, this part typically remains unexplained, thus constituting a lower bound on unobserved heterogeneity. Next, the potential impact of heterogeneity on CHD hazard rates in several large countries was investigated. CHD rates increase with age but the increase attenuates with age. Presuming this attenuation to be largely caused by heterogeneity, an approximate upper bound on σ was derived. Taking together both bounds, unobserved heterogeneity in studies without imaging information can be described by a shape parameter in the range σ = 1–2. It substantially contributes to observed age-dependences of hazard ratios and may lead to underestimation of hazard ratios by a factor of about two. Therefore, analysis of studies for primary CHD risk assessment should account for unobserved heterogeneity.
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data
Authors: Arpi Magdalena Navarro Torres , Simpson T. Ian
Published: June 2022

Autism Spectrum Disorders (ASD) have a strong, yet heterogeneous, genetic component. Among the various methods that are being developed to help reveal the underlying molecular aetiology of the disease one approach that is gaining popularity is the combination of gene expression and clinical genetic data, often using the SFARI-gene database, which comprises lists of curated genes considered to have causative roles in ASD when mutated in patients. We build a gene co-expression network to study the relationship between ASD-specific transcriptomic data and SFARI genes and then analyse it at different levels of granularity. No significant evidence is found of association between SFARI genes and differential gene expression patterns when comparing ASD samples to a control group, nor statistical enrichment of SFARI genes in gene co-expression network modules that have a strong correlation with ASD diagnosis. However, classification models that incorporate topological information from the whole ASD-specific gene co-expression network can predict novel SFARI candidate genes that share features of existing SFARI genes and have support for roles in ASD in the literature. A statistically significant association is also found between the absolute level of gene expression and SFARI’s genes and Scores, which can confound the analysis if uncorrected. We propose a novel approach to correct for this that is general enough to be applied to other problems affected by continuous sources of bias. It was found that only co-expression network analyses that integrate information from the whole network are able to reveal signatures linked to ASD diagnosis and novel candidate genes for the study of ASD, which individual gene or module analyses fail to do. It was also found that the influence of SFARI genes permeates not only other ASD scoring systems, but also lists of genes believed to be involved in other neurodevelopmental disorders.
A rapid and high sensitivity RNA detection based on NASBA and G4-ThT fluorescent biosensor
Authors: Guoshuai Jia , Xiaomeng Xu , Zengdan Guo , Xingxing Hu , Qi Pan , Hanbing Zhu , Yi Wang
Published: June 2022

In recent years, various newly emerged and re-emerged RNA viruses have seriously threatened the global public health. There is a pressing need for rapid and reliable nucleic acid–based assays for detecting viral RNA. Here, we successfully developed a highly sensitive, easy-to-operate G4-ThT-NASBA system to detect viral RNA that no need for labeled primers and probes. Next, we tested the system for detecting the Classical Swine Fever Virus (CSFV), an RNA virus that causes a highly contagious disease in domestic pigs and wild boar and easily causes huge economic losses. Results showed that the system, integrated the G4-ThT fluorescent biosensor and NASBA (Nuclear acid sequence-based amplification),is capable to detect as little as 2 copies/μL of viral RNA without interfering by other swine viral RNA. Moreover, we were able to detect CSFV RNA within 2 h in serum samples taken from the field in a real-time mode. These findings indicate that the G4-ThT-NASBA system is a rapid, high sensitivity and easy-to-operate technique for RNA detection. The method also has the real-time detection capability which may be easily integrated in a highly automated system such as microfluidic chips.
Adipocere formation in biofilms as a first step in soft tissue preservation
Authors: Mähler Bastian , Janssen Kathrin , Tahoun Mariam , Tomaschek Frank , Schellhorn Rico , Müller Christa E. , Bierbaum Gabriele , Rust Jes
Published: June 2022

The preservation of soft tissue in the fossil record is mostly due to the replacement of organic structures by minerals (e.g. calcite, aragonite or apatite) called pseudomorphs. In rare cases soft tissues were preserved by pyrite. We assume that adipocere, as the shaping component, might be a preliminary stage in the pyritisation of soft tissues under anaerobic conditions. Using high-performance liquid chromatography coupled to ultraviolet and mass spectrometric detection (HPLC–UV/MS) and confocal Raman spectroscopy (CRS) we were able to demonstrate the transformation of the hepatopancreas (digestive gland) of the crayfish Cambarellus diminutus [Hobbs 1945] into adipocere within only 9 days, just inside a biofilm. Microorganisms (bacteria and fungi) which were responsible for the biofilm (Sphaerotilus [Kutzig 1833] and Pluteus [Fries 1857]) and maybe the adipocere formation (Clostridium [Prazmowski 1880]) were detected by 16S rRNA gene amplicon sequencing. Furthermore, micro-computed tomography (µ-CT) analyses revealed a precipitation of calcite and further showed that in animals with biofilm formation calcite precipitates in finer grained crystals than in individuals without biofilm formation, and that the precipitates were denser and replicated the structures of the cuticles better than the coarse precipitates.
The impact of the ST131 clone on recurrent ESBL-producing E. coli urinary tract infection: a prospective comparative study
Authors: Lindblom Anna , Kiszakiewicz Camilla , Kristiansson Erik , Yazdanshenas Shora , Kamenska Nina , Karami Nahid , Åhrén Christina
Published: June 2022

The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is of great concern. Almost one third of patients with UTI, develop recurrent UTI (RUTI). We followed 297 patients for one year after their first episode of UTI due to ESBL-E. coli. Our aim was to evaluate the impact of the globally dominant sequence type (ST)131 clone and its clades, on the risk of subsequent recurrences with ESBL-E. coli. Isolates from patients developing RUTI (68/297) were compared with those from patients with sporadic UTI (SUTI, 229/297). No association was found between RUTI and the two most prevalent phylogroups B2 and D, blaCTX-M genes, or resistance profile. Half of the patients with RUTI were infected with ST131 isolates. Clade C2 were in dominance (50/119) among ST131 isolates. They were more common in patients with RUTI than SUTI (28% vs 13%) and multivariate analysis showed an increased odds-ratio (OR = 2.21, p = 0.033) for recurrences in patients infected with these isolates as compared to non-ST131 isolates. Detecting specific biomarkers, as ST131 clade C2, in ESBL-E. coli UTI isolates may aid in prediction of RUTI and improve diagnostics and care of patients with a risk of ESBL-E. coli recurrences.
Building reliable radiomic models using image perturbation
Authors: Teng Xinzhi , Zhang Jiang , Zwanenburg Alex , Sun Jiachen , Huang Yuhua , Lam Saikit , Zhang Yuanpeng , Li Bing , Zhou Ta , Xiao Haonan , Liu Chenyang , Li Wen , Han Xinyang , Ma Zongrui , Li Tian , Cai Jing
Published: June 2022

Radiomic model reliability is a central premise for its clinical translation. Presently, it is assessed using test–retest or external data, which, unfortunately, is often scarce in reality. Therefore, we aimed to develop a novel image perturbation-based method (IPBM) for the first of its kind toward building a reliable radiomic model. We first developed a radiomic prognostic model for head-and-neck cancer patients on a training (70%) and evaluated on a testing (30%) cohort using C-index. Subsequently, we applied the IPBM to CT images of both cohorts (Perturbed-Train and Perturbed-Test cohort) to generate 60 additional samples for both cohorts. Model reliability was assessed using intra-class correlation coefficient (ICC) to quantify consistency of the C-index among the 60 samples in the Perturbed-Train and Perturbed-Test cohorts. Besides, we re-trained the radiomic model using reliable RFs exclusively (ICC > 0.75) to validate the IPBM. Results showed moderate model reliability in Perturbed-Train (ICC: 0.565, 95%CI 0.518–0.615) and Perturbed-Test (ICC: 0.596, 95%CI 0.527–0.670) cohorts. An enhanced reliability of the re-trained model was observed in Perturbed-Train (ICC: 0.782, 95%CI 0.759–0.815) and Perturbed-Test (ICC: 0.825, 95%CI 0.782–0.867) cohorts, indicating validity of the IPBM. To conclude, we demonstrated capability of the IPBM toward building reliable radiomic models, providing community with a novel model reliability assessment strategy prior to prospective evaluation.
Resting-state functional connectivity and socioemotional processes in male perpetrators of intimate partner violence against women
Authors: Amaoui Sofia , Martín-Pérez Cristina , Marín-Morales Agar , Bueso-Izquierdo Natalia , García-León María Ángeles , Pérez-García Miguel , Verdejo-Román Juan
Published: June 2022

Intimate partner violence against women (IPVAW) is a serious and overwhelming public concern. Neuroimaging techniques have provided insights into the brain mechanisms underlying IPVAW perpetration. The purpose of this study is to examine the resting-state functional connectivity (rsFC) involving the process of social decision-making of male perpetrators. Twenty-six male perpetrators convicted for an IPVAW crime were compared to 29 men convicted for crimes other than IPVAW (other offenders) and 29 men with no criminal records (non-offenders) using a seed-based approach. Seeds were located in areas involved in reflective (prefrontal), impulsive (amygdala and striatum) and interoceptive (insula) processing. Then, as an exploratory analysis, the connectivity networks on male perpetrators were correlated with measures of executive functions and socioemotional self-report measures. Male perpetrators in comparison to other offenders and non-offenders, presented higher rsFC between prefrontal, limbic, brainstem, temporal and basal ganglia areas. Also male perpetrators showed higher rsFC between insula, default mode network and basal ganglia, while lower rsFC was found between prefrontal and motor areas and between amygdala, occipital and parietal areas. Exploratory correlations suggest that the specific rsFC in male perpetrators might be more related to socioemotional processes than to executive functions. These results showed that male perpetrators present a specific rsFC in brain systems that are essential for an adaptive social decision-making.
Incentive motivation improves numerosity discrimination in children and adolescents
Authors: Spliethoff Luca , Li Shu-Chen , Dix Annika
Published: June 2022

We recently showed that incentive motivation improves the precision of the Approximate Number System (ANS) in young adults. To shed light on the development of incentive motivation, the present study investigated whether this effect and its underlying mechanisms may also be observed in younger samples. Specifically, seven-year-old children (n = 23; 12 girls) and 14-year-old adolescents (n = 30; 15 girls) performed a dot comparison task with monetary reward incentives. Both age groups showed higher accuracy in a reward compared to a neutral condition and, similarly, higher processing efficiency as revealed by the drift rate parameter of the EZ-diffusion model. Furthermore, in line with the Incentive Salience Hypothesis, phasic pupil dilations—indicating the activation of the brain’s salience network—were greater in incentivized trials in both age groups. Together these finding suggest that incentive modulation improves numerosity discrimination in children and adolescents by enhancing the perceptual saliency of numerosity information. However, the observed reward anticipation effects were less pronounced in children relative to adolescents. Furthermore, unlike previous findings regarding young adults, the decision thresholds of children and adolescents were not raised by the monetary reward, which may indicate a more protracted development of incentive regulation of response caution than perceptual evidence accumulation.
Robust antibacterial activity of functionalized carbon nanotube- levofloxacine conjugate based on in vitro and in vivo studies
Authors: Hassani Marzieh , Tahghighi Azar , Rohani Mahdi , Hekmati Malak , Ahmadian Maryam , Ahmadvand Hassan
Published: June 2022

A new nano-antibiotic was synthesized from the conjugation of multi-walled carbon nanotubes with levofloxacin (MWCNT-LVX) through covalent grafting of drug with surface-modified carbon nanotubes in order to achieve an effective, safe, fast-acting nano-drug with the minimal side effects. This study is the first report on the evaluation of in vitro cell viability and antibacterial activity of nano-antibiotic along in addition to the in vivo antibacterial activity in a burn wound model. The drug-loading and release profile at different pH levels was determined using an ultraviolet–visible spectrometer. MWCNT-LVX was synthesized by a simple, reproducible and cost-effective method for the first time and characterized using various techniques, such as scanning electron microscope, transmission electron microscopy, and Brunauer–Emmett–Teller analysis, and so forth. The noncytotoxic nano-antibiotic showed more satisfactory in vitro antibacterial activity against Staphylococcus aureus compared to Pseudomona aeruginosa. The novel synthetic nano-drug possessed high loading capacity and pH-sensitive release profile; resultantly, it exhibited very potent bactericidal activity in a mouse S. aureus wound infection model compared to LVX. Based on the results, the antibacterial properties of the drug enhanced after conjugating with surface-modified MWCNTs. The nano-antibiotic has great industrialization potential for the simple route of synthesis, no toxicity, proper drug loading and release, low effective dose, and strong activity against wound infections. In virtue of unique properties, MWCNTs can serve as a controlled release and delivery system for drugs. The easy penetration to biological membranes and barriers can also increase the drug delivery at lower doses compared to the main drug alone, which can lead to the reduction of its side effects. Hence, MWCNTs can be considered a promising nano-carrier of LVX in the treatment of skin infections.
Simplified quantum optical Stokes observables and Bell’s theorem
Authors: Schlichtholz Konrad , Woloncewicz Bianka , Żukowski Marek
Published: June 2022

