bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of spore inoculum and confirmation of pathway genetic blueprint of T13αH and DBAT from a Taxol-producing endophytic fungus
Authors: Chakravarthi Balabhadrapatruni V. S. K. , Singh Satpal , Kamalraj Subban , Gupta Vijai Kumar , Jayabaskaran Chelliah 
Published: December 2020

AbstractTaxol (paclitaxel), a plant-derived anticancer drug, has been among the most successful anticancer drugs of natural origin. Endophytic fungi have been proposed as a prominent alternative source for Taxol and its intermediate Baccatin III, however the very low yields remain a hinderance to their commercial utilization. Significant research efforts towards this end are underway globally. Here, we report the results on our earlier reported Taxol-producing endophytic fungus, Fusarium solani from the standpoint of spores as seed inoculum and media selection for enhanced Taxol and baccatin III yields. Spores produced on M1D medium with 94.76% viability were used for further media optimization for Taxol and Baccatin III production in five different liquid media under static and shaker condition at different cultivation days. Taxol and Baccatin III when quantified through competitive inhibition enzyme immunoassay (CIEIA), showed maximum production at 136.3 µg L−1 and 128.3 µg L−1, respectively in the modified flask basal broth (MFBB) under shaking condition. Further, two important genes of this pathway, namely taxane 13α-hydroxylase (T13αH) and 10-deacetylbaccatin III-10-β-O-acetyltransferase (DBAT) have been identified in this fungus. These findings are hoped to assist in further manipulation and metabolic engineering of the parent F. solani strain towards the enhanced production of Taxol and baccatin III.
Time dynamics of COVID-19
Authors: Carroll Cody , Bhattacharjee Satarupa , Chen Yaqing , Dubey Paromita , Fan Jianing , Gajardo Álvaro , Zhou Xiner , Müller Hans-Georg , Wang Jane-Ling 
Published: December 2020

AbstractWe apply tools from functional data analysis to model cumulative trajectories of COVID-19 cases across countries, establishing a framework for quantifying and comparing cases and deaths across countries longitudinally. It emerges that a country’s trajectory during an initial first month “priming period” largely determines how the situation unfolds subsequently. We also propose a method for forecasting case counts, which takes advantage of the common, latent information in the entire sample of curves, instead of just the history of a single country. Our framework facilitates to quantify the effects of demographic covariates and social mobility on doubling rates and case fatality rates through a time-varying regression model. Decreased workplace mobility is associated with lower doubling rates with a roughly 2 week delay, and case fatality rates exhibit a positive feedback pattern.
Exploring the effect of UV-C radiation on earthworm and understanding its genomic integrity in the context of H2AX expression
Authors: Subbiahanadar Chelladurai Karthikeyan , Selvan Christyraj Jackson Durairaj , Azhagesan Ananthaselvam , Paulraj Vennila Devi , Jothimani Muralidharan , Yesudhason Beryl Vedha , Chellathurai Vasantha Niranjan , Ganesan Mijithra , Rajagopalan Kamarajan , Venkatachalam Saravanakumar , Benedict Johnson , John Samuel Jemima Kamalapriya , Selvan Christyraj Johnson Retnaraj Samuel 
Published: December 2020

AbstractMaintaining genomic stability is inevitable for organism survival and it is challenged by mutagenic agents, which include ultraviolet (UV) radiation. Whenever DNA damage occurs, it is sensed by DNA-repairing proteins and thereby performing the DNA-repair mechanism. Specifically, in response to DNA damage, H2AX is a key protein involved in initiating the DNA-repair processes. In this present study, we investigate the effect of UV-C on earthworm, Perionyx excavatus and analyzed the DNA-damage response. Briefly, we expose the worms to different doses of UV-C and find that worms are highly sensitive to UV-C. As a primary response, earthworms produce coelomic fluid followed by autotomy. However, tissue inflammation followed by death is observed when we expose worm to increased doses of UV-C. In particular, UV-C promotes damages in skin layers and on the contrary, it mediates the chloragogen and epithelial outgrowth in intestinal tissues. Furthermore, UV-C promotes DNA damages followed by upregulation of H2AX on dose-dependent manner. Our finding confirms DNA damage caused by UV-C is directly proportional to the expression of H2AX. In short, we conclude that H2AX is present in the invertebrate earthworm, which plays an evolutionarily conserved role in DNA damage event as like that in higher animals.
Insights into the chemistry of the amphibactin–metal (M3+) interaction and its role in antibiotic resistance
Authors: Kaipanchery Vidya , Sharma Anamika , Albericio Fernando , de la Torre Beatriz G. 
Published: December 2020

AbstractWe have studied the diversity and specificity of interactions of amphibactin produced by Vibrio genus bacterium (Vibriosp. HC0601C5) with iron and various metal ions in + 3 oxidation state in an octahedral (Oh) environment. To survive in the iron-deficient environment of their host, pathogenic bacteria have devised various efficient iron acquisition strategies. One such strategy involves the production of low molecular weight peptides called siderophores, which have a strong affinity and specificity to chelate Fe3+and can thus facilitate uptake of this metal in order to ensure iron requirements. The Fe uptake by amphibactin and the release of iron inside the cell have been studied. Comparison of the interaction of different transition metal ions (M3+) with amphibactin has been studied and it reveals that Co and Ga form stable complexes with this siderophore. The competition of Co and Ga with Fe impedes iron uptake by bacteria, thereby preventing infection.
Seroprevalence of hepatitis B virus and hepatitis C virus infection among Malaysian population
Authors: Muhamad Nor Asiah , Ab.Ghani Rimah Melati , Abdul Mutalip Mohd Hatta , Muhammad Eida Nurhadzira , Mohamad Haris Hasmah , Mohd Zain Rozainanee , Abdullah Noraidatulakma , Muhammad Azami Nor Azila , Abd Jalal Nazihah , Ismail Norliza , Mhd Yusuf Nurul Ain , Othman Raihannah , Kamalul Arifin Azwa Shawani , Abdullah Mohd Shaharom , Kamaruddin Mohd Arman , Abu Hassan Muhammad Radzi , Aris Tahir , Jamal Rahman 
Published: December 2020

AbstractMalaysia is a country with an intermediate endemicity for hepatitis B. As the country moves toward hepatitis B and C elimination, population-based estimates are necessary to understand the burden of hepatitis B and C for evidence-based policy-making. Hence, this study aims to estimate the prevalence of hepatitis B and C in Malaysia. A total of 1458 participants were randomly selected from The Malaysian Cohort (TMC) aged 35 to 70 years between 2006 and 2012. All blood samples were tested for hepatitis B and C markers including hepatitis B surface antigen (HBsAg), anti-hepatitis B core antibody (anti-HBc), antibodies against hepatitis C virus (anti-HCV). Those reactive for hepatitis C were further tested for HCV RNA genotyping. The sociodemographic characteristics and comorbidities were used to evaluate their associated risk factors. Descriptive analysis and multivariable analysis were done using Stata 14. From the samples tested, 4% were positive for HBsAg (95% CI 2.7–4.7), 20% were positive for anti-HBc (95% CI 17.6–21.9) and 0.3% were positive for anti-HCV (95% CI 0.1–0.7). Two of the five participants who were reactive for anti-HCV had the HCV genotype 1a and 3a. The seroprevalence of HBV and HCV infection in Malaysia is low and intermediate, respectively. This population-based study could facilitate the planning and evaluation of the hepatitis B and C control program in Malaysia.
Exploring the genetic variability and diversity of pearl millet core collection germplasm for grain nutritional traits improvement
Authors: Govindaraj Mahalingam , Rai Kedar N. , Kanatti Anand , Upadhyaya Hari D. , Shivade Harshad , Rao Aluri S. 
Published: December 2020

AbstractImproving essential nutrient content in staple food crops through biofortification breeding can overcome the micronutrient malnutrition problem. Genetic improvement depends on the availability of genetic variability in the primary gene pool. This study was aimed to ascertain the magnitude of variability in a core germplasm collection of diverse origin and predict pearl millet biofortification prospects for essential micronutrients. Germplasm accessions were evaluated in field trials at ICRISAT, India. The accessions differed significantly for all micronutrients with over two-fold variation for Fe (34–90 mg kg−1), Zn (30–74 mg kg−1), and Ca (85–249 mg kg−1). High estimates of heritability (> 0.81) were observed for Fe, Zn, Ca, P, Mo, and Mg. The lower magnitude of genotype (G) × environment (E) interaction observed for most of the traits implies strong genetic control for grain nutrients. The top-10 accessions for each nutrient and 15 accessions, from five countries for multiple nutrients were identified. For Fe and Zn, 39 accessions, including 15 with multiple nutrients, exceeded the Indian cultivars and 17 of them exceeded the biofortification breeding target for Fe (72 mg kg−1). These 39 accessions were grouped into 5 clusters. Most of these nutrients were positively and significantly associated among themselves and with days to 50% flowering and 1000-grain weight (TGW) indicating the possibility of their simultaneous improvement in superior agronomic background. The identified core collection accessions rich in specific and multiple-nutrients would be useful as the key genetic resources for developing biofortified and agronomically superior cultivars.
Assessment of a dried blood spot C-reactive protein method to identify disease flares in rheumatoid arthritis patients
Authors: D’Cruz Leon G. , McEleney Kevin G. , Cochrane Chris , Tan Kyle B. C. , Shukla Priyank , Gardiner Philip V. , Small Dawn , Zhang Shu-Dong , Gibson David S. 
Published: December 2020

AbstractRheumatoid arthritis (RA) is characterised by painful, stiff and swollen joints. RA features sporadic ‘flares’ or inflammatory episodes—mostly occurring outside clinics—where symptoms worsen and plasma C-reactive protein (CRP) becomes elevated. Poor control of inflammation results in higher rates of irreversible joint damage, increased disability, and poorer quality of life. Flares need to be accurately identified and managed. A method comparison study was designed to assess agreement between CRP values obtained by dried blood spot (DBS) versus conventional venepuncture sampling. The ability of a weekly DBS sampling and CRP test regime to detect flare outside the clinic was also assessed. Matched venepuncture and finger lancet DBS samples were collected from n = 100 RA patients with active disease at baseline and 6 weeks (NCT02809547). A subset of n = 30 RA patients submitted weekly DBS samples over the study period. Patient demographics, including self-reported flares were recorded. DBS sample CRP measurements were made by enzyme-linked immunosorbent assay, and venepuncture samples by a reference immunoturbometric assay. Data was compared between sample types by Bland–Altman and weighted Deming regression analyses. Flare detection sensitivity and specificity were compared between ‘minimal’ baseline and 6 week sample CRP data and the ‘continuous’ weekly CRP data. Baseline DBS ELISA assay CRP measures yielded a mean positive bias of 2.693 ± 8.640 (95% limits of agreement − 14.24 to 19.63%), when compared to reference assay data. Deming regression revealed good agreement between the DBS ELISA method and reference assay data, with baseline data slope of 0.978 and intercept -0.153. The specificity of ‘continuous’ area under the curve (AUC) CRP data (72.7%) to identify flares, was greater than ‘minimal’ AUC CRP data (54.5%). This study indicates reasonable agreement between DBS and the reference method, especially at low to mid-range CRP values. Importantly, longitudinal CRP measurement in RA patients helps to clearly identify flare and thus could assist in remote monitoring strategies and may facilitate timely therapeutic intervention.Trial registration: The Remote Arthritis Disease Activity MonitoR (RADAR) study was registered on 22/06/2016 at ClinicalTrials.gov Identifier: NCT02809547. https://clinicaltrials.gov/ct2/show/NCT02809547.
Fermi surface and kink structures in $$\hbox {Sr}_{{4}}\hbox {Ru}_{{3}}\hbox {O}_{{10}}$$ revealed by synchrotron-based ARPES
Authors: Ngabonziza Prosper , Carleschi Emanuela , Zabolotnyy Volodymyr , Taleb-Ibrahimi Amina , Bertran François , Fittipaldi Rosalba , Granata Veronica , Cuoco Mario , Vecchione Antonio , Doyle Bryan Patrick 
Published: December 2020

AbstractThe low-energy electronic structure, including the Fermi surface topology, of the itinerant metamagnet $$\hbox {Sr}_{{4}}\hbox {Ru}_{{3}}\hbox {O}_{{10}}$$

Sr
4

Ru
3

O
10

is investigated for the first time by synchrotron-based angle-resolved photoemission. Well-defined quasiparticle band dispersions with matrix element dependencies on photon energy or photon polarization are presented. Four bands crossing the Fermi-level, giving rise to four Fermi surface sheets are resolved; and their complete topography, effective mass as well as their electron and hole character are determined. These data reveal the presence of kink structures in the near-Fermi-level band dispersion, with energies ranging from 30 to 69 meV. Together with previously reported Raman spectroscopy and lattice dynamic calculation studies, the data suggest that these kinks originate from strong electron–phonon coupling present in $$\hbox {Sr}_{{4}}\hbox {Ru}_{{3}}\hbox {O}_{{10}}$$

Sr
4

Ru
3

O
10

. Considering that the kink structures of $$\hbox {Sr}_{{4}}\hbox {Ru}_{{3}}\hbox {O}_{{10}}$$

Sr
4

Ru
3

O
10

are similar to those of the other three members of the Ruddlesden Popper structured ruthenates, the possible universality of strong coupling of electrons to oxygen-related phonons in $$\hbox {Sr}_{n+1}\hbox {Ru}_{{n}}\hbox {O}_{3n+1}$$

Sr

n
+
1

Ru
n

O

3
n
+
1

compounds is proposed.
Deletion of the nuclear receptor RORα in macrophages does not modify the development of obesity, insulin resistance and NASH
Authors: L’homme Laurent , Sermikli Benan Pelin , Molendi-Coste Olivier , Fleury Sébastien , Quemener Sandrine , Le Maître Mathilde , Joseph Marie-Laure , Pineau Laurent , Duhem Christian , Gross Barbara , Vallez Emmanuelle , Tailleux Anne , Staels Bart , Dombrowicz David 
Published: December 2020

AbstractRetinoic acid receptor-related orphan receptor-alpha (RORα) is a transcription factor from the nuclear receptor family expressed by immune cells and involved in the development of obesity, insulin resistance (IR) and non-alcoholic steatohepatitis (NASH). It was recently reported that mice deficient for RORα in macrophages develop more severe NASH upon high fat diet (HFD) feeding due to altered Kupffer cell function. To better understand the role of RORα in obesity and IR, we independently generated a macrophage RORα-deficient mouse line. We report that RORα deletion in macrophages does not impact on HFD-induced obesity and IR. Surprisingly, we did not confirm an effect on NASH development upon HFD feeding nor in the more severe and obesity-independent choline-deficient, L-amino acid-defined diet model. Our results therefore show that RORα deletion in macrophages does not alter the development of obesity and IR and question its role in NASH.
Synergistic anti-biofilm effects of Brassicaceae plant extracts in combination with proteinase K against Escherichia coli O157:H7
Authors: Hu Wen Si , Min Nam Da , Kim Joo-Sung , Koo Ok Kyung 
Published: December 2020

AbstractBacteria can form biofilms, complex microbial communities protected from environmental stress, on food contact surfaces. Brassicaceae plant has been shown to contain bioactive compounds with antimicrobial activities. The objective of this study was to evaluate the synergistic effects of Brassicaceae species and proteinase K against E. coli O157:H7 biofilm. We determined the minimum biofilm inhibitory concentration, the fractional inhibitory concentration indexes, and the synergistic inhibitory effect of Raphanus sativus var. longipinnatus, R. sativus, and Brassica oleracea var. acephala extracts with proteinase K on E. coli O157:H7. The biofilm showed a 49% reduction with 2 mg/mL R. sativus. The combination of proteinase K 25 µg/mL significantly increased the effect of 2 mg/mL R. sativus var. longipinnatus and the combined treatment yielded up to 2.68 log reduction on stainless steel coupons. The results showed that the combination of R. sativus var. longipinnatus extract and proteinase K could serve as an anti-biofilm agent with synergistic effects for inhibiting E. coli O157:H7 biofilm on stainless steel surfaces.
Recent land use and management changes decouple the adaptation of livestock diversity to the environment
Authors: Velado-Alonso Elena , Morales-Castilla Ignacio , Gómez-Sal Antonio 
Published: December 2020

