Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentially expressed lncRNAs and miRNAs with associated ceRNA networks in aged mice with postoperative cognitive dysfunction

Postoperative cognitive dysfunction (POCD) is a common postoperative complication observed in elderly patients. Using microarray analyses, we comprehensively compared long non-coding RNA (lncRNA), messenger RNA (mRNA), and microRNA (miRNA) expression profiles in hippocampal tissues from a mouse model of POCD and control mice. A total of 175 lncRNAs, 117 mRNAs, and 26 miRNAs were differentially expressed between POCD and control mice. Gene ontology (GO) and KEGG pathway enrichment analyses were performed to explore the principal functions of dysregulated genes. Correlated coding-noncoding co-expression (CNC) and competing endogenous RNA (ceRNA) expression networks were constructed using bioinformatics methods. lncRNA NONMMUT000708 correlated positively with expression of the inflammation-related gene Hif3a. lncRNAs NONMMUT043249 and NONMMUT028705 mediated gene expression by binding the transcription factor cAMP response element-binding protein (CREB). The constructed ceRNA network suggested lncRNA NONMMUT055714 binds competitively with miR-7684-5p, increasing expression of its target gene, Sorl1. Finally, eight dysregulated lncRNAs, four miRNAs, and ten mRNAs were confirmed via quantitative real-time polymerase chain reaction (PCR) in 10 POCD-healthy mouse paired samples. These results suggest that lncRNAs and miRNAs are involved in POCD pathogenesis and progression. Our ceRNA network will improve understanding of lncRNA-mediated ceRNA regulatory mechanisms operating during the pathogenesis of POCD.
LATE SPECTRAL EVOLUTION OF THE EJECTA AND REVERSE SHOCK IN SN 1987A

We present observations with the Very Large Telescope and Hubble Space Telescope (HST) of the broad emission lines from the inner ejecta and reverse shock of SN 1987A from 1999 February until 2012 January (days 4381–9100 after explosion). We detect broad lines from Hα, Hβ, Mg i], Na i, [O i], [Ca ii], and a feature at ∼9220 Å. We identify the latter line with Mg ii λλ9218, 9244, which is most likely pumped by Lyα fluorescence. Hα and Hβ both have a centrally peaked component extending to ∼4500 km s−1 and a very broad component extending to ≳ 11, 000 km s−1, while the other lines have only the central component. The low-velocity component comes from unshocked ejecta, heated mainly by X-rays from the circumstellar environment, whereas the very broad component comes from faster ejecta passing through the reverse shock, created by the collision with the circumstellar ring. The flux in Hα from the reverse shock has increased by a factor of four to six from 2000 to 2007. After that there is a tendency of flattening of the light curve, similar to what may be seen in the optical lines from the shocked ring. The core component seen in Hα, [Ca ii], and Mg ii has experienced a similar increase, which is consistent with that found from HST photometry. The energy deposition of the external X-rays is calculated using explosion models for SN 1987A and we predict that the outer parts of the unshocked ejecta will continue to brighten because of this. The external X-ray illumination also explains the edge-brightened morphology of the ejecta seen in the HST images. We finally discuss evidence for dust in the ejecta from line asymmetries.
RSS-eye: Human-assisted indoor localization without radio maps

The pervasive diffusion of smartphones is boosting indoor positioning solutions and location-based services. We propose a novel methodology to perform indoor positioning of mobile users by the estimation of angles of arrival from access points whose locations are known. Angles of arrival are estimated by correlating WiFi RSSI measurements with data coming from a digital compass, which is provided by most current handsets. Our system has minimal requirements in terms of infrastructure and mobile hardware. The system neither needs calibration, nor radio maps but requires the user to perform a gesture when an estimation is needed. The resulting on-demand localization has advantages in terms of privacy and power efficiency. Initial experimental results, even under severe multipath conditions, show good accuracy in terms of angle of arrival estimation and promising results on localization.
Distributed under Creative Commons Cc-by 4.0 Mirmod: a Tool for Identification and Analysis of 5 ′ and 3 ′ Mirna Modifications in next Generation Sequencing Small Rna Data

In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5 ′ and 3 ′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at
Physical performance of elite and subelite Spanish female futsal players

The aim of this study was to determine the parameters distinguishing top female futsal players from lower level players. Twenty-seven female futsal players participated in the study, composed of professional first division (elite; n = 15) players and semi-professional second division players (sub-elite; n = 14). Active and passive straight leg raise tests, isokinetic strength of the knee extensor and flexor muscles at 60° · s-1 angular velocity, squat and counter movement jumps, 30 m sprint, 30 m agility, repeated sprint ability test and maximum ball speed during shooting were measured. The elite players were more agile and kicked harder than sub-elite players in maximum ball speed during the shooting test (P ≤ 0.05). However, no significant differences between teams were observed in active and passive hamstring flexibility, jumping ability, repeated sprint ability test, 30 m sprint time, H/Q ratio and absolute and relative torque from 60° · s-1 angular velocity. Based on these findings we conclude that agility and maximum ball speed during shooting may be important determinant factors of Spanish female futsal actions and could distinguish ability at high-level games.
CMOS Humidity Sensor System Using Carbon Nitride Film as Sensing Materials

An integrated humidity sensor system with nano-structured carbon nitride film as humidity sensing material is fabricated by a 0.8 μm analog mixed CMOS process. The integrated sensor system consists of differential humidity sensitive field effect transistors (HUSFET), temperature sensor, and operational amplifier. The process contains two poly, two metal and twin well technology. To form CNx film on Si3N4/Si substrate, plasma etching is performed to the gate area as well as trenches. CNx film is deposited by reactive RF magnetron sputtering method and patterned by the lift-off technique. The drain current is proportional to the dielectric constant, and the sensitivity is 2.8 μA/%RH.
Effect of insemination regimen on embryo production in superovulated cows

Three experiments tested the effects of six insemination regimens on embryo production in superovulated cows. One, two or three inseminations with one unit of semen at each time produced the same percentage fertilised (74, 68 and 74 per cent, P = 0.673) and the same number of fertilised embryos (8.2, 6.3 and 9.1, P = 0.136). However, the one and two inseminations group had less transferable (P = 0.008) and total (P = 0.051) embryos (3.9/9.6 and 3.9/8.9) than the three inseminations group (6.8/13.2). The percentage transferable remained the same (42, 45 and 58 per cent, P = 0.161). When two units of semen were used at the first or middle insemination and one, two and three inseminations were compared, the percentage fertilised (65, 77 and 77 per cent, P = 0.082) and the number fertilised (7.0, 7.4 and 8.6, P = 0.565) were again the same but the number (P = 0.047) and percentage transferable (P = 0.000) increased between the one and two inseminations (3.8 vs 5.7 and 30 per cent vs 54 per cent). The increase in transferable embryos with multiple inseminations could not be explained physiologically, but is of concern since transferable embryos are the "sales product' of superovulation. Two inseminations with one unit of semen was as effective as two inseminations with three units of semen, in terms of percentage fertilised (68 and 70 per cent, P = 0.762), number fertilised (10.3 and 8.3, P = 0.582), transferable embryos (6.7 and 5.7 P = 0.532), percentage transferable (44 and 46 per cent, P = 0.737) and total embryos recovered (14.8 and 12.7, P = 0.54). (ABSTRACT TRUNCATED AT 250 WORDS)
Comparison and evaluation of dust detection algorithms using MODