bluuebunny/crossref_metadata_2025_split huggingface dataset:
microRNA-25 as a novel modulator of circadian Period2 gene oscillation
Authors: Park Inah , Kim Doyeon , Kim Jeongah , Jang Sangwon , Choi Mijung , Choe Han Kyoung , Choe Youngshik , Kim Kyungjin 
Published: September 2020

AbstractCircadian clock controls an organism’s biological rhythm and regulates its physiological processes in response to external time cues. Most living organisms have their own time-keeping mechanism that is maintained by transcriptional–translational autoregulatory feedback loops involving several core clock genes, such as Period. Recent studies have found the relevance between the modulation of circadian oscillation and posttranscriptional modifications by microRNAs (miRNAs). However, there are limited studies on candidate miRNAs that regulate circadian oscillation. Here, we characterize the functions of novel miRNA-25 regulating circadian Period2 (Per2) expression. Using several in silico algorithms, we identified novel miR-25-3p that, together with miR-24-3p, targets the Per2 gene. Luciferase reporter assays validated that miR-25-3p and miR-24-3p repressed Per2 expression and confirmed their predicted binding sites in the 3′-untranslated region (UTR) of Per2 mRNA. Real-time bioluminescence analyses using Per2::Luc mouse embryonic fibroblasts confirmed that PER2 protein oscillation patterns were responsive to miR-25-3p and miR-24-3. The overexpression of miR-25-3p or miR-24-3p resulted in the dampening and period shortening of the PER2::LUC oscillation, while inhibition of either miRNA increased the relative amplitude of the PER2::LUC oscillation. Notably, endogenous miR-25-3p expression in the suprachiasmatic nucleus (SCN) showed no circadian rhythmicity, but the expression levels differed in various brain regions and peripheral tissues. These results suggest that the posttranscriptional regulation of miR-25-3p and miR-24-3p may differ according to Per2 gene expression in different tissue regions. In summary, we found that novel miR-25-3p was involved in fine-tuning circadian rhythmicity by regulating Per2 oscillation at the posttranscriptional level and that it functioned synergistically with miR-24-3p to affect Per2 oscillation.
Independent iron and light limitation in a low-light-adapted Prochlorococcus from the deep chlorophyll maximum
Authors: Hawco Nicholas J , Fu Feixue , Yang Nina , Hutchins David A , John Seth G 
Published: September 2020

Abstract
Throughout the open ocean, a minimum in dissolved iron concentration (dFe) overlaps with the deep chlorophyll maximum (DCM), which marks the lower limit of the euphotic zone. Maximizing light capture in these dim waters is expected to require upregulation of Fe-bearing photosystems, further depleting dFe and possibly leading to co-limitation by both iron and light. However, this effect has not been quantified for important phytoplankton groups like Prochlorococcus, which contributes most of the productivity in the oligotrophic DCM. Here, we present culture experiments with Prochlorococcus strain MIT1214, a member of the Low Light 1 ecotype isolated from the DCM in the North Pacific subtropical gyre. Under a matrix of iron and irradiance matching those found at the DCM, the ratio of Fe to carbon in Prochlorococcus MIT1214 cells ranged from 10–40 × 10−6 mol Fe:mol C and increased with light intensity and growth rate. These results challenge theoretical models predicting highest Fe:C at lowest light intensity, and are best explained by a large photosynthetic Fe demand that is not downregulated at higher light. To sustain primary production in the DCM with the rigid Fe requirements of low-light-adapted Prochlorococcus, dFe must be recycled rapidly and at high efficiency.
A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium,Microcoleus vaginatus
Authors: Nelson Corey , Giraldo-Silva Ana , Garcia-Pichel Ferran 
Published: September 2020

AbstractMicrocoleus vaginatus plays a prominent role as both primary producer and pioneer in biocrust communities from dryland soils. And yet, it cannot fix dinitrogen, essential in often nitrogen-limited drylands. But a diazotroph-rich “cyanosphere” has been described in M. vaginatus, hinting that there exists a C for N exchange between the photoautotroph and heterotrophic diazotrophs. We provide evidence for this by establishing such a symbiosis in culture and by showing that it is selective and dependent on nitrogen availability. In natural populations, provision of nitrogen resulted in loss of diazotrophs from the cyanosphere of M. vaginatus compared to controls, but provision of phosphorus did not. Co-culturing of pedigreed cyanosphere diazotroph isolates with axenic M. vaginatus resulted in copious growth in C and N-free medium, but co-culture with non-cyanosphere diazotrophs or other heterotrophs did not. Unexpectedly, bundle formation in M. vaginatus, diacritical to the genus but not seen in axenic culture, was restored in vitro by imposed nitrogen limitation or, even more strongly, by co-culture with diazotrophic partners, implicating this trait in the symbiosis. Our findings provide direct evidence for a symbiotic relationship between M. vaginatus and its cyanosphere and help explain how it can be a global pioneer in spite of its genetic shortcomings.
Determining dimensionalities and multiplicities of crystal nets
Authors: Gao Hao , Wang Junjie , Guo Zhaopeng , Sun Jian 
Published: September 2020

AbstractLow-dimensional materials have attracted significant attention over the past decade. To discover new low-dimensional materials, high-throughput screening methods for structures with target dimensionality have been applied in different materials databases. For this purpose, the reliability of dimensionality identification is therefore highly important. In this work, we find that the existence of self-penetrating nets may lead to incorrect results by previous methods. Instead of this, we use the quotient graph to analyse the topologies of structures and compute their dimensionalities. Based on the quotient graph, we can calculate not only the dimensionality but also the multiplicity of self-penetrating structures. As a demonstration, we screened the Crystallography Open Database using the method and find hundreds of structures with different dimensionalities and high multiplicities up to 11. Some of the self-penetrating materials may have application values in gas storage, selective catalysis or photocatalysis because of their high gas sorption capacities and various electronic structures.
Tick populations from endemic and non-endemic areas in Germany show differential susceptibility to TBEV
Authors: Liebig Katrin , Boelke Mathias , Grund Domenic , Schicht Sabine , Springer Andrea , Strube Christina , Chitimia-Dobler Lidia , Dobler Gerhard , Jung Klaus , Becker Stefanie 
Published: September 2020

AbstractTick-borne encephalitis virus (TBEV) is endemic in twenty-seven European countries, transmitted via the bite of an infected tick. TBEV is the causative agent of one of the most important viral diseases of the central nervous system (CNS). In Germany, 890 human cases were registered between the years 2018–2019. The castor bean tick, Ixodes ricinus, is the TBEV vector with the highest importance in Central Europe, including Germany. Despite the nationwide distribution of this tick species, risk areas of TBEV are largely located in Southern Germany. To increase our understanding of TBEV-tick interactions, we collected ticks from different areas within Germany (Haselmühl/Bavaria, Hanover/Lower Saxony) and infected them via an in vitro feeding system. A TBEV isolate was obtained from an endemic focus in Haselmühl. In two experimental series conducted in 2018 and 2019, ticks sampled in Haselmühl (TBEV focus) showed higher artificial feeding rates, as well as higher TBEV infections rates than ticks from the non-endemic area (Hanover). Other than the tick origin, year and month of the infection experiment as well as co-infection with Borrelia spp., had a significant impact on TBEV Haselmühl infection rates. Taken together, these findings suggest that a specific adaptation of the tick populations to their respective TBEV virus isolates or vice versa, leads to higher TBEV infection rates in those ticks. Furthermore, co-infection with other tick-borne pathogens such as Borrelia spp. can lower TBEV infection rates in specific populations.
Long-term cognitive impairment after ICU treatment: a prospective longitudinal cohort study (Cog-I-CU)
Authors: Müller Annekatrin , von Hofen-Hohloch Judith , Mende Meinhard , Saur Dorothee , Fricke Christopher , Bercker Sven , Petros Sirak , Classen Joseph 
Published: September 2020

AbstractIn this prospective cohort study we aimed to investigate the trajectory of the cognitive performance of patients after discharge from an intensive care unit (ICU). Special consideration was given to patients with suspected premorbid cognitive impairment who might be at risk for the development of dementia. Clinical characteristics were collected until discharge. The premorbid cognitive state was estimated by a structured interview with a close relative. Cognitive outcome was assessed using the Consortium to Establish a Registry of Alzheimer’s Disease (CERAD) Plus battery and the Stroop Color and Word Test at the time of discharge from ICU and 9 months later. The results of the study group were compared to an established healthy control group and to normative data. A total number of 108 patients were finally included. At the time of discharge, patients underperformed the healthy control group. In linear regression models, delirium during the ICU stay and the factor premorbid cognitive impairment were associated with poorer cognitive outcome (p = 0.047 and p = 0.001). After 9 months, in 6% of patients without evidence of premorbid cognitive impairment long-lasting deficits were found. In patients with suspected premorbid cognitive impairment, performance in tests of executive function failed to improve.
Hepatic lipocalin 2 promotes liver fibrosis and portal hypertension
Authors: Chen Jiegen , Argemi Josepmaria , Odena Gemma , Xu Ming-Jiang , Cai Yan , Massey Veronica , Parrish Austin , Vadigepalli Rajanikanth , Altamirano Jose , Cabezas Joaquin , Gines Pere , Caballeria Juan , Snider Natasha , Sancho-Bru Pau , Akira Shizuo , Rusyn Ivan , Gao Bin , Bataller Ramon 
Published: September 2020

