bluuebunny/crossref_metadata_2025 huggingface dataset:
A class I odorant receptor enhancer shares a functional motif with class II enhancers
Authors: Iwata Tetsuo , Tomeoka Satoshi , Hirota Junji
Published: January 2021

In the mouse, 129 functional class I odorant receptor (OR) genes reside in a ~ 3 megabase huge gene cluster on chromosome 7. The J element, a long-range cis-regulatory element governs the singular expression of class I OR genes by exerting its effect over the whole cluster. To elucidate the molecular mechanisms underlying class I-specific enhancer activity of the J element, we analyzed the J element sequence to determine the functional region and essential motif. The 430-bp core J element, that is highly conserved in mammalian species from the platypus to humans, contains a class I-specific conserved motif of AAACTTTTC, multiple homeodomain sites, and a neighboring O/E-like site, as in class II OR-enhancers. A series of transgenic reporter assays demonstrated that the class I-specific motif is not essential, but the 330-bp core J-H/O containing the homeodomain and O/E-like sites is necessary and sufficient for class I-specific enhancer activity. Further motif analysis revealed that one of homeodomain sequence is the Greek Islands composite motif of the adjacent homeodomain and O/E-like sequences, and mutations in the composite motif abolished or severely reduced class I-enhancer activity. Our results demonstrate that class I and class II enhancers share a functional motif for their enhancer activity.
Controlled release evaluation of paracetamol loaded amine functionalized mesoporous silica KCC1 compared to microcrystalline cellulose based tablets
Authors: Pishnamazi Marieh , Hafizi Hamid , Pishnamazi Mahboubeh , Marjani Azam , Shirazian Saeed , Walker Gavin M.
Published: January 2021

In the pharmaceutical manufacturing, drug release behavior development is remained as one of the main challenges to improve the drug effectiveness. Recently, more focus has been done on using mesoporous silica materials as drug carriers for prolonged and superior control of drug release in human body. In this study, release behavior of paracetamol is developed using drug-loaded KCC-1-NH2 mesoporous silica, based on direct compaction method for preparation of tablets. The purpose of this study is to investigate the utilizing of pure KCC-1 mesoporous silica (KCC-1) and amino functionalized KCC-1 (KCC-1-NH2) as drug carriers in oral solid dosage formulations compared to common excipient, microcrystalline cellulose (MCC), to improve the control of drug release rate by manipulating surface chemistry of the carrier. Different formulations of KCC-1 and KCC-NH2 are designed to investigate the effect of functionalized mesoporous silica as carrier on drug controlled-release rate. The results displayed the remarkable effect of KCC-1-NH2 on drug controlled-release in comparison with the formulation containing pure KCC-1 and formulation including MCC as reference materials. The pure KCC-1 and KCC-1-NH2 are characterized using different evaluation methods such as FTIR, SEM, TEM and N2 adsorption analysis.
Allele-specific expression of Parkinson’s disease susceptibility genes in human brain
Authors: Langmyhr Margrete , Henriksen Sandra Pilar , Cappelletti Chiara , van de Berg Wilma D. J. , Pihlstrøm Lasse , Toft Mathias
Published: January 2021

Genome-wide association studies have identified genetic variation in genomic loci associated with susceptibility to Parkinson’s disease (PD), the most common neurodegenerative movement disorder worldwide. We used allelic expression profiling of genes located within PD-associated loci to identify cis-regulatory variation affecting gene expression. DNA and RNA were extracted from post-mortem superior frontal gyrus tissue and whole blood samples from PD patients and controls. The relative allelic expression of transcribed SNPs in 12 GWAS risk genes was analysed by real-time qPCR. Allele-specific expression was identified for 9 out of 12 genes tested (GBA, TMEM175, RAB7L1, NUCKS1, MCCC1, BCKDK, ZNF646, LZTS3, and WDHD1) in brain tissue samples. Three genes (GPNMB, STK39 and SIPA1L2) did not show significant allele-specific effects. Allele-specific effects were confirmed in whole blood for three genes (BCKDK, LZTS3 and MCCC1), whereas two genes (RAB7L1 and NUCKS1) showed brain-specific allelic expression. Our study supports the hypothesis that changes to the cis-regulation of gene expression is a major mechanism behind a large proportion of genetic associations in PD. Interestingly, allele-specific expression was also observed for coding variants believed to be causal variants (GBA and TMEM175), indicating that splicing and other regulatory mechanisms may be involved in disease development.
Establishment of a long-term stable β-cell line and its application to analyze the effect of Gcg expression on insulin secretion
Authors: Miyazaki Satsuki , Tashiro Fumi , Tsuchiya Takashi , Sasaki Kazuki , Miyazaki Jun-ichi
Published: January 2021

A pancreatic β-cell line MIN6 was previously established in our lab from an insulinoma developed in an IT6 transgenic mouse expressing the SV40 T antigen in β-cells. This cell line has been widely used for in vitro analysis of β-cell function, but tends to lose the mature β-cell features, including glucose-stimulated insulin secretion (GSIS), in long-term culture. The aim of this study was to develop a stable β-cell line that retains the characteristics of mature β-cells. Considering that mice derived from a cross between C3H and C57BL/6 strains are known to exhibit higher insulin secretory capacity than C57BL/6 mice, an IT6 male mouse of this hybrid background was used to isolate insulinomas, which were independently cultured. After 7 months of continuous culturing, we obtained the MIN6-CB4 β-cell line, which stably maintains its GSIS. It has been noted that β-cell lines express the glucagon (Gcg) gene at certain levels. MIN6-CB4 cells were utilized to assess the effects of differentialGcgexpression on β-cell function. Our data show the functional importance ofGcgexpression and resulting basal activation of the GLP-1 receptor in β-cells. MIN6-CB4 cells can serve as an invaluable tool for studying the regulatory mechanisms of insulin secretion, such as the GLP-1/cAMP signaling, in β-cells.
Vision-based egg quality prediction in Pacific bluefin tuna (Thunnus orientalis) by deep neural network
Authors: Ienaga Naoto , Higuchi Kentaro , Takashi Toshinori , Gen Koichiro , Tsuda Koji , Terayama Kei
Published: January 2021

Closed-cycle aquaculture using hatchery produced seed stocks is vital to the sustainability of endangered species such as Pacific bluefin tuna (Thunnus orientalis) because this aquaculture system does not depend on aquaculture seeds collected from the wild. High egg quality promotes efficient aquaculture production by improving hatch rates and subsequent growth and survival of hatched larvae. In this study, we investigate the possibility of a simple, low-cost, and accurate egg quality prediction system based only on photographic images using deep neural networks. We photographed individual eggs immediately after spawning and assessed their qualities, i.e., whether they hatched normally and how many days larvae survived without feeding. The proposed system predicted normally hatching eggs with higher accuracy than human experts. It was also successful in predicting which eggs would produce longer-surviving larvae. We also analyzed the image aspects that contributed to the prediction to discover important egg features. Our results suggest the applicability of deep learning techniques to efficient egg quality prediction, and analysis of early developmental stages of development.
The antimicrobial capacity of Cistus salviifolius and Punica granatum plant extracts against clinical pathogens is related to their polyphenolic composition
Authors: Álvarez-Martínez Francisco Javier , Rodríguez Juan Carlos , Borrás-Rocher Fernando , Barrajón-Catalán Enrique , Micol Vicente
Published: January 2021

Antimicrobial resistance poses a serious threat to human health worldwide. Plant compounds may help to overcome antibiotic resistance due to their potential resistance modifying capacity. Several botanical extracts and pure polyphenolic compounds were screened against a panel of eleven bacterial isolates with clinical relevance. The two best performing agents, Cistus salviifolius (CS) and Punica granatum (GP) extracts, were tested against 100 Staphylococcus aureus clinical isolates, which resulted in average MIC50 values ranging between 50–80 µg/mL. CS extract, containing hydrolyzable tannins and flavonoids such as myricetin and quercetin derivatives, demonstrated higher activity against methicillin-resistant S. aureus isolates. GP extract, which contained mostly hydrolyzable tannins, such as punicalin and punicalagin, was more effective against methicillin-sensitive S. aureus isolates. Generalized linear model regression and multiple correspondence statistical analysis revealed a correlation between a higher susceptibility to CS extract with bacterial resistance to beta-lactam antibiotics and quinolones. On the contrary, susceptibility to GP extract was related with bacteria sensitive to quinolones and oxacillin. Bacterial susceptibility to GP and CS extracts was linked to a resistance profile based on cell wall disruption mechanism. In conclusion, a differential antibacterial activity against S. aureus isolates was observed depending on antibiotic resistance profile of isolates and extract polyphenolic composition, which may lead to development of combinatorial therapies including antibiotics and botanical extracts.
Generation of proliferating human adult hepatocytes using optimized 3D culture conditions
Authors: Rose Sophie , Ezan Frédéric , Cuvellier Marie , Bruyère Arnaud , Legagneux Vincent , Langouët Sophie , Baffet Georges
Published: January 2021

Generating the proliferation of differentiated normal adult human hepatocytes is a major challenge and an expected central step in understanding the microenvironmental conditions that regulate the phenotype of human hepatocytes in vitro. In this work, we described optimized 3D culture conditions of primary human hepatocytes (PHH) to trigger two waves of proliferation and we identified matrix stiffness and cell–cell interactions as the main actors necessary for this proliferation. We demonstrated that DNA replication and overexpression of cell cycle markers are modulate by the matrix stiffness while PHH cultured in 3D without prior cellular interactions did not proliferate. Besides, we showed that PHH carry out an additional cell cycle after transient inhibition of MAPK MER1/2-ERK1/2 signaling pathway. Collagen cultured hepatocytes are organized as characteristic hollow spheroids able to maintain survival, cell polarity and hepatic differentiation for long-term culture periods of at least 28 days. Remarkably, we demonstrated by transcriptomic analysis and functional experiments that proliferating cells are mature hepatocytes with high detoxication capacities. In conclusion, the advanced 3D model described here, named Hepoid, is particularly relevant for obtaining normal human proliferating hepatocytes. By allowing concomitant proliferation and differentiation, it constitutes a promising tool for many pharmacological and biotechnological applications.
Time to peak and full width at half maximum in MR perfusion: valuable indicators for monitoring moyamoya patients after revascularization
Authors: Huang Adam , Lee Chung-Wei , Liu Hon-Man
Published: January 2021

Moyamoya disease (MMD) is a chronic, steno-occlusive cerebrovascular disorder of unknown etiology. Surgical treatment is the only known effective method to restore blood flow to affected areas of the brain. However, there are lack of generally accepted noninvasive tools for therapeutic outcome monitoring. As dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) is the standard MR perfusion imaging technique in the clinical setting, we investigated a dataset of nineteen pediatric MMD patients with one preoperational and multiple periodic DSC MRI examinations for four to thirty-eight months after indirect revascularization. A rigid gamma variate model was used to derive two nondeconvolution-based perfusion parameters: time to peak (TTP) and full width at half maximum (FWHM) for monitoring transitional bolus delay and dispersion changes respectively. TTP and FWHM values were normalized to the cerebellum. Here, we report that 74% (14/19) of patients improve in both TTP and FWHM measurements, and whereof 57% (8/14) improve more noticeably on FWHM. TTP is in good agreement with Tmax in estimating bolus delay. Our study data also suggest bolus dispersion estimated by FWHM is an additional, informative indicator in pediatric MMD monitoring.
Differential effects of sodium chloride and monosodium glutamate on kidney of adult and aging mice
Authors: Celestino Michele , Balmaceda Valdez Valeria , Brun Paola , Castagliuolo Ignazio , Mucignat-Caretta Carla
Published: January 2021

Monosodium Glutamate (MSG) is used as flavour enhancer, with potential beneficial effects due to its nutritional value. Given the decline in kidney functions during aging, we investigated the impact of MSG voluntary intake on the kidney of male mice, aged 6 or 18 months. For 2 months, they freely consumed water (control group), sodium chloride (0.3% NaCl) or MSG (1% MSG) in addition to standard diet. Young animals consuming sodium chloride presented signs of proteinuria, hyperfiltration, enhanced expression and excretion of Aquaporin 2 and initial degenerative reactions suggestive of fibrosis, while MSG-consuming mice were similar to controls. In old mice, aging-related effects including proteinuria and increased renal corpuscle volume were observed in all groups. At an advanced age, MSG caused no adverse effects on the kidney compared to controls, despite the presence of a sodium moiety, similar to sodium chloride. These data show that prolonged MSG intake in mice has less impact on kidney compared to sodium chloride, that already in young animals induced some effects on kidney, possibly related to hypertension.
Ephrin A4-ephrin receptor A10 signaling promotes cell migration and spheroid formation by upregulating NANOG expression in oral squamous cell carcinoma cells
Authors: Chen Yu-Lin , Yen Yi-Chen , Jang Chuan-Wei , Wang Ssu-Han , Huang Hsin-Ting , Chen Chung-Hsing , Hsiao Jenn-Ren , Chang Jang-Yang , Chen Ya-Wen
Published: January 2021

Ephrin type-A receptor 10 (EPHA10) has been implicated as a potential target for breast and prostate cancer therapy. However, its involvement in oral squamous cell carcinoma (OSCC) remains unclear. We demonstrated that EPHA10 supports in vivo tumor growth and lymphatic metastasis of OSCC cells. OSCC cell migration, epithelial mesenchymal transition (EMT), and sphere formation were found to be regulated by EPHA10, and EPHA10 was found to drive expression of some EMT- and stemness-associated transcription factors. Among EPHA10 ligands, exogenous ephrin A4 (EFNA4) induced the most OSCC cell migration and sphere formation, as well as up-regulation of SNAIL, NANOG, and OCT4. These effects were abolished by extracellular signal-regulated kinase (ERK) inhibition and NANOG knockdown. Also, EPHA10 was required for EFNA4-induced cell migration, sphere formation, and expression of NANOG and OCT4 mRNA. Our microarray dataset revealed that EFNA4 mRNA expression was associated with expression of NANOG and OCT4 mRNA, and OSCC patients showing high co-expression of EFNA4 with NANOG or OCT4 mRNA demonstrated poor recurrence-free survival rates. Targeting forward signaling of the EFNA4-EPHA10 axis may be a promising therapeutic approach for oral malignancies, and the combination of EFNA4 mRNA and downstream gene expression may be a useful prognostic biomarker for OSCC.
Intermedin facilitates hepatocellular carcinoma cell survival and invasion via ERK1/2-EGR1/DDIT3 signaling cascade
Authors: Xiao Fei , Li Hongyu , Feng Zhongxue , Huang Luping , Kong Lingmiao , Li Min , Wang Denian , Liu Fei , Zhu Zhijun , Wei Yong’gang , Zhang Wei
Published: January 2021

As one of the most malignant cancer types, hepatocellular carcinoma (HCC) is highly invasive and capable of metastasizing to distant organs. Intermedin (IMD), an endogenous peptide belonging to the calcitonin family, has been suggested playing important roles in cancer cell survival and invasion, including in HCC. However, how IMD affects the behavior of HCC cells and the underlying mechanisms have not been fully elucidated. Here, we show that IMD maintains an important homeostatic state by activating the ERK1/2-EGR1 (early growth response 1) signaling cascade, through which HCC cells acquire a highly invasive ability via significantly enhanced filopodia formation. The inhibition of IMD blocks the phosphorylation of ERK1/2, resulting in EGR1 downregulation and endoplasmic reticulum stress (ER) stress, which is evidenced by the upregulation of ER stress marker DDIT3 (DNA damage-inducible transcript 3). The high level of DDIT3 induces HCC cells into an ER-stress related apoptotic pathway. Along with our previous finding that IMD plays critical roles in the vascular remodeling process that improves tumor blood perfusion, IMD may facilitate the acquisition of increased invasive abilities and a survival benefit by HCC cells, and it is easier for HCC cells to obtain blood supply via the vascular remodeling activities of IMD. According to these results, blockade of IMD activity may have therapeutic potential in the treatment of HCC.
CrAssphage and its bacterial host in cat feces
Authors: Li Yanpeng , Gordon Emilia , Shean Ryan C. , Idle Amanda , Deng Xutao , Greninger Alexander L. , Delwart Eric
Published: January 2021

CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages’ cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat’s feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.
Laser-induced melting of two-dimensional dusty plasma system in RF discharge
Authors: Vasilieva E. V. , Petrov O. F. , Vasiliev M. M.
Published: January 2021

We present a detailed analysis of experimental study, which shows clear evidence of a two-stage melting process of a quasi-two-dimensional dusty plasma system in a high-frequency gas discharge. We accurately calculated global parameters of the orientational and translational order, as well as their susceptibilities to determine two critical points, related to “solid-to-hexatic” and “hexatic-to-liquid” phase transitions. The nature of the emerging defects and changes in their mutual concentration, in addition to the estimate of core energy of free dislocations also counts in favor of the formation of an intermediate hexatic phase. These results are fully consistent with the Berezinsky–Kosterlitz–Thouless theory.
Serum fibroblast growth factor 21 levels after out of hospital cardiac arrest are associated with neurological outcome
Authors: Pekkarinen Pirkka T. , Skrifvars Markus B. , Lievonen Ville , Jakkula Pekka , Albrecht Laura , Loisa Pekka , Tiainen Marjaana , Pettilä Ville , Reinikainen Matti , Hästbacka Johanna
Published: January 2021

Fibroblast growth factor (FGF) 21 is a marker associated with mitochondrial and cellular stress. Cardiac arrest causes mitochondrial stress, and we tested if FGF 21 would reflect the severity of hypoxia-reperfusion injury after cardiac arrest. We measured serum concentrations of FGF 21 in 112 patients on ICU admission and 24, 48 and 72 h after out-of-hospital cardiac arrest with shockable initial rhythm included in the COMACARE study (NCT02698917). All patients received targeted temperature management for 24 h. We defined 6-month cerebral performance category 1–2 as good and 3–5 as poor neurological outcome. We used samples from 40 non-critically ill emergency room patients as controls. We assessed group differences with the Mann Whitney U test and temporal differences with linear modeling with restricted maximum likelihood estimation. We used multivariate logistic regression to assess the independent predictive value of FGF 21 concentration for neurologic outcome. The median (inter-quartile range, IQR) FGF 21 concentration was 0.25 (0.094–0.91) ng/ml in controls, 0.79 (0.37–1.6) ng/ml in patients at ICU admission (P < 0.001 compared to controls) and peaked at 48 h [1.2 (0.46–2.5) ng/ml]. We found no association between arterial blood oxygen partial pressure and FGF 21 concentrations. We observed with linear modeling an effect of sample timepoint (F 5.6, P < 0.01), poor neurological outcome (F 6.1, P = 0.01), and their interaction (F 3.0, P = 0.03), on FGF 21 concentration. In multivariate logistic regression analysis, adjusting for relevant clinical covariates, higher average FGF 21 concentration during the first 72 h was independently associated with poor neurological outcome (odds ratio 1.60, 95% confidence interval 1.10–2.32). We conclude that post cardiac arrest patients experience cellular and mitochondrial stress, reflected as a systemic FGF 21 response. This response is higher with a more severe hypoxic injury but it is not exacerbated by hyperoxia.
The impact of Pain-related emotions on migraine
Authors: Kim Seonghoon , Bae Dae-Woong , Park Sang-Gue , Park Jeong-Wook
Published: January 2021