We discuss a simplified form of Stokes operators for quantum optical fields that involve the known concept of binning. Behind polarization analyzer photon numbers (more generally intensities) are measured. We have two outputs, say, for horizontal and vertical polarization. If the value obtained in horizontal output is greater than in vertical one we put 1. Otherwise, we put − 1. For equal photon numbers, we put 0. Such observables do not have all properties of the Stokes operators, but can be employed in Bell type measurements, involving polarization analyzers. They are especially handy for states of undefined number of photons, e.g. squeezed vacuum and their realisation is intuitive. We show that our observables can lead to quite robust violations of associated Bell inequalities. We formulate a strongly supported numerically conjecture that one can observe with this approach violations of local realism for the four mode squeezed vacuum for all pumping powers (i.e. gain values).
piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode
Authors: Suleiman Mona , Kounosu Asuka , Murcott Ben , Dayi Mehmet , Pawluk Rebecca , Yoshida Akemi , Viney Mark , Kikuchi Taisei , Hunt Vicky L.
Published: June 2022

The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21–22 nt long sRNAs with a 5′ uridine (21-22Us) and a 5′ monophosphate, and (ii) 27 nt long sRNAs with a 5′ guanine/adenine (27GAs) and a 5′ modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.
Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer
Authors: Vlaar Judith M. , Borgman Anouska , Kalkhoven Eric , Westland Denise , Besselink Nicolle , Shale Charles , Faltas Bishoy M. , Priestley Peter , Kuijk Ewart , Cuppen Edwin
Published: June 2022

Bladder cancer has a high recurrence rate and low survival of advanced stage patients. Few genetic drivers of bladder cancer have thus far been identified. We performed in-depth structural variant analysis on whole-genome sequencing data of 206 metastasized urinary tract cancers. In ~ 10% of the patients, we identified recurrent in-frame deletions of exons 8 and 9 in the aryl hydrocarbon receptor gene (AHRΔe8-9), which codes for a ligand-activated transcription factor. Pan-cancer analyses show that AHRΔe8-9 is highly specific to urinary tract cancer and mutually exclusive with other bladder cancer drivers. The ligand-binding domain of the AHRΔe8-9 protein is disrupted and we show that this results in ligand-independent AHR-pathway activation. In bladder organoids, AHRΔe8-9 induces a transformed phenotype that is characterized by upregulation of AHR target genes, downregulation of differentiation markers and upregulation of genes associated with stemness and urothelial cancer. Furthermore, AHRΔe8-9 expression results in anchorage independent growth of bladder organoids, indicating tumorigenic potential. DNA-binding deficient AHRΔe8-9 fails to induce transformation, suggesting a role for AHR target genes in the acquisition of the oncogenic phenotype. In conclusion, we show that AHRΔe8-9 is a novel driver of urinary tract cancer and that the AHR pathway could be an interesting therapeutic target.
Severity of underweight and risk of fracture: a Korean nationwide population-based cohort study
Authors: Han Sangsoo , Park Jiwon , Nah Sangun , Jang Hae-Dong , Han Kyungdo , Hong Jae-Young
Published: June 2022

Underweight is an important modifiable risk factor for fractures. However, there have been few large cohort studies regarding the relationship between underweight and fracture in the general population. We investigated the risk of fracture development according to underweight severity in a large population cohort. This nationwide cohort study included 2,896,320 people aged ≥ 40 years who underwent national health checkups in 2009 and were followed up to identify the incidence of fracture until December 31, 2018. After applying the exclusion criteria that included overweight and obese individuals, the study population was divided according to body mass index (BMI) into normal weight (18.5 ≤ BMI < 23.0), mild underweight (17.5 ≤ BMI < 18.5), moderate underweight (16.5 ≤ BMI < 17.5), and severe underweight (BMI < 16.5) groups. Cox proportional hazards regression analyses were performed to calculate the hazard ratios for risk of fracture according to underweight severity. Severely underweight participants had a 28% increased fracture risk (adjusted hazard ratio [HR] 1.28, 95% confidence interval [CI] 1.20–1.37) compared with those of normal weight. In addition, fracture risk was increased by 14% in individuals with moderate underweight (adjusted HR 1.14, 95% CI 1.08–1.19) and 9% in those with mild underweight (adjusted HR 1.09, 95% CI 1.06–1.13). The severity of underweight was significantly associated with risk of fracture.
Ketone body 3-hydroxybutyrate enhances adipocyte function
Authors: Nishitani Shigeki , Fukuhara Atsunori , Tomita Issei , Kume Shinji , Shin Jihoon , Okuno Yosuke , Otsuki Michio , Maegawa Hiroshi , Shimomura Iichiro
Published: June 2022