AbstractAdvanced fibrosis and portal hypertension influence short-term mortality. Lipocalin 2 (LCN2) regulates infection response and increases in liver injury. We explored the role of intrahepatic LCN2 in human alcoholic hepatitis (AH) with advanced fibrosis and portal hypertension and in experimental mouse fibrosis. We found hepatic LCN2 expression and serum LCN2 level markedly increased and correlated with disease severity and portal hypertension in patients with AH. In control human livers, LCN2 expressed exclusively in mononuclear cells, while its expression was markedly induced in AH livers, not only in mononuclear cells but also notably in hepatocytes. Lcn2−/− mice were protected from liver fibrosis caused by either ethanol or CCl4 exposure. Microarray analysis revealed downregulation of matrisome, cell cycle and immune related gene sets in Lcn2−/− mice exposed to CCl4, along with decrease in Timp1 and Edn1 expression. Hepatic expression of COL1A1, TIMP1 and key EDN1 system components were elevated in AH patients and correlated with hepatic LCN2 expression. In vitro, recombinant LCN2 induced COL1A1 expression. Overexpression of LCN2 increased HIF1A that in turn mediated EDN1 upregulation. LCN2 contributes to liver fibrosis and portal hypertension in AH and could represent a new therapeutic target.
Visual-reward driven changes of movement during action execution
Authors: Marti-Marca Angela , Deco Gustavo , Cos Ignasi 
Published: September 2020

AbstractMotor decision-making is often described as a sequential process, beginning with the assessment of available options and leading to the execution of a selected movement. While this view is likely to be accurate for decisions requiring significant deliberation, it would seem unfit for choices between movements in dynamic environments. In this study, we examined whether and how non-selected motor options may be considered post-movement onset. We hypothesized that a change in reward at any point in time implies a dynamic reassessment of options, even after an initial decision has been made. To test this, we performed a decision-making task in which human participants were instructed to execute a reaching movement from an origin to a rectangular target to attain a reward. Reward depended on arrival precision and on the specific distribution of reward presented along the target. On a third of trials, we changed the initial reward distribution post-movement onset. Our results indicated that participants frequently change their initially selected movements when a change is associated with an increase in reward. This process occurs quicker than overall, average reaction times. Finally, changes in movement are not only dependent on reward but also on the current state of the motor apparatus.
The structure of first-cousin marriages in Brazil
Authors: Otto Paulo A. , Lemes Renan B. , Farias Allysson A. , Weller Mathias , Lima Shirley O. A. , Albino Victor Alves , Marques-Alves Yanna K. , Pardono Eliete , Bocangel Magnolia A. P. , Santos Silvana 
Published: September 2020

AbstractThis paper deals with the frequency and structure of first-cousin marriages, by far the most important and frequent type of consanguineous mating in human populations. Based on the analysis of large amounts of data from the world literature and from large Brazilian samples recently collected, we suggest some explanations for the asymmetry of sexes among the parental sibs of first-cousin marriages. We suggest also a simple manner to correct the method that uses population surnames to assess the different Wright fixation indexes FIS, FST and FIT taking into account not only alternative methods of surname transmission, but also the asymmetries that are almost always observed in the distribution of sexes among the parental sibs of first-cousins.
Correlated chromosomal periodicities according to the growth rate and gene expression
Authors: Liu Liu , Kurokawa Masaomi , Nagai Motoki , Seno Shigeto , Ying Bei-Wen 
Published: September 2020

AbstractLinking genetic information to population fitness is crucial to understanding living organisms. Despite the abundant knowledge of the genetic contribution to growth, the overall patterns/features connecting genes, their expression, and growth remain unclear. To reveal the quantitative and direct connections, systematic growth assays of single-gene knockoutEscherichia colistrains under both rich and poor nutritional conditions were performed; subsequently, the resultant growth rates were associated with the original expression levels of the knockout genes in the parental genome. Comparative analysis of growth and the transcriptome identified not only the nutritionally differentiated fitness cost genes but also a significant correlation between the growth rates of the single-gene knockout strains and the original expression levels of these knockout genes in the parental strain, regardless of the nutritional variation. In addition, the coordinated chromosomal periodicities of the wild-type transcriptome and the growth rates of the strains lacking the corresponding genes were observed. The common six-period periodicity was somehow attributed to the essential genes, although the underlying mechanism remains to be addressed. The correlated chromosomal periodicities associated with the gene expression-growth dataset were highly valuable for bacterial growth prediction and discovering the working principles governing minimal genetic information.
Electromagnetic surface waves supported by a resistive metasurface-covered metamaterial structure
Authors: Yaqoob M. Z. , Ghaffar A. , Alkanhal Majeed A. S. , Naz M. Y. , Alqahtani Ali H. , Khan Y. 
Published: September 2020