AbstractNative livestock breeds, i.e. those autochthonous to a specific region, are locally adapted domesticated animals that conserve genetic resources, guaranty food security and provide agroecosystem services. Native breeds are largely threatened worldwide by agricultural intensification and rural areas abandonment processes related to recent changes in production schemes and planning. Yet, our gap of knowledge regarding livestock breed-environment relationships may prevent the design of successful conservation measures. In this work, we analyse the links between livestock diversity -i.e. richness of native breeds- and a selection of environmental factors that express at broad scales, with a temporal perspective. We compare native breeds distributional patterns before and after the agricultural intensification, in the context of land-use change in mainland Spain. Our results confirm the existence of strong associations between the distribution of native livestock breeds and environmental factors. These links, however, weaken for contemporary distributions. In fact, changes in breed distribution reflect a shift towards more productive environments. Finally, we found that the areas having higher breed richness are undergoing land abandonment processes. Succeeding in the conservation of threatened native breeds will require going beyond merely genetic and production-oriented views. Ecological and sociocultural perspectives should also be accounted for as global change processes are determinant for livestock agrobiodiversity.
A minimalist model to measure interactions between proteins and synaptic vesicles
Authors: Perego Eleonora , Reshetniak Sofiia , Lorenz Charlotta , Hoffmann Christian , Milovanović Dragomir , Rizzoli Silvio O. , Köster Sarah 
Published: December 2020

AbstractProtein dynamics in the synaptic bouton are still not well understood, despite many quantitative studies of synaptic structure and function. The complexity of the synaptic environment makes investigations of presynaptic protein mobility challenging. Here, we present an in vitro approach to create a minimalist model of the synaptic environment by patterning synaptic vesicles (SVs) on glass coverslips. We employed fluorescence correlation spectroscopy (FCS) to measure the mobility of monomeric enhanced green fluorescent protein (mEGFP)-tagged proteins in the presence of the vesicle patterns. We observed that the mobility of all eleven measured proteins is strongly reduced in the presence of the SVs, suggesting that they all bind to the SVs. The mobility observed in these conditions is within the range of corresponding measurements in synapses of living cells. Overall, our simple, but robust, approach should enable numerous future studies of organelle-protein interactions in general.
Glioma and temozolomide induced alterations in gut microbiome
Authors: Patrizz Anthony , Dono Antonio , Zorofchian Soheil , Hines Gabriella , Takayasu Takeshi , Husein Nuruddin , Otani Yoshihiro , Arevalo Octavio , Choi H. Alex , Savarraj Jude , Tandon Nitin , Ganesh Bhanu P. , Kaur Balveen , McCullough Louise D. , Ballester Leomar Y. , Esquenazi Yoshua 
Published: December 2020

AbstractThe gut microbiome is fundamental in neurogenesis processes. Alterations in microbial constituents promote inflammation and immunosuppression. Recently, in immune-oncology, specific microbial taxa have been described to enhance the effects of therapeutic modalities. However, the effects of microbial dysbiosis on glioma are still unknown. The aim of this study was to explore the effects of glioma development and Temozolomide (TMZ) on fecal microbiome in mice and humans. C57BL/6 mice were implanted with GL261/Sham and given TMZ/Saline. Fecal samples were collected longitudinally and analyzed by 16S rRNA sequencing. Fecal samples were collected from healthy controls as well as glioma patients at diagnosis, before and after chemoradiation. Compared to healthy controls, mice and glioma patients demonstrated significant differences in beta diversity, Firmicutes/Bacteroides (F/B) ratio, and increase of Verrucomicrobia phylum and Akkermansia genus. These changes were not observed following TMZ in mice. TMZ treatment in the non-tumor bearing mouse-model diminished the F/B ratio, increase Muribaculaceae family and decrease Ruminococcaceae family. Nevertheless, there were no changes in Verrucomicrobia/Akkermansia. Glioma development leads to gut dysbiosis in a mouse-model, which was not observed in the setting of TMZ. These findings seem translational to humans and warrant further study.
A residual dense network assisted sparse view reconstruction for breast computed tomography
Authors: Fu Zhiyang , Tseng Hsin Wu , Vedantham Srinivasan , Karellas Andrew , Bilgin Ali 
Published: December 2020

AbstractTo develop and investigate a deep learning approach that uses sparse-view acquisition in dedicated breast computed tomography for radiation dose reduction, we propose a framework that combines 3D sparse-view cone-beam acquisition with a multi-slice residual dense network (MS-RDN) reconstruction. Projection datasets (300 views, full-scan) from 34 women were reconstructed using the FDK algorithm and served as reference. Sparse-view (100 views, full-scan) projection data were reconstructed using the FDK algorithm. The proposed MS-RDN uses the sparse-view and reference FDK reconstructions as input and label, respectively. Our MS-RDN evaluated with respect to fully sampled FDK reference yields superior performance, quantitatively and visually, compared to conventional compressed sensing methods and state-of-the-art deep learning based methods. The proposed deep learning driven framework can potentially enable low dose breast CT imaging.