Ketone bodies, including 3HBA, are endogenous products of fatty acid oxidation, and Hmgcs2 is the first rate-limiting enzyme of ketogenesis. From database analysis and in vivo and in vitro experiments, we found that adipose tissue and adipocytes express Hmgcs2, and that adipocytes produce and secrete 3HBA. Treatment with 3HBA enhanced the gene expression levels of the antioxidative stress factors, PPARγ, and lipogenic factors in adipose tissue in vivo and in adipocytes in vitro, accompanied by reduced ROS levels. Knockdown of endogenous Hmgcs2 in adipocytes markedly decreased 3HBA levels in adipocytes and decreased the gene expression levels of the antioxidative stress factors, PPARγ, and lipogenic factors with increased ROS levels. Conversely, overexpression of Hmgcs2 in adipocytes increased 3HBA secretion from adipocytes and enhanced the gene expression levels of the antioxidative stress factors, PPARγ, and lipogenic factors. These results demonstrate that 3HBA plays significant roles in enhancing the physiological function of adipocytes.
Water quality assessment of east Tiaoxi River, China, based on a comprehensive water quality index model and Monte-Carlo simulation
Authors: Jin Wei , Li Yuan , Lu Li , Zhang Dong , He Shanying , Shentu Jiali , Chai Qiwei , Huang Lei
Published: June 2022

The comprehensive water quality index (CWQI) reflects the comprehensive pollution status of rivers through mathematical statistics of several water quality indicators. Using computational mathematical simulations, high-confidence CWQI predictions can be obtained based on limited water quality monitoring samples. At present, most of the CWQI reported in the literature are based on conventional indicators such as nitrogen and phosphorus levels, and do not include the petroleum hydrocarbons levels. This article takes a typical river in eastern China as an example, based on the 1-year monitoring at 20 sampling sets, a CWQI containing five factors, TN, NH4+-N, TP, ∑n-Alks, and ∑PAHs was established, and further predicted by a Monte-Carlo model. The predicted CWQI for each monitoring section is above 0.7, indicating that most of the monitoring sections are moderately polluted, and some sections are seriously polluted. The Spearman rank correlation coefficient analysis results show that TN, ∑PAHs, and ∑n-Alks are the main factors influencing the water quality, especially the petroleum hydrocarbons have a significant impact on the middle and lower reaches due to shipping. In the future, more attention should be paid to petroleum hydrocarbon organic pollutants in the water quality evaluation of similar rivers.
Predictivity of daily gait speed using tri-axial accelerometers for two-year incident disability among Japanese older adults
Authors: Takayanagi Naoto , Sudo Motoki , Yamashiro Yukari , Chiba Ippei , Lee Sangyoon , Niki Yoshifumi , Shimada Hiroyuki
Published: June 2022

Gait speed is an important indicator of functional decline in older adults. Recently, daily gait speed has been assessed using accelerometers. However, it is unclear whether this parameter can predict the decline in functional abilities. This study investigates whether daily gait speed can be a predictor of incident disability risk as well as in-laboratory gait speed. A sample of 1860 older adults (Male: 728, Female: 1132; 70.1 ± 6.2 years) were instructed to wear accelerometers on the waist. The association between daily gait speed for two weeks and incident disability during a two-year period was analyzed by using the cut-off value for screening prefrailty in the previous study (106.3 cm/s). Furthermore, the associations with in-laboratory gait speed (cut-off value: 100 cm/s), number of steps (cut-off value: 6342.2 steps/day), and incident disability were also analyzed. Cox proportional hazards analysis showed a significant hazard ratio of low daily gait speed (HR, 2.97; p = 0.02) comparable to that of low in-laboratory gait speed (HR: 2.53; p = 0.01). Conversely, the number of steps had no significant association with incident disability (HR: 1.99; p = 0.12). These results suggest that daily gait speed can be a predictor of incident disability risk in older adults.
Identification of an inflammatory response signature associated with prognostic stratification and drug sensitivity in lung adenocarcinoma
Authors: Song Congkuan , Lu Zilong , Lai Kai , Li Donghang , Hao Bo , Xu Chenzhen , Pan Shize , Li Ning , Geng Qing
Published: June 2022

Increasing evidence has confirmed the close connection between inflammatory response and tumorigenesis. However, the relationship between inflammatory response genes (IRGs) and the prognosis of lung adenocarcinoma (LUAD) as well as the response to drug therapy remains poorly investigated. Here, we comprehensively analyzed IRGs RNA expression profiling and clinical features of over 2000 LUAD patients from 12 public datasets. The Cox regression method and LASSO analysis were combined to develop a novel IRG signature for risk stratification and drug efficacy prediction in LUAD patients. Enriched pathways, tumor microenvironment (TME), genomic and somatic mutation landscape in different subgroups were evaluated and compared with each other. This established IRG signature including 11 IRGs (ADM, GPC3, IL7R, NMI, NMURI, PSEN1, PTPRE, PVR, SEMA4D, SERPINE1, SPHK1), could well categorize patients into significantly different prognostic subgroups, and have better predictive in independently assessing survival as compared to a single clinical factor. High IRG scores (IRGS) patients might benefit more from immunotherapy and chemotherapy. Comprehensive analysis uncovered significant differences in enriched pathways, TME, genomic and somatic mutation landscape between the two subgroups. Additionally, integrating the IRGS and TNM stage, a reliable prognostic nomogram was developed to optimize survival prediction, and validated in an independent external dataset for clinical application. Take together, the proposed IRG signature in this study is a promising biomarker for risk stratification and drug efficacy prediction in LUAD patients. This study may be meaningful for explaining the responses of clinical therapeutic drugs and providing new strategies for administrating sufferer of LUAD.
Assessing the impact of land use land cover change on regulatory ecosystem services of subtropical scrub forest, Soan Valley Pakistan
Authors: Ghafoor Gul Zareen , Sharif Faiza , Shahid Memuna Ghafoor , Shahzad Laila , Rasheed Rizwan , Khan Amin Ul Haq
Published: June 2022

This study investigated the effect of land use land cover (LULC) changes on carbon sequestration in the Hayat-ul-Mir subtropical scrub reserve forest, Pakistan. Supervised maximum likelihood classification of Landsat satellite imagery was done to assess spatio-temporal changes in LULC during 2007, 2013 and 2019. The CA–Markov model was used to simulate LULC of 2030. Spatial LULC data and carbon pools data was processed in Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) carbon model to investigate the effect of LULC on future carbon dynamics. The analysis revealed increase in cover of A. modesta and O. ferruginea and decrease in agriculture, built up and barren area of forest during 2007–2019 and 2030. The analysis also showed that the forest would additionally sequester 111 Mg C with an overall Net Present Value of $4112.05 in year 2030. The analysis revealed LULC changes on 25% area with increase and decrease in the value of ecosystem service (at some location) from carbon storage and loss as CO2 emissions respectively depending on the type of LULC converted. The study is helpful in identifying areas of potential carbon sequestration to maximize net benefits from management interventions.
The metaxenia effects of different pollen grains on secondary metabolites enzymes and sugars of ‘Piarom’ date palm fruit
Authors: Shahsavar Ali Reza , Shahhosseini Asma
Published: June 2022

In this research, the characteristics of pollen were studied in eight pollinating cultivars of date palm, namely, ‘Shahani’, ‘Kabkab’, ‘Zahedi’, ‘Beraem’, ‘Faryab’, ‘Sheikhali’, ‘Fard’ and ‘Jarvis’. The characteristics were compared and metaxenia effects were evaluated on secondary metabolites, enzymes and other biochemical compounds of ‘Piarom’ date fruits. The evaluations were carried out during four stages of fruit growth and development. The pollen of these eight pollinating cultivars were compared in terms of carbohydrates, proteins, starch, total phenol, flavonoids, pectin methyl esterase, and amylase enzymes. According to the results, the pollen of ‘Sheikhali’, ‘Fard’, ‘Zahedi’ and ‘Shahani’ cultivars contained more of the above compounds, compared to the other cultivars. Regarding the effects of pollen on the composition of ‘Piarom’ date fruits, ‘Fard’ and ‘Sheikhali’ pollen produced the lowest amount of soluble tannin, which resulted in a better quality of ‘Piarom’ date fruits. Pollen was also obtained from ‘Sheikhali’ and ‘Fard’ cultivars for evaluations, showing that they led to the highest amounts of glucose and fructose in the fruits. Regarding the sucrose amount, ‘Jarvis’ and ‘Shikhali’ produced the best results. Pollen of ‘Sheikhali’ and ‘Fard’ cultivars caused the lowest amount of chlorophyll at the different stages of fruit growth, indicating a better decomposition of fruit chlorophyll and, as a result, better fruit quality. Pollen of ‘Sheikhali’ and ‘Fard’ cultivars produced the highest amounts of secondary metabolites such as total phenol, carotenoids and anthocyanin at the different stages of fruit development. The pollen of ‘Fard’ and ‘Sheikhali’ cultivars produced the highest levels of polygalacturonase, cellulase and invertase enzymes at different growth stages of the ‘Piarom’ date fruit. Regarding cellulase enzyme, fruits of the ‘Zahedi’ cultivar had more cellulase than the fruits of ‘Sheikhali’. In general, the pollen of ‘Fard’ and ‘Sheikhali, in comparison with other cultivars, improved the quantity and quality of ‘Piarom’ date fruits, due to their metaxenia properties.
Predicting driving speed from psychological metrics in a virtual reality car driving simulation
Authors: Ju Uijong , Williamson John , Wallraven Christian
Published: June 2022

Why do some people tend to drive faster than others? Personality characteristics such as the evaluation of risk to oneself or to others, impulsivity, adherence to norms, but also other personal factors such as gender, age, or driving experience all may play a role in determining how fast people drive. Since driving speed is a critical factor underlying accident prevalence, identifying the psychological metrics to predict individual driving speed is an important step that could aid in accident prevention. To investigate this issue, here, we used an immersive virtual reality driving simulation to analyze average driving speed. A total of 124 participants first took a comprehensive set of personality and background questionnaires and a behavioral risk-taking measure. In the virtual reality experiment, participants were required to navigate a difficult driving course in a minimally-restricted, non-urban setting in order to provide baseline results for speed selection. Importantly, we found that sensation seeking and gender significantly predicted the average driving speed, and that sensation seeking and age were able to predict the maximum driving speed.
Biosynthesis of exopolysaccharide from waste molasses using Pantoea sp. BCCS 001 GH: a kinetic and optimization study
Authors: Niknezhad Seyyed Vahid , Kianpour Sedigheh , Jafarzadeh Sina , Alishahi Mohsen , Najafpour Darzi Ghasem , Morowvat Mohammad Hossein , Ghasemi Younes , Shavandi Amin
Published: June 2022

The bacterium Pantoea sp. BCCS 001 GH produces an exopolysaccharide (EPS) named Pantoan through using sugar beet molasses (SBM) as an inexpensive and widely available carbon source. This study aims to investigate the kinetics and optimization of the Pantoan biosynthesis using Pantoea sp. BCCS 001 GH in submerged culture. During kinetics studies, the logistic model and Luedeking–Piret equation are precisely fit with the obtained experimental data. The response surface methodology (RSM)-central composite design (CCD) method is applied to evaluate the effects of four factors (SBM, peptone, Na2HPO4, and Triton X-100) on the concentration of Pantoan in batch culture of Pantoea sp. BCCS 001 GH. The experimental and predicted maximum Pantoan production yields are found 9.9 ± 0.5 and 10.30 g/L, respectively, and the best prediction factor concentrations are achieved at 31.5 g/L SBM, 2.73 g/L peptone, 3 g/L Na2HPO4, and 0.32 g/L Triton X-100 after 48 h of submerged culture fermentation, at 30 °C. The functional groups and major monosaccharides (glucose and galactose) of a purified Pantoan are described and confirmed by 1HNMR and FTIR. The produced Pantoan is also characterized by thermogravimetric analysis and the rheological properties of the biopolymer are investigated. The present work guides the design and optimization of the Pantoea sp. BCCS 001 GH culture media, to be fine-tuned and applied to invaluable EPS, which can be applicable in food and biotechnology applications.
Design of a multi-epitope vaccine candidate against Brucella melitensis
Authors: Li Min , Zhu Yuejie , Niu Ce , Xie Xinru , Haimiti Gulishati , Guo Wenhong , Yu Mingkai , Chen Zhiqiang , Ding Jianbing , Zhang Fengbo
Published: June 2022

Brucella is a typical facultative intracellular bacterium that can cause zoonotic infections. For Brucella, it is difficult to eliminate with current medical treatment. Therefore, a multi-epitope vaccine (MEV) should be designed to prevent Brucella infection. For this purpose, we applied the reverse vaccinology approach from Omp10, Omp25, Omp31 and BtpB. Finally, we obtained 13 cytotoxic T lymphocyte (CTL) epitopes, 17 helper T lymphocyte (HTL) epitopes, 9 linear B cell epitopes, and 2 conformational B cell epitopes for further study. To keep the protein folded normally, we linked AAY, GPGPG, and KK to CTL epitopes, HTL epitopes, and B cell epitopes, respectively. The N-terminal of the vaccine peptide is supplemented with appropriate adjuvants to enhance immunogenicity. To evaluate its immunogenicity, stability, safety, and feasibility, a final MEV containing 806 amino acids was constructed by linking linkers and adjuvants. In addition, molecular docking and molecular dynamics simulations were performed to verify the affinity and stability of the MEV-TLR4. Then, codon adaptation and in silico cloning studies were carried out to identify the possible codons for expressing the MEV. In animal experiments, the results demonstrated that the MEV had high immunogenicity. Collectively, this study provided a theoretical basis for the development of a Brucella vaccine.
σ-Aromaticity in planar pentacoordinate aluminium and gallium clusters
Authors: Kalita Amlan J. , Sarmah Kangkan , Yashmin Farnaz , Borah Ritam R. , Baruah Indrani , Deka Rinu P. , Guha Ankur K.
Published: June 2022

