bluuebunny/crossref_metadata_2025 huggingface dataset:
Artificial miRNA mediated resistance in tobacco against Jatropha leaf curl Gujarat virus by targeting RNA silencing suppressors
Authors: More Prashant , Agarwal Parinita , Anand Abhishek , Sanan-Mishra Neeti , Agarwal Pradeep K.
Published: January 2021

The leaf curl disease of Jatropha caused by geminiviruses results in heavy economic losses. In the present study, we report the identification of a new strain of a Jatropha leaf curl Gujarat virus (JLCuGV), which encodes six ORFs with each one having RNA silencing suppressor activity. Therefore, three artificial microRNAs (amiRNAs; C1/C4, C2/C3 and V1/V2) were designed employing overlapping regions, each targeting two ORFs of JLCuGV genomic DNA and transformed in tobacco. The C1/C4 and C2/C3 amiRNA transgenics were resistant while V1/V2 amiRNA transgenics were tolerant against JLCuGV. The relative level of amiRNA inversely related to viral load indicating a correlation with disease resistance. The assessment of photosynthetic parameters suggests that the transgenics perform significantly better in response to JLCuGV infiltration as compared to wild type (WT). The metabolite contents were not altered remarkably in amiRNA transgenics, but sugar metabolism and tricarboxylic acid (TCA) cycle showed noticeable changes in WT on virus infiltration. The overall higher methylation and demethylation observed in amiRNA transgenics correlated with decreased JLCuGV accumulation. This study demonstrates that amiRNA transgenics showed enhanced resistance to JLCuGV while efficiently maintaining normalcy in their photosynthesis and metabolic pathways as well as homeostasis in the methylation patterns.
The pineapple MADS-box gene family and the evolution of early monocot flower
Authors: Hu Juan , Chang Xiaojun , Zhang Ying , Yu Xianxian , Qin Yuan , Sun Yun , Zhang Liangsheng
Published: January 2021

Unlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple ‘ABCDE’ model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes’ role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.
Shape and rate of movement of the invasion front of Xylella fastidiosa spp. pauca in Puglia
Authors: Kottelenberg David , Hemerik Lia , Saponari Maria , van der Werf Wopke
Published: January 2021

In 2013, Xylella fastidiosa spp. pauca was first reported in Puglia, Italy, causing the olive quick decline syndrome (OQDS). Since then the disease has spread, prompting the initiation of management measures to contain the outbreak. Estimates of the shape of the disease front and the rate of area expansion are needed to inform management, e.g. the delineation of buffer zones. However, empirical estimates of the invasion front and the rate of spread of OQDS are not available. Here, we analysed the hundreds of thousands of records of monitoring data on disease occurrence in Puglia to estimate the shape of the invasion front and the rate of movement of the front. The robustness of estimation was checked using simulation. The shape of the front was best fitted by a logistic function while using a beta-binomial error distribution to model variability around the expected proportion of infected trees. The estimated rate of movement of the front was 10.0 km per year (95% confidence interval: 7.5–12.5 km per year). This rate of movement is at the upper limit of previous expert judgements. The shape of the front was flatter than expected. The fitted model indicates that the disease spread started approximately in 2008. This analysis underpins projections of further disease spread and the need for preparedness in areas that are still disease free.
Comparative analysis of visit and home blood pressure in a pilot trial on the effect of 18% sodium substitute salt on blood pressure
Authors: Liu Ting , Rao Huakun , Wang Meixian , Xu Huini , Wang Wen , Li Ge , Wang Hao , Mu Lihong
Published: January 2021

Aim to compare the home blood pressure monitoring (HBPM) and visit blood pressure monitoring in a clinical phase I single-arm pilot trial. The 18% sodium substitute salt was used in 43 hypertensives for 8 weeks, and visited once a week, while weekly visit blood (VBP) pressure, daily home blood pressure (HBP) and urine test results before and after intervention were collected. 43 hypertensive patients were recruited, 4 were lost. And enrolled 39 patients for analysis. The VBP were lower than morning HBP and night HBP (P < 0.05). And VBP was good correlated with morning BP (SBP: r = 0.692, P < 0.001, DBP: r = 0.789, P < 0.001) and night BP (SBP: r = 0.571, P < 0.001, DBP: r = 0.738, P < 0.001). The results of mixed linear model analysis showed that patients' visit SBP (− 11.4 mmHg, 95% CI: − 17.0 to − 5.7, P < 0.001), morning home SBP (− 10.0 mmHg, 95% CI: − 16.4 to − 3.6, P = 0.003) and night home SBP (− 10.2 mmHg, 95% CI: − 15.8 to − 4.6, P = 0.001) decreased significantly, after intervention. Both HBP and VBP showed that 18% substitute salt intervention could decrease the blood pressure of hypertensives. Medication led to VBP lower than HBP, but the two still had a good correlation.

Trial registration: NCT03226327. Registered 21 July 2017—Retrospectively registered, http://www.clinicaltrials.gov.
A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota
Authors: Palumbo Fabio , Squartini Andrea , Barcaccia Gianni , Macolino Stefano , Pornaro Cristina , Pindo Massimo , Sturaro Enrico , Ramanzin Maurizio
Published: January 2021

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms’ interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.
Comprehensive surveillance data suggest a prominent role of parvovirus B19 infection in Belarus and the presence of a third subtype within subgenotype 1a
Authors: Yermalovich Marina A. , Dronina Alina M. , Semeiko Galina V. , Samoilovich Elena O. , Khrustalev Vladislav V. , Sausy Aurelie , Hübschen Judith M.
Published: January 2021

Human parvovirus B19 (B19V) infection is not notifiable in Belarus and its most common clinical presentation erythema infectiosum (EI) is often difficult to distinguish from other exanthematous diseases. The objective of this study was to provide comprehensive data about EI epidemiology in Belarus based on the serological and molecular investigation of samples from measles and rubella discarded cases collected between 2005 and 2019. Overall, 4919 sera were investigated for IgM antibodies against B19V and the positive cases were analysed according to year, season and age. B19V DNA was amplified by PCR in a total of 238 sera from all over the country, and sequenced for phylogenetic analyses. B19V infection was confirmed in 1377 (27.8%) measles and rubella discarded cases. Two high incidence periods and a seasonal increase of EI between mid-February to mid-July were identified. Children from 4 to 6 and from 7 to 10 years of age represented the largest groups of patients (22.51% and 22.66% of all cases, respectively), followed by adults between 20 and 29 years of age (14.23%). Among the 238 B19Vs sequenced, one belonged to subgenotype 3b and 237 to subgenotype 1a with 81 (34.2%) clustering with subtypes 1a1 and 153 (64.6%) with 1a2. Three strains (1.2%) formed an additional, well-supported cluster suggesting the presence of another subtype of 1a, tentatively named 1a3. The epidemiological and molecular analyses highlighted not only the prominent role of B19V in exanthematous diseases in Belarus, but also suggested a previously underestimated diversity of subgenotype 1a sequences with a third subtype 1a3.
Local scattering ultrasound imaging
Authors: Velichko Alexander , Villaverde Eduardo Lopez , Croxford Anthony J.
Published: January 2021

Ultrasonic imaging is a widely used tool for detection, localisation and characterisation of material inhomogeneities with important applications in many fields. This task is particularly challenging when imaging in a complex medium, where the ultrasonic wave is scattered by the material microstructure, preventing detection and characterisation of weak targets. Fundamentally, the maximum information that can be experimentally obtained from each material region consists of a set of reflected signals for different incident waves. However, these data are not directly accessible from the raw measurements, which represent a superposition of reflections from all scatterers in the medium. Here we show, that a complete set of transmitter–receiver data encodes sufficient information in order to achieve full spatio–temporal separation of transmitter–receiver data, corresponding to different local scattering areas. We show that access to the local scattering data can provide valuable benefits for many applications. More importantly, this technique enables fundamentally new approaches, exploiting the angular distribution of the scattering amplitude and phase of each local scattering region. Here we demonstrate how the local scattering directivity can be used to build the local scattering image, releasing the full potential and richness of the transmit–receive data. As a proof of concept, we demonstrate the detection of small inclusions in various highly scattering materials using numerical and experimental examples. The described principles are very general and can be applied to any research field where the phased array technology is employed.
Addition of probiotics to antibiotics improves the clinical course of pneumonia in young people without comorbidities: a randomized controlled trial
Authors: Lee Chang Hun , Choi Yunjung , Seo Seung Young , Kim Seong-Hun , Kim In Hee , Kim Sang Wook , Lee Soo Teik , Lee Seung Ok
Published: January 2021

This study was aimed at investigating the clinical efficacy of probiotics in pneumonia patients. To this end, we enrolled 80 participants diagnosed with pneumonia at Naval Pohang Hospital, Pohang, Korea, from May 2016 to January 2017. The participants were randomly assigned to the control and probiotic groups depending on whether they received probiotics. All participants clinically improved but 22.6% of the participants complained of abnormal stool habits after pneumonia treatment. In comparison, fever duration was significantly shorter in the probiotic group, and the group exhibited an improved general condition. The probiotic group also showed better stool characteristics according to the Bristol stool scale (P = 0.009). Notably, the serum hs-CRP levels were significantly lower in the probiotic group at 2 weeks of treatment (P = 0.015), and all participants in the probiotic group achieved their levels within the normal range. Flow cytometry was used to analyze T-helper 17 (Th17) cells and regulatory T cells (Tregs). Tregs were promoted and the Th17 cell/Treg ratio was suppressed after 2 weeks of treatment in the probiotic group (P = 0.007 and 0.037, respectively). This study demonstrated that probiotics improved clinical symptoms and normalized inflammatory biomarker levels in patients with pneumonia. Early infection and inflammation recovery may be due to the immunomodulatory effects of probiotics by facilitating the subset of Tregs and suppressing the Th17 cell/Treg ratio.
An alternative approach to produce versatile retinal organoids with accelerated ganglion cell development
Authors: Wagstaff Ellie L. , ten Asbroek Anneloor L. M. A. , ten Brink Jacoline B. , Jansonius Nomdo M. , Bergen Arthur A. B.
Published: January 2021

Genetically complex ocular neuropathies, such as glaucoma, are a major cause of visual impairment worldwide. There is a growing need to generate suitable human representative in vitro and in vivo models, as there is no effective treatment available once damage has occured. Retinal organoids are increasingly being used for experimental gene therapy, stem cell replacement therapy and small molecule therapy. There are multiple protocols for the development of retinal organoids available, however, one potential drawback of the current methods is that the organoids can take between 6 weeks and 12 months on average to develop and mature, depending on the specific cell type wanted. Here, we describe and characterise a protocol focused on the generation of retinal ganglion cells within an accelerated four week timeframe without any external small molecules or growth factors. Subsequent long term cultures yield fully differentiated organoids displaying all major retinal cell types. RPE, Horizontal, Amacrine and Photoreceptors cells were generated using external factors to maintain lamination.
Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Authors: Relvas M. , Regueira-Iglesias A. , Balsa-Castro C. , Salazar F. , Pacheco J. J. , Cabral C. , Henriques C. , Tomás I.
Published: January 2021

The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota’s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.
Heat-related illness risk and associated personal and environmental factors of construction workers during work in summer
Authors: Kakamu Takeyasu , Endo Shota , Hidaka Tomoo , Masuishi Yusuke , Kasuga Hideaki , Fukushima Tetsuhito
Published: January 2021

Heat-related illness (HRI) is a common occupational injury, especially in construction workers. To explore the factors related to HRI risk in construction workers under hot outdoor working conditions, we surveyed vital and environmental data of construction workers in the summer season. Sixty-one workers joined the study and the total number of days when their vital data during working hours and environmental data were recorded was 1165. Heart rate with high-risk HRI was determined using the following formula: 180 − 0.65 × age. As a result of the logistic regression analysis, age, working area, maximum skin temperature, and heart rate immediately after warming up were significantly positively related, and experience of construction was significantly negatively related to heart rate with high-risk HRI. Heart rate immediately after warming up may indicate morning fatigue due to reasons such as insufficient sleep, too much alcohol intake the night before, and sickness. Asking morning conditions may lead to the prevention of HRI. For occupational risk management, monitoring of environmental and personal conditions is required.
Differential effects on human cytochromes P450 by CRISPR/Cas9-induced genetic knockout of cytochrome P450 reductase and cytochrome b5 in HepaRG cells
Authors: Heintze Tamara , Klein Kathrin , Hofmann Ute , Zanger Ulrich M.
Published: January 2021

HepaRG cells are increasingly accepted as model for human drug metabolism and other hepatic functions. We used lentiviral transduction of undifferentiated HepaRG cells to deliver Cas9 and two alternative sgRNAs targeted at NADPH:cytochrome P450 oxidoreductase (POR), the obligate electron donor for microsomal cytochromes P450 (CYP). Cas9-expressing HepaRGVC (vector control) cells were phenotypically similar to wild type HepaRG cells and could be differentiated into hepatocyte-like cells by DMSO. Genetic POR-knockout resulted in phenotypic POR knockdown of up to 90% at mRNA, protein, and activity levels. LC–MS/MS measurement of seven CYP-activities showed differential effects of POR-knockdown with CYP2C8 being least and CYP2C9 being most affected. Further studies on cytochrome b5 (CYB5), an alternative NADH-dependent electron donor indicated particularly strong support of CYP2C8-dependent amodiaquine N-deethylation by CYB5 and this was confirmed by genetic CYB5 single- and POR/CYB5 double-knockout. POR-knockdown also affected CYP expression on mRNA and protein level, with CYP1A2 being induced severalfold, while CYP2C9 was strongly downregulated. In summary our results show that POR/NADPH- and CYB5/NADH-electron transport systems influence human drug metabolizing CYPs differentially and differently than mouse Cyps. Our Cas9-expressing HepaRGVC cells should be suitable to study the influence of diverse genes on drug metabolism and other hepatic functions.
Identifying priority core habitats and corridors for effective conservation of brown bears in Iran
Authors: Mohammadi A. , Almasieh K. , Nayeri D. , Ataei F. , Khani A. , López-Bao J. V. , Penteriani V. , Cushman S. A.
Published: January 2021

Iran lies at the southernmost range limit of brown bears globally. Therefore, understanding the habitat associations and patterns of population connectivity for brown bears in Iran is relevant for the species’ conservation. We applied species distribution modeling to predict habitat suitability and connectivity modeling to identify population core areas and corridors. Our results showed that forest density, topographical roughness, NDVI and human footprint were the most influential variables in predicting brown bear distribution. The most crucial core areas and corridor networks for brown bear are concentrated in the Alborz and Zagros Mountains. These two core areas were predicted to be fragmented into a total of fifteen isolated patches if dispersal of brown bear across the landscape is limited to 50,000 cost units, and aggregates into two isolated habitat patches if the species is capable of dispersing 400,000 cost units. We found low overlap between corridors, and core habitats with protected areas, suggesting that the existing protected area network may not be adequate for the conservation of brown bear in Iran. Our results suggest that effective conservation of brown bears in Iran requires protection of both core habitats and the corridors between them, especially outside Iran’s network of protected areas.
Estimation of Basin-scale turbulence distribution in the North Pacific Ocean using CTD-attached thermistor measurements
Authors: Goto Yasutaka , Yasuda Ichiro , Nagasawa Maki , Kouketsu Shinya , Nakano Toshiya
Published: January 2021

A recently developed technique for microstructure measurement based on a fast-response thermistor mounted on a conductivity-temperature-depth equipment was used on eight cruises to obtain 438 profiles. Thus, the spatial distribution of turbulent dissipation rates across the North Pacific sea floor was illustrated, and was found out to be related to results obtained using tide-induced energy dissipation and density stratification. The observed turbulence distribution was then compared with the dissipation rate based on a high-resolution numerical ocean model with tidal forcing, and discrepancies and similarities between the observed and modelled distributions were described. The turbulence intensity from observation showed that the numerical model was overestimated, and could be refined by comparing it with the observed basin-scale dissipation rate. This new method makes turbulence observations much easier and wider, significantly improving our knowledge regarding ocean mixing.
Lipid droplet biogenesis and COX-2 pathway activation are triggered by Barrett’s esophagus and adenocarcinoma, but not esophageal squamous cell carcinoma risk factors
Authors: Carrossini N. , Meireles Da Costa N. , Andrade-Barreto E. , Sousa V. P. L. , Nicolau-Neto P. , Souza-Santos P. T. , Mansur G. R. , Wernersbach L. , Bozza P. T. , Viola J. P. B. , Ribeiro Pinto Luis Felipe
Published: January 2021

Esophageal cancer (EC) is an aggressive disease, presenting two main histological subtypes: adenocarcinoma (EAC) and squamous cell carcinoma (ESCC). The two EC subtypes widely differ concerning virtually all factors. ESCC development is mainly associated with tobacco and alcohol abuse, whereas obesity and chronic gastroesophageal reflux disease (GERD) are important risk factors not only for EAC, but also for for Barrett’s esophagus (BE), an intestinal metaplasia that precedes EAC. Obesity triggers ectopic lipid droplets (LD) accumulation in non-adipose tissues. LD are organelles involved in cell metabolism, signaling, proliferation and production of inflammatory mediators. Therefore, the aim of this work was to investigate LD occurrence and role in EC. This study shows progressive LD levels increase along EAC development, in esophageal samples from non-obese through obese individuals, as well as BE, and EAC patients, whereas no significant changes were observed in ESCC samples, when compared to non-tumor samples. Additionally, in order to mimic BE and EAC risk factors exposure, a non-tumor esophageal cell line was incubated with oleic acid (OA) and acidified medium and/or deoxycholic acid (DCA), revealing a significant increment in LD amount as well as in COX-2 and CXCL-8 expression, and in IL-8 secretion. Further, COX-2 expression and LD amount presented a significant positive correlation and were detected co-localized in EAC, but not in ESCC, suggesting that LD may be the site for eicosanoid production in EAC. In conclusion, this study shows that obesity, and BE- and EAC-associated inflammatory stimuli result in a gradual increase of LD, that may be responsible for orchestrating inflammatory mediators’ production and/or action, thus contributing to BE and EAC genesis and progression.
A role for orphan nuclear receptor liver receptor homolog-1 (LRH-1, NR5A2) in primordial follicle activation
Authors: Meinsohn Marie-Charlotte , Hughes Camilla H. K. , Estienne Anthony , Saatcioglu Hatice D. , Pépin David , Duggavathi Raj , Murphy Bruce D.
Published: January 2021

Liver receptor homolog-1 (NR5A2) is expressed specifically in granulosa cells of developing ovarian follicles where it regulates the late stages of follicle development and ovulation. To establish its effects earlier in the trajectory of follicular development, NR5A2 was depleted from granulosa cells of murine primordial and primary follicles. Follicle populations were enumerated in neonates at postnatal day 4 (PND4) coinciding with the end of the formation of the primordial follicle pool. The frequency of primordial follicles in PND4 conditional knockout (cKO) ovaries was greater and primary follicles were substantially fewer relative to control (CON) counterparts. Ten-day in vitro culture of PND4 ovaries recapitulated in vivo findings and indicated that CON mice developed primary follicles in the ovarian medulla to a greater extent than did cKO animals. Two subsets of primordial follicles were observed in wildtype ovaries: one that expressed NR5A2 and the second in which the transcript was absent. Neither expressed the mitotic marker. KI-67, indicating their developmental quiescence. RNA sequencing on PND4 demonstrated that loss of NR5A2 induced changes in 432 transcripts, including quiescence markers, inhibitors of follicle activation, and regulators of cellular migration and epithelial-to-mesenchymal transition. These experiments suggest that NR5A2 expression poises primordial follicles for entry into the developing pool.
Bulk-edge correspondence of classical diffusion phenomena
Authors: Yoshida Tsuneya , Hatsugai Yasuhiro
Published: January 2021

We elucidate that diffusive systems, which are widely found in nature, can be a new platform of the bulk-edge correspondence, a representative topological phenomenon. Using a discretized diffusion equation, we demonstrate the emergence of robust edge states protected by the winding number for one- and two-dimensional systems. These topological edge states can be experimentally accessible by measuring diffusive dynamics at edges. Furthermore, we discover a novel diffusion phenomenon by numerically simulating the distribution of temperatures for a honeycomb lattice system; the temperature field with wavenumber $$\pi $$
π
cannot diffuse to the bulk, which is attributed to the complete localization of the edge state.
Revisiting cosmic microwave background radiation using blackbody radiation inversion
Authors: Konar Koustav , Bose Kingshuk , Paul R. K.
Published: January 2021

Blackbody radiation inversion is a mathematical process for the determination of probability distribution of temperature from measured radiated power spectrum. In this paper a simple and stable blackbody radiation inversion is achieved by using an analytical function with three determinable parameters for temperature distribution. This inversion technique is used to invert the blackbody radiation field of the cosmic microwave background, the remnant radiation of the hot big bang, to infer the temperature distribution of the generating medium. The salient features of this distribution are investigated and analysis of this distribution predicts the presence of distortion in the cosmic microwave background spectrum.
Predictors for development of denosumab-induced hypocalcaemia in cancer patients with bone metastases determined by ordered logistic regression analysis
Authors: Kanbayashi Yuko , Sakaguchi Koichi , Hongo Fumiya , Ishikawa Takeshi , Tabuchi Yusuke , Ukimura Osamu , Takayama Koichi , Taguchi Tetsuya
Published: January 2021

This retrospective study was undertaken to identify predictors for the development of hypocalcaemia even with prophylactic administration of calcium and vitamin D, and to help guide future strategies to improve the safety, efficacy, and QOL of patients receiving denosumab. Between January 2016 and February 2020, a total of 327 advanced cancer patients at our hospital who were receiving denosumab were enrolled. Variables associated with the development of hypocalcaemia were extracted from the clinical records. The level of hypocalcaemia was evaluated using CTCAE version 5. Multivariate ordered logistic regression analysis was performed to identify predictors for the development of hypocalcaemia. Optimal cut off thresholds were determined using ROC analysis. Values of P < 0.05 (2-tailed) were considered significant. 54 patients have developed hypocalcemia (≥ Grade 1). Significant factors identified included concomitant use of vonoprazan [odds ratio (OR) = 3.74, 95% confidence interval (CI) 1.14–12.26; P = 0.030], dexamethasone (OR = 2.45, 95%CI 1.14–5.42; P = 0.022), pre-treatment levels of serum calcium (OR = 0.27, 95%CI 0.13–0.54; P < 0.001), ALP/100 (OR = 1.04, 95%CI 1.01–1.07; P = 0.003), and haemoglobin (OR = 0.79, 95%CI 0.68–0.93; P = 0.004). ROC curve analysis revealed that the threshold for pre-treatment levels of serum calcium was ≤ 9.3 mg/dL, ALP was ≥ 457 U/L, and haemoglobin was ≤ 10.4 g/dL. In conclusion, concomitant use of vonoprazan or dexamethasone, and pre-treatment levels of serum calcium (low), ALP (high) and haemoglobin (low) were identified as significant predictors for the development of denosumab-induced hypocalcaemia.
Insulator-to-half metal transition and enhancement of structural distortions in $$\text {Lu}_2 \text {NiIrO}_6$$ double perovskite oxide via hole-doping
Authors: Nazir Safdar
Published: January 2021

Using density functional theory calculations, we found that recently high-pressure synthesized double perovskite oxide $$\text {Lu}_2 \text {NiIrO}_6$$

Lu
2

NiIrO
6

exhibits ferrimagnetic (FiM) Mott-insulating state having an energy band gap of 0.20 eV which confirms the experimental observations (Feng et al. in Inorg Chem 58:397–404, 2019). Strong antiferromagnetic superexchange interactions between high-energy half-filled $$\text {Ni}^{+2}$$

Ni

+
2

-$$e_g^2\uparrow$$

e
g
2

↑

and low-energy partially filled $$\text {Ir}^{+4}\,t_{2g}^3\uparrow t_{2g}^2\downarrow$$

Ir

+
4

t

2
g

3

↑

t

2
g

2

↓

orbitals, results in a FiM spin ordering. Besides, the effect of 3d transition metal (TM = Cr, Mn, and Fe) doping with 50% concentration at Ni sites on its electronic and magnetic properties is explored. It is established that smaller size cation-doping at the B site enhances the structural distortion, which further gives strength to the FiM ordering temperature. Interestingly, our results revealed that all TM-doped structures exhibit an electronic transition from Mott-insulating to a half-metallic state with effective integral spin moments. The admixture of Ir 5d orbitals in the spin-majority channel are mainly responsible for conductivity, while the spin minority channel remains an insulator. Surprisingly, a substantial reduction and enhancement of spin moment are found on non-equivalent Ir and oxygen ions, respectively. This leads the Ir ion in a mixed-valence state of $$+4$$

+
4

and $$+5$$

+
5

in all doped systems having configurations of $$5d^5$$

5

d
5

($$t_{2g}^3\uparrow t_{2g}^2\downarrow$$

t

2
g

3

↑

t

2
g

2

↓

) and $$5d^4$$

5

d
4

($$t_{2g}^2\uparrow t_{2g}^2\downarrow$$

t

2
g

2

↑

t

2
g

2

↓

), respectively. Hence, the present work proposes that doping engineering with suitable impurity elements could be an effective way to tailor the physical properties of the materials for their technological potential utilization in advanced spin devices.
Insulin resistance is associated with poor functional outcome after acute ischemic stroke in non-diabetic patients
Authors: Chang Yoonkyung , Kim Chi Kyung , Kim Min-Kyung , Seo Woo‐Keun , Oh Kyungmi
Published: January 2021

Insulin resistance is associated with the occurrence of stroke and atherosclerotic disease. However, the relationship between insulin resistance and the prognosis of acute ischemic stroke in non-diabetic patients is unclear. We hypothesized that insulin resistance might affect short-term functional recovery after acute ischemic stroke in non-diabetic patients. Between May 2014 and December 2016, 1377 consecutive patients with acute ischemic stroke were enrolled from a prospectively maintained stroke registry. After excluding patients with transient ischemic attacks (TIA), pre-stroke disabilities, diabetes mellitus, and patients with incomplete evaluations, 517 patients were included in the study. The homeostasis model assessment of insulin resistance (HOMA-IR) score was used to evaluate the degree of insulin resistance. The patients with the highest quartile of log HOMA-IR index scores were younger and had higher fasting blood glucose, total cholesterol, triglycerides, low-density lipoprotein, and HbA1c levels. Multivariable logistic regression analysis revealed that log HOMA-IR scores were independently associated with poor prognosis after adjusting for age and sex and p < 0.1 in univariable analysis. Insulin resistance was associated with the poor functional outcome of non-diabetic stroke patients. This evidence supports treating insulin resistance in acute ischemic stroke patients with blood glucose levels within the normal range.
Physicochemical characterization and rheological properties of magnetic elastomers containing different shapes of corroded carbonyl iron particles
Authors: Burhannuddin Nurul Liyana , Nordin Nur Azmah , Mazlan Saiful Amri , Aziz Siti Aishah Abdul , Kuwano Noriyuki , Jamari Siti Khumaira Mohd , Ubaidillah
Published: January 2021

Carbonyl iron particles (CIPs) is one of the key components in magnetic rubber, known as magnetorheological elastomer (MRE). Apart from the influence of their sizes and concentrations, the role of the particle’ shape is pronounced worthy of the attention for the MRE performance. However, the usage of CIPs in MRE during long-term applications may lead to corrosion effects on the embedded CIPs, which significantly affects the performance of devices or systems utilizing MRE. Hence, the distinctions between the two types of MRE embedded in different shapes of spherical and plate-like CIPs, at both conditions of non-corroded and corroded CIPs were investigated in terms of the field-dependent rheological properties of MRE. The plate-like shape was produced from spherical CIPs through a milling process using a rotary ball mill. Then, both shapes of CIPs individually subjected to an accelerated corrosion test in diluted hydrochloric (HCl) at different concentrations, particularly at 0.5, 1.0, and 1.5 vol.% for 30 min of immersion time. Eight samples of CIPs, including non-corroded for both CIPs shapes, were characterized in terms of a morphological study by field emission scanning electron microscope (FESEM) and magnetic properties via vibrating sample magnetometer (VSM). The field-dependent rheological properties of MREs were analyzed the change in the dynamic modulus behavior of MREs via rheometer. From the application perspective, this finding may be useful for the system to be considered that provide an idea to prolong the performance MRE by utilizing the different shapes of CIPs even when the material is fading.
Corticosteroid treatment has no effect on hospital mortality in COVID-19 patients
Authors: Albani Filippo , Fusina Federica , Granato Enza , Capotosto Cristina , Ceracchi Claudia , Gargaruti Riccardo , Santangelo Giovanni , Schiavone Luca , Taranto Maria Salvatrice , Tosati Cinzia , Vavassori Elena , Natalini Giuseppe
Published: January 2021

Since the start of the novel coronavirus 2019 (COVID-19) pandemic, corticosteroid use has been the subject of debate. The available evidence is uncertain, and knowledge on the subject is evolving. The aim of our cohort study was to evaluate the association between corticosteroid therapy and hospital mortality, in patients hospitalized with COVID-19 after balancing for possible confounders. One thousand four hundred forty four patients were admitted to our hospital with a positive RT-PCR test for SARS-CoV-2, 559 patients (39%) were exposed to corticosteroids during hospital stay, 844 (61%) were not exposed to corticosteroids. In the cohort of patients exposed to corticosteroids, 171 (30.6%) died. In the cohort of patients not exposed to corticosteroids, 183 (21.7%) died (unadjusted p < 0.001). Nonetheless, exposure to corticosteroids was not associated with in-hospital mortality after balancing with overlap weight propensity score (adjusted p = 0.25). Patients in the corticosteroids cohort had a reduced risk of ICU admission (adjusted p < 0.001). Treatment with corticosteroids did not affect hospital mortality in patients with COVID-19 after balancing for confounders. A possible advantage of corticosteroid therapy was to reduce Intensive Care Unit admission, which could be useful in reducing pressure on Intensive Care Units in times of limited resources, as during the COVID-19 pandemic.
Internetwork connectivity of molecular networks across species of life
Authors: Mahajan Tarun , Dar Roy D.
Published: January 2021

Molecular interactions are studied as independent networks in systems biology. However, molecular networks do not exist independently of each other. In a network of networks approach (called multiplex), we study the joint organization of transcriptional regulatory network (TRN) and protein–protein interaction (PPI) network. We find that TRN and PPI are non-randomly coupled across five different eukaryotic species. Gene degrees in TRN (number of downstream genes) are positively correlated with protein degrees in PPI (number of interacting protein partners). Gene–gene and protein–protein interactions in TRN and PPI, respectively, also non-randomly overlap. These design principles are conserved across the five eukaryotic species. Robustness of the TRN–PPI multiplex is dependent on this coupling. Functionally important genes and proteins, such as essential, disease-related and those interacting with pathogen proteins, are preferentially situated in important parts of the human multiplex with highly overlapping interactions. We unveil the multiplex architecture of TRN and PPI. Multiplex architecture may thus define a general framework for studying molecular networks. This approach may uncover the building blocks of the hierarchical organization of molecular interactions.
Strategically positioning cooperators can facilitate the contagion of cooperation
Authors: Yang Guoli , Cavaliere Matteo , Zhu Cheng , Perc Matjaž
Published: January 2021

The spreading of cooperation in structured population is a challenging problem which can be observed at different scales of social and biological organization. Generally, the problem is studied by evaluating the chances that few initial invading cooperators, randomly appearing in a network, can lead to the spreading of cooperation. In this paper we demonstrate that in many scenarios some cooperators are more influential than others and their initial positions can facilitate the spreading of cooperation. We investigate six different ways to add initial cooperators in a network of cheaters, based on different network-based measurements. Our research reveals that strategically positioning the initial cooperators in a population of cheaters allows to decrease the number of initial cooperators necessary to successfully seed cooperation. The strategic positioning of initial cooperators can also help to shorten the time necessary for the restoration of cooperation. The optimal ways in which the initial cooperators should be placed is, however, non-trivial in that it depends on the degree of competition, the underlying game, and the network structure. Overall, our results show that, in structured populations, few cooperators, well positioned in strategically chosen places, can spread cooperation faster and easier than a large number of cooperators that are placed badly.
Simulation of infrared spectra of trace impurities in silicon wafers based on the multiple transmission–reflection infrared method
Authors: Lu Xiaobin
Published: January 2021

The content of trace impurities, such as interstitial oxygen and substitutional carbon, in silicon is crucial in determining the mechanical and physical characteristics of silicon wafers. The traditional infrared (IR) method is adopted as a normal means to analyse their concentration at home and abroad, but there are two problems. The first problem is the poor representativeness of a single local sampling point because the impurity distribution in a solid sample is not as uniform as that in a liquid sample. The second problem is that interference fringes appear in the infrared spectra of the sample due to the thin wafer (≤ 300 μm thick). Based on this, controversial issues existed regarding the measured trace impurity concentrations between wafer manufacturers and solar cell assembly businessmen who used silicon sheets made by the former. Therefore, multiple transmission-reflection (MTR) infrared (IR) spectroscopy was proposed to solve the problems mentioned above. In the MTR setup, because light passes through different parts of the silicon chip several times, multiple sampling points make the final result more representative. Moreover, the optical path is lengthened, and the corresponding absorbance is enhanced. In addition to amplification of weak signals, the MTR-IR method can eliminate interference fringes via the integrating sphere effect of its special configuration. The signal-to-noise ratio of the corresponding spectrum is considerably improved due to the aforementioned dual effects. Thus, the accuracy and sensitivity of the detection method for trace impurities in silicon chips are greatly increased. In this study, silicon wafers were placed in the MTR setup, and then, their relative properties at room temperature were investigated. The corresponding theoretical calculation and simulation of infrared spectra of silicon chips were provided. This affords an optional method for the semiconductor material industry to analyse trace impurities in their chips.
Human α-synuclein overexpression in a mouse model of Parkinson’s disease leads to vascular pathology, blood brain barrier leakage and pericyte activation
Authors: Elabi Osama , Gaceb Abderahim , Carlsson Robert , Padel Thomas , Soylu-Kucharz Rana , Cortijo Irene , Li Wen , Li Jia-Yi , Paul Gesine
Published: January 2021

The pathological hallmark of Parkinson’s disease (PD) is the formation of Lewy bodies containing aggregated alpha-synuclein (α-syn). Although PD is associated with these distinct histological changes, other pathological features such as microvascular alterations have been linked to neurodegeneration. These changes need to be investigated as they create a hostile brain microenvironment and may contribute to the development and progression of the disease. We use a human α-syn overexpression mouse model that recapitulates some of the pathological features of PD in terms of progressive aggregation of human α-syn, impaired striatal dopamine fiber density, and an age-dependent motor deficit consistent with an impaired dopamine release. We demonstrate for the first time in this model a compromised blood–brain barrier integrity and dynamic changes in vessel morphology from angiogenesis at earlier stages to vascular regression at later stages. The vascular alterations are accompanied by a pathological activation of pericytes already at an early stage without changing overall pericyte density. Our data support and further extend the occurrence of vascular pathology as an important pathophysiological aspect in PD. The model used provides a powerful tool to investigate disease-modifying factors in PD in a temporal sequence that might guide the development of new treatments.
A justification of the invariance of the speed of light by quantum theoretical considerations
Authors: Cordin Michael
Published: January 2021

Abstract phenomena can often be analysed in a visually clear way by thought experiments. In the present work a new thought experiment is analysed, which describes the emission of a photon by a special mechanism. The analysis leads to the finding, that there is a natural connection between the energy-time uncertainty and the Heisenberg position-momentum uncertainty principle. A deeper analysis of this thought experiment, especially with regard to a justification of the Doppler effect from the uncertainty principle, leads to the conclusion, that the speed of light is invariant. Therefore it seems reasonable to assume, that the origin of relativistic laws lies in non-relativistic quantum mechanics.
Correction: Effect of the formulation and structure of monoglyceride-based gels on the viability of probiotic Lactobacillus rhamnosus upon in vitro digestion
Authors: Melchior Sofia , Marino Marilena , D'Este Francesca , Innocente Nadia , Nicoli Maria Cristina , Calligaris Sonia
Published: January 2021

Correction for ‘Effect of the formulation and structure of monoglyceride-based gels on the viability of probiotic Lactobacillus rhamnosus upon in vitro digestion’ by Sofia Melchior et al., Food Funct., 2021, DOI: 10.1039/D0FO01788D.
Shape factors in the binding of soft fluorescent nanoshuttles with target receptors
Authors: Cozza Concetta , Raymo Françisco M. , Pietropaolo Adriana
Published: January 2021

We predicted the binding of fluorescent nanoparticles with a target receptor through free-energy and ECD spectra simulations. In a stable binding complex, the ECD spectra of the binding monomer and the receptor binding pocket turn out to be superimposable.
Correction: An ultrahigh thermal conductive graphene flexible paper
Authors: Ding Jiheng , Zhao Hongran , Wang Qiaolei , Dou Huimin , Chen Hao , Yu Haibin
Published: January 2021

Correction for ‘An ultrahigh thermal conductive graphene flexible paper’ by Jiheng Ding et al., Nanoscale, 2017, 9, 16871–16878, DOI: 10.1039/C7NR06667H.
The effect of complexing agents in chemical solution deposition of metal chalcogenide thin films
Authors: Sengupta Sucheta , Aggarwal Rinki , Golan Yuval
Published: January 2021

This review article gives an overview of different complexing agents used during chemical deposition of metal chalcogenide thin films and their role in controlling the resultant morphology by effective complexation of the metal ion.
Detection of kidney disease biomarkers based on fluorescence technology
Authors: Yao Bicheng , Giel Marie-Claire , Hong Yuning
Published: January 2021

This review summarizes the recent progress in the development of fluorescent probes and methods for the detection of biomarkers for the diagnosis of kidney diseases.
Synthesis and antimicrobial activity of some novel 1,2-dihydro-[1,2,4]triazolo[1,5-a]pyrimidines bearing amino acid moiety
Authors: Mohamed Mounir A. A. , Bekhit Adnan A. , Abd Allah Omyma A. , Kadry Asmaa M. , Ibrahim Tamer M. , Bekhit Salma A. , Amagase Kikuko , El-Saghier Ahmed M. M.
Published: January 2021

A new series of [1,2,4]-triazole bearing amino acid derivatives were synthesized under green chemistry conditions and evaluated for their antimicrobial activities.