The response to pain is highly individual and can be influenced by complex emotional perception. This study aims to investigate the status of the pain-related emotional response, and the influence on headache characteristics and disability in migraine. We studied the pain-related emotional response in 145 consecutive migraine patients using the Pain Anxiety Symptoms Scale (PASS), the Pain Catastrophizing Scale (PCS), and the Pain Sensitivity Questionnaire (PSQ) and compared them with 106 healthy controls. We investigated the relationship between emotional factors and migraine characteristics. The effect of pain-related emotion on migraine-related disability assessed with the Headache Impact Test-6 (HIT-6) and the Migraine Disability Assessment (MIDAS). Migraine patients showed significantly higher scores on total PASS (p < 0.001), PCS (p < 0.001) and PSQ (p = 0.002) compared to the healthy controls. The HIT-6 was weakly correlated with PASS (r = 0.390,p < 0.001) and PCS (r = 0.354,p < 0.001). PASS-Total (p = 0.001), headache frequency (p = 0.003), and HADS-Anxiety (p = 0.028) were independent variables associated with HIT-6. Headache frequency (p < 0.001) was an independent variable associated with MIDAS. The structural equation model indicated that headache severity has direct loading on emotion and subsequently influenced migraine-related disability. Disability has a significant effect on the frequency of abortive medication use. Migraine patients have altered emotional responses to pain perception. Pain-related anxiety made an important contribution to headache-related disability. The present results suggest that the management of disability by considering various pain-related emotional factors may be necessary for the therapeutic aspects of migraine.
Domain randomization-enhanced deep learning models for bird detection
Authors: Mao Xin , Chow Jun Kang , Tan Pin Siang , Liu Kuan-fu , Wu Jimmy , Su Zhaoyu , Cheong Ye Hur , Ooi Ghee Leng , Pang Chun Chiu , Wang Yu-Hsing
Published: January 2021

Automatic bird detection in ornithological analyses is limited by the accuracy of existing models, due to the lack of training data and the difficulties in extracting the fine-grained features required to distinguish bird species. Here we apply the domain randomization strategy to enhance the accuracy of the deep learning models in bird detection. Trained with virtual birds of sufficient variations in different environments, the model tends to focus on the fine-grained features of birds and achieves higher accuracies. Based on the 100 terabytes of 2-month continuous monitoring data of egrets, our results cover the findings using conventional manual observations, e.g., vertical stratification of egrets according to body size, and also open up opportunities of long-term bird surveys requiring intensive monitoring that is impractical using conventional methods, e.g., the weather influences on egrets, and the relationship of the migration schedules between the great egrets and little egrets.
Assessment of differential intraocular pressure response to dexamethasone treatment in perfusion cultured Indian cadaveric eyes
Authors: Haribalaganesh Ravinarayanan , Gowri Priya Chidambaranathan , Sharmila Rajendrababu , Krishnadas Subbaiah , Muthukkaruppan Veerappan , Willoughby Colin E. , Senthilkumari Srinivasan
Published: January 2021

The purpose of the present study was to assess the differential intraocular pressure response (IOP) to dexamethasone (DEX) treatment at two dose levels (100 or 500 nM) in perfusion cultured Indian cadaveric eyes to investigate glucocorticoid (GC) responsiveness. In a human organ-cultured anterior segment (HOCAS) set-up, the eye pressure was monitored for every 24 h post DEX infusion (100 or 500 nM) or 0.1% ethanol treatment for 7 days after baseline stabilization. The expression of DEX-inducible proteins such as myocilin and fibronectin in HOCAS-TM tissues was assessed by immunostaining. Elevated IOP was observed in 6/16 eyes [Mean ± SEM (mΔIOP): 15.50 ± 1.96 mmHg; 37.5% responders] and 3/15 eyes (Mean ± SEM mΔIOP: 10 ± 0.84 mmHg; 20% responders) in 100 nM and 500 nM dose groups respectively. Elevated IOP in GC responder eyes was substantiated with a significant increase in myocilin (11.8-fold; p = 0.0002) and fibronectin (eightfold; p = 0.04) expression as compared to vehicle-treated eyes by immunofluorescence analysis. This is the first study reporting the GC responsiveness in Indian cadaveric eyes. The observed GC response rate was comparable with the previous studies and hence, this model will enable us to investigate the relationship between differential gene expression and individual GC responsiveness in our population.
Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)
Authors: Vinayan M. T. , Seetharam K. , Babu Raman , Zaidi P. H. , Blummel M. , Nair Sudha K.
Published: January 2021

Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits—in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson’s correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set.
Expression and function of the cdgD gene, encoding a CHASE–PAS-DGC-EAL domain protein, in Azospirillum brasilense
Authors: Cruz-Pérez José Francisco , Lara-Oueilhe Roxana , Marcos-Jiménez Cynthia , Cuatlayotl-Olarte Ricardo , Xiqui-Vázquez María Luisa , Reyes-Carmona Sandra Raquel , Baca Beatriz Eugenia , Ramírez-Mata Alberto
Published: January 2021

The plant growth-promoting bacterium Azospirillum brasilense contains several genes encoding proteins involved in the biosynthesis and degradation of the second messenger cyclic-di-GMP, which may control key bacterial functions, such as biofilm formation and motility. Here, we analysed the function and expression of the cdgD gene, encoding a multidomain protein that includes GGDEF-EAL domains and CHASE and PAS domains. An insertional cdgD gene mutant was constructed, and analysis of biofilm and extracellular polymeric substance production, as well as the motility phenotype indicated that cdgD encoded a functional diguanylate protein. These results were correlated with a reduced overall cellular concentration of cyclic-di-GMP in the mutant over 48 h compared with that observed in the wild-type strain, which was recovered in the complemented strain. In addition, cdgD gene expression was measured in cells growing under planktonic or biofilm conditions, and differential expression was observed when KNO3 or NH4Cl was added to the minimal medium as a nitrogen source. The transcriptional fusion of the cdgD promoter with the gene encoding the autofluorescent mCherry protein indicated that the cdgD gene was expressed both under abiotic conditions and in association with wheat roots. Reduced colonization of wheat roots was observed for the mutant compared with the wild-type strain grown in the same soil conditions. The Azospirillum-plant association begins with the motility of the bacterium towards the plant rhizosphere followed by the adsorption and adherence of these bacteria to plant roots. Therefore, it is important to study the genes that contribute to this initial interaction of the bacterium with its host plant.
RETRACTED ARTICLE: Chitosan hydrogel/silk fibroin/Mg(OH)2 nanobiocomposite as a novel scaffold with antimicrobial activity and improved mechanical properties
Authors: Eivazzadeh-Keihan Reza , Radinekiyan Fateme , Aliabadi Hooman Aghamirza Moghim , Sukhtezari Sima , Tahmasebi Behnam , Maleki Ali , Madanchi Hamid
Published: January 2021

Herein, a novel nanobiocomposite scaffold based on modifying synthesized cross-linked terephthaloyl thiourea-chitosan hydrogel (CTT-CS hydrogel) substrate using the extracted silk fibroin (SF) biopolymer and prepared Mg(OH)2 nanoparticles was designed and synthesized. The biological capacity of this nanobiocomposite scaffold was evaluated by cell viability method, red blood cells hemolytic and anti-biofilm assays. According to the obtained results from 3 and 7 days, the cell viability of CTT-CS/SF/Mg(OH)2 nanobiocomposite scaffold was accompanied by a considerable increment from 62.5 to 89.6% respectively. Furthermore, its low hemolytic effect (4.5%), and as well, the high anti-biofilm activity and prevention of the P. aeruginosa biofilm formation confirmed its promising hemocompatibility and antibacterial activity. Apart from the cell viability, blood biocompatibility, and antibacterial activity of CTT-CS/SF/Mg(OH)2 nanobiocomposite scaffold, its structural features were characterized using spectral and analytical techniques (FT-IR, EDX, FE-SEM and TG). As well as, given the mechanical tests, it was indicated that the addition of SF and Mg(OH)2 nanoparticles to the CTT-CS hydrogel could improve its compressive strength from 65.42 to 649.56 kPa.
Increased levels of pentraxins protein and cytokines bear good association in patients with severe dengue infection
Authors: Patra Goutam , Saha Bibhuti , Mukhopadhyay Sumi
Published: January 2021

Dengue is an arboviral infection with high rates of morbidity and mortality throughout the tropics and sub-tropics. This work studied the status of pentraxin (CRP/SAP) protein, ferritin, TNF-α and IL-1β levels in Dengue patients of different pathophysiological manifestations. Accordingly, clinically confirmed Dengue cases (n = 97) were enrolled and subsequently blood parameters were studied by Haematology cell counter and Biochemistry Autoanalyser. CRP, SAP, ferritin, TNF-α and IL-1β ELISA were done in all the samples by using standard ELISA kits. Statistical Analysis was done in all the experiments. The levels of CRP (p < 0.0001), SAP (p < 0.0001), ferritin (p < 0.0001), TNF-α (p < 0.0001) and IL-1β (p < 0.0001) were high in patients with Severe Dengue as compared to Dengue without warning signs. High levels of SGOT, SGPT and decreased platelet counts were found in severe patients as compared to Healthy donor. CRP/SAP as well as TNF-α/IL-1β were independently associated with both dengue severity and overall disease manifestation. Statistically significant increased CRP, SAP, ferritin, TNF-α and IL-1β titres were correlated in patients with severe clinical manifestations as compared to mild disease forms of dengue. Elevated levels of pentraxin, TNF-α/IL-1β in blood during dengue infection could act as an early predictor in Severe Dengue infection.
3D enamel profilometry reveals faster growth but similar stress severity in Neanderthal versus Homo sapiens teeth
Authors: McGrath Kate , Limmer Laura Sophia , Lockey Annabelle-Louise , Guatelli-Steinberg Debbie , Reid Donald J. , Witzel Carsten , Bocaege Emmy , McFarlin Shannon C. , El Zaatari Sireen
Published: January 2021

Early life stress disrupts growth and creates horizontal grooves on the tooth surface in humans and other mammals, yet there is no consensus for their quantitative analysis. Linear defects are considered to be nonspecific stress indicators, but evidence suggests that intermittent, severe stressors create deeper defects than chronic, low-level stressors. However, species-specific growth patterns also influence defect morphology, with faster-growing teeth having shallower defects at the population level. Here we describe a method to measure the depth of linear enamel defects and normal growth increments (i.e., perikymata) from high-resolution 3D topographies using confocal profilometry and apply it to a diverse sample ofHomo neanderthalensisandH. sapiensanterior teeth. Debate surrounds whether Neanderthals exhibited modern human-like growth patterns in their teeth and other systems, with some researchers suggesting that they experienced more severe childhood stress. Our results suggest that Neanderthals have shallower features thanH. sapiensfrom the Upper Paleolithic, Neolithic, and medieval eras, mirroring the faster growth rates in Neanderthal anterior teeth. However, when defect depth is scaled by perikymata depth to assess their severity, Neolithic humans have less severe defects, while Neanderthals and the otherH. sapiensgroups show evidence of more severe early life growth disruptions.
Gene expression in blood reflects smoking exposure among cancer-free women in the Norwegian Women and Cancer (NOWAC) postgenome cohort
Authors: Baiju Nikita , Sandanger Torkjel M. , Sætrom Pål , Nøst Therese H.
Published: January 2021