Planar hypercoordinate structures are gaining immense attention due to the shift from common paradigm. Herein, our high level ab initio calculations predict that planar pentacoordinate aluminium and gallium centres in Cu5Al2+and Cu5Ga2+clusters are global minima in their singlet ground states. These clusters are thermodynamically and kinetically very stable. Detailed electronic structure analyses reveal the presence of σ-aromaticity which is the driving force for the stability of the planar form.
Data-driven spatiotemporal assessment of the event-size distribution of the Groningen extraction-induced seismicity catalogue
Authors: Muntendam-Bos A. G. , Grobbe N.
Published: June 2022

For induced seismicity, the non-stationary, heterogeneous character of subsurface stress perturbations can be a source of spatiotemporal variations in the scaling of event sizes; one of the critical parameters controlling seismic hazard and risk. We demonstrate and test a systematic, statistical, penalized-likelihood approach to analysing both spatial and temporal variations in event size distributions. The methodology used is transferable to the risk analysis of any subsurface operation, especially for small earthquake catalogues. We explore the whole solution space and circumvent conventional, arbitrary choices that require a priori knowledge of these variations. We assess the effect of possible bias in the derivation, e.g., due to tapering of the earthquake-size distribution, correlation between the b-value and the magnitude of completeness and correlation between the b-value and the largest magnitude observed. We analyse the spatiotemporal variations in the earthquake-size distribution of the Groningen induced seismicity catalogue (December 1991–November 16, 2021). We find statistically significant spatial variations without any compelling, statistical evidence of a temporal variation. Furthermore, we find that the largest magnitudes observed are inconsistent with the sampling statistics of an unconstrained earthquake-size distribution. Current risk assessment models likely overestimate the probability of larger magnitude events (M ≥ 3.0) and thus the risk posed.
A computerized diagnostic model for automatically evaluating placenta accrete spectrum disorders based on the combined MR radiomics-clinical signatures
Authors: Zhu Hao , Yin Xuan , Wang Haijie , Wang Yida , Liu Xuefen , Wang Chenglong , Li Xiaotian , Lu Yuanyuan , Yang Guang , Zhang He
Published: June 2022

We aimed to establish a computerized diagnostic model to predict placenta accrete spectrum (PAS) disorders based on T2-weighted MR imaging. We recruited pregnant women with clinically suspected PAS disorders between January 2015 and December 2018 in our institution. All preoperative T2-weighted imaging (T2WI) MR images were manually outlined on the picture archive communication system terminal server. A nnU-Net network for automatic segmentation and the corresponding radiomics features extracted from the segmented region were applied to build a radiomics-clinical model for PAS disorders identification. Taking the surgical or pathological findings as the reference standard, we compared this computerized model’s diagnostic performance in detecting PAS disorders. In the training cohort, our model combining both radiomics and clinical characteristics yielded an accuracy of 0.771, a sensitivity of 0.854, and a specificity of 0.750 in identifying PAS disorders. In the testing cohort, this model achieved a segmentation mean Dice coefficient of 0.890 and yielded an accuracy of 0.825, a sensitivity of 0.830 and a specificity of 0.822. In the external validation cohort, this computer-aided diagnostic model yielded an accuracy of 0.690, a sensitivity of 0.929 and a specificity of 0.467 in identifying placenta increta. In the present study, a machine learning model based on preoperative T2WI-based imaging had high accuracy in identifying PAS disorders in respect of surgical and histological findings.
Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation
Authors: Krishnan Jaya , Wang Yan , Kenzior Olga , Hassan Huzaifa , Olsen Luke , Tsuchiya Dai , Kenzior Alexander , Peuß Robert , Xiong Shaolei , Wang Yongfu , Zhao Chongbei , Rohner Nicolas
Published: June 2022

Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (Scherer et al. in J Exp Med 97:695–710, 1953). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with comprehensive biochemical and molecular characterization of the cell lines, which reflect key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.