AbstractThis study examines the analytical and numerical solution of electromagnetic surface waves supported by a resistive metasurface-covered grounded metamaterial structure. To simulate the metamaterial, the Kramers–Kronig relation based on the causality principle is used, while the modeling of the resistive metasurface has been done by implementing the impedance boundary conditions. The analytical expressions for the field phasors of surface waves are developed for the transverse magnetic (TM) polarized mode and transverse electric (TE) polarized mode. The characteristic equations are computed for both modes, and the unknown propagation constant is evaluated numerically in the kernel. After computation, the dispersion curves, electric field profiles, effective mode index ($$N_{eff}$$

N

eff

), and phase speeds ($$v_{p}$$

v
p

) are presented for both the TM and TE polarized modes. To study the tunability of surface waves, the influence of the thickness of the metamaterial slab ($$d$$
d
), effective permittivity of the metamaterial ($$\varepsilon_{1}$$

ε
1

), thickness of the resistive metasurface ($$t$$
t
), and effective permittivity of the metasurface ($$\varepsilon_{r}$$

ε
r

) on all the numerical results has been studied. However, the geometrical parameters are found to be more sensitive to the effective mode index ($$N_{eff}$$

N

eff

) and phase speed ($$v_{p}$$

v
p

) of the surface waves. The results are consistent with the published results, which reflects the accuracy of the work. It is concluded that the appropriate choice of parameters can be used to achieve surface waves with the desired characteristics in the GHz range. The present work may have potential applications in surface waveguide design, surface wave speed controllers, surface communication devices, and light trapping configurations.
Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties
Authors: Furukawa Ryutaro , Toma Wakako , Yamazaki Koji , Akanuma Satoshi 
Published: September 2020

AbstractEnzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.
The conservation value of admixed phenotypes in a critically endangered species complex
Authors: Sadanandan Keren R. , Low Gabriel W. , Sridharan Sheeraja , Gwee Chyi Yin , Ng Elize Y. X. , Yuda Pramana , Prawiradilaga Dewi M. , Lee Jessica G. H. , Tritto Anaïs , Rheindt Frank E. 
Published: September 2020

AbstractIn today’s environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.
Automated thermal imaging for the detection of fatty liver disease
Authors: Brzezinski Rafael Y. , Levin-Kotler Lapaz , Rabin Neta , Ovadia-Blechman Zehava , Zimmer Yair , Sternfeld Adi , Finchelman Joanna Molad , Unis Razan , Lewis Nir , Tepper-Shaihov Olga , Naftali-Shani Nili , Balint-Lahat Nora , Safran Michal , Ben-Ari Ziv , Grossman Ehud , Leor Jonathan , Hoffer Oshrit 
Published: September 2020

AbstractNon-alcoholic fatty liver disease (NAFLD) comprises a spectrum of progressive liver pathologies, ranging from simple steatosis to non-alcoholic steatohepatitis (NASH), fibrosis and cirrhosis. A liver biopsy is currently required to stratify high-risk patients, and predicting the degree of liver inflammation and fibrosis using non-invasive tests remains challenging. Here, we sought to develop a novel, cost-effective screening tool for NAFLD based on thermal imaging. We used a commercially available and non-invasive thermal camera and developed a new image processing algorithm to automatically predict disease status in a small animal model of fatty liver disease. To induce liver steatosis and inflammation, we fed C57/black female mice (8 weeks old) a methionine-choline deficient diet (MCD diet) for 6 weeks. We evaluated structural and functional liver changes by serial ultrasound studies, histopathological analysis, blood tests for liver enzymes and lipids, and measured liver inflammatory cell infiltration by flow cytometry. We developed an image processing algorithm that measures relative spatial thermal variation across the skin covering the liver. Thermal parameters including temperature variance, homogeneity levels and other textural features were fed as input to a t-SNE dimensionality reduction algorithm followed by k-means clustering. During weeks 3,4, and 5 of the experiment, our algorithm demonstrated a 100% detection rate and classified all mice correctly according to their disease status. Direct thermal imaging of the liver confirmed the presence of changes in surface thermography in diseased livers. We conclude that non-invasive thermal imaging combined with advanced image processing and machine learning-based analysis successfully correlates surface thermography with liver steatosis and inflammation in mice. Future development of this screening tool may improve our ability to study, diagnose and treat liver disease.