Active smoking has been linked to modulated gene expression in blood. However, there is a need for a more thorough understanding of how quantitative measures of smoking exposure relate to differentially expressed genes (DEGs) in whole-blood among ever smokers. This study analysed microarray-based gene expression profiles from whole-blood samples according to smoking status and quantitative measures of smoking exposure among cancer-free women (n = 1708) in the Norwegian Women and Cancer postgenome cohort. When compared with never smokers and former smokers, current smokers had 911 and 1082 DEGs, respectively and their biological functions could indicate systemic impacts of smoking.LRRN3was associated with smoking status with the lowest FDR-adjusted p-value. When never smokers and all former smokers were compared, no DEGs were observed, butLRRN3was differentially expressed when never smokers were compared with former smokers who quit smoking ≤ 10 years ago. Further,LRRN3was positively associated with smoking intensity, pack-years, and comprehensive smoking index score among current smokers; and negatively associated with time since cessation among former smokers. Consequently,LRRN3expression in whole-blood is a molecular signal of smoking exposure that could supplant self-reported smoking data in further research targeting blood-based markers related to the health effects of smoking.
Anomalous shape effect of nanosized helium bubble on the elastic field in irradiated tungsten
Authors: Huang Xinlong , Lv Chenyangtao , Chu Haijian
Published: January 2021

Bubble pressure and elastic response in helium-irradiated tungsten are systematically investigated in this study. An anomalous shape effect is found that the radial normal stress and mean stress distributions around a nanosized void or bubble are far from the spherical symmetry, which is ascribed to polyhedral geometry characteristic of the nanosized bubble and physical mechanism transition from crystal surfaces dominated to the surface ledges and triple junctions dominated. Molecular simulation shows that Young–Laplace equation is not suitable for directly predicting equilibrium pressure for nanosized bubble in crystals. Consequently, a new criterion of average radial normal stress of spherical shell is proposed to polish the concept of equilibrium pressure of helium bubbles. Moreover, the dependences of bubble size, temperature and helium/vacancy ratio (He/Vac ratio) on the bubble pressure are all documented, which may provide an insight into the understanding of mechanical properties of helium-irradiated tungsten.
Evolution of ribosomal protein network architectures
Authors: Timsit Youri , Sergeant-Perthuis Grégoire , Bennequin Daniel
Published: January 2021

To perform an accurate protein synthesis, ribosomes accomplish complex tasks involving the long-range communication between its functional centres such as the peptidyl transfer centre, the tRNA bindings sites and the peptide exit tunnel. How information is transmitted between these sites remains one of the major challenges in current ribosome research. Many experimental studies have revealed that some r-proteins play essential roles in remote communication and the possible involvement of r-protein networks in these processes have been recently proposed. Our phylogenetic, structural and mathematical study reveals that of the three kingdom’s r-protein networks converged towards non-random graphs where r-proteins collectively coevolved to optimize interconnection between functional centres. The massive acquisition of conserved aromatic residues at the interfaces and along the extensions of the newly connected eukaryotic r-proteins also highlights that a strong selective pressure acts on their sequences probably for the formation of new allosteric pathways in the network.
Summary of the COVID-19 epidemic and estimating the effects of emergency responses in China
Authors: Tao Junwen , Ma Yue , Luo Caiying , Huang Jiaqi , Zhang Tao , Yin Fei
Published: January 2021

Coronavirus disease-2019 (COVID-19) pandemic has affected millions of people since December 2019. Summarizing the development of COVID-19 and assessing the effects of control measures are very critical to China and other countries. A logistic growth curve model was employed to compare the development of COVID-19 before and after the emergency response took effect. We found that the number of confirmed cases peaked 9–14 days after the first detection of an imported case, but there was a peak lag in the province where the outbreak was concentrated. Results of the growth curves indicated that the fitted cumulative confirmed cases were close to the actual observed cases, and the R2 of all models was above 0.95. The average growth rate decreased by 44.42% nationally and by 32.5% outside Hubei Province. The average growth rate in the 12 high-risk areas decreased by 29.9%. The average growth rate of cumulative confirmed cases decreased by approximately 50% after the emergency response. Areas with frequent population migration have a high risk of outbreak. The emergency response taken by the Chinese government was able to effectively control the COVID-19 outbreak. Our study provides references for other countries and regions to control the COVID-19 outbreak.
The effects of maternal separation on behaviours under social-housing environments in adult male C57BL/6 mice
Authors: Endo Nozomi , Makinodan Manabu , Mannari-Sasagawa Takayo , Horii-Hayashi Noriko , Somayama Nami , Komori Takashi , Kishimoto Toshifumi , Nishi Mayumi
Published: January 2021

Adverse experience in early life can affect the formation of neuronal circuits during postnatal development and exert long-lasting influences on neural functions that can lead to the development of a variety of psychiatric disorders including depression, anxiety disorders, and post-traumatic stress disorder. Many studies have demonstrated that daily repeated maternal separation, an animal model of early-life stress, can induce impairments in emotional behaviours and cognitive function during adolescence and adulthood. However, the behavioural phenotypes of maternally separated mice under long-term group-housing conditions are largely unknown. In this study, we applied our newly developed assay system to investigate the effects of maternal separation on behaviours under group-housing conditions during four days of continuous observations. Using our system, we found that repeated maternal separation resulted in inappropriate social distance from cagemates, altered approach preferences to others, and induced a lower rank in the time spent on the running wheel under group-housing conditions in adult male mice. Focussing on these behavioural abnormalities that appear in an environment with a social context will be important insights to understand the pathogenesis of psychiatric disorders.
Magnetic domains oscillation in the brain with neurodegenerative disease
Authors: Kletetschka Gunther , Bazala Robert , Takáč Marian , Svecova Eva
Published: January 2021

Geomagnetic fields interfere with the accumulation of iron in the human brain. Magnetic sensing of the human brain provides compelling evidence of new electric mechanisms in human brains and may interfere with the evolution of neurodegenerative diseases. We revealed that the human brain may have a unique susceptibility to conduct electric currents as feedback of magnetic dipole fluctuation in superparamagnetic grains. These grains accumulate and grow with brain aging. The electric feedback creates an electronic noise background that depends on geomagnetic field intensity and may compromise functional stability of the human brain, while induced currents are spontaneously generated near superparamagnetic grains. Grain growth due to an increase of iron mobility resulted in magnetic remanence enhancement during the final years of the studied brains.
Collapsed mitochondrial cristae in goat spermatozoa due to mercury result in lethality and compromised motility along with altered kinematic patterns
Authors: Kushawaha Bhawna , Yadav Rajkumar Singh , Swain Dilip Kumar , Kumari Priyambada , Kumar Akhilesh , Yadav Brijesh , Anand Mukul , Yadav Sarvajeet , Singh Dipty , Garg Satish Kumar
Published: January 2021

Earlier we have reported mercury-induced alterations in functional dynamics of buck spermatozoa through free radicals-mediated oxidative stress and spontaneous acrosome reaction. Based on our earlier findings, we aimed to investigate the effect of mercury exposure on motility, kinematic patterns, DNA damage, apoptosis and ultra-structural alterations in goat spermatozoa following in vitro exposure to different concentrations (0.031–1.25 µg/ml) of mercuric chloride for 15 min and 3 h. Following exposure of sperm cells to 0.031 µg/ml of mercuric chloride for 3 h, livability and motility of sperms was significantly reduced along with altered kinematic patterns, significant increase in per cent necrotic sperm cells and number of cells showing DNA damage; and this effect was dose- and time-dependent. Contrary to up-regulation of Bax gene after 3 h in control group, there was significant increase in expression of Bcl-2 in mercury-treated groups. Transmission electron microscopy studies revealed rifts and nicks in plasma and acrosomal membrane, mitochondrial sheath, and collapsed mitochondria with loss of helical organization of mitochondria in the middle piece of spermatozoa. Our findings evidently suggest that mercury induces necrosis instead of apoptosis and targets the membrane, acrosome, mid piece of sperms; and the damage to mitochondria seems to be responsible for alterations in functional and kinematic attributes of spermatozoa.
Temperature induced changes in the optical properties of skin in vivo
Authors: Iorizzo Tyler W. , Jermain Peter R. , Salomatina Elena , Muzikansky Alona , Yaroslavsky Anna N.
Published: January 2021

Knowledge of temperature-induced changes of skin optical properties is required for accurate dosimetry of photothermal treatments. We determined and compared in vivo optical properties of mouse ear skin at different temperatures. The diffuse reflectance, total and diffuse transmittance were measured in the spectral range from 400 to 1650 nm using an integrating sphere spectrometer at the temperatures of 25 °C, 36 °C and 60 °C. Target temperatures were attained and maintained using an automated heater equipped with a sensor for feed-back and control. Temperature and temperature induced morphological changes of skin were monitored using an infrared thermal camera and reflectance confocal microscopy, respectively. An inverse Monte Carlo technique was utilized to determine absorption, scattering, and anisotropy factors from the measured quantities. Our results indicate significant differences between the optical properties of skin at different temperatures. Absorption and scattering coefficients increased, whereas anisotropy factors decreased with increasing temperature. Changes in absorption coefficients indicate deoxygenation of hemoglobin, and a blue shift of water absorption bands. Confocal imaging confirmed that our observations can be explained by temperature induced protein denaturation and blood coagulation. Monitoring spectral responses of treated tissue may become a valuable tool for accurate dosimetry of light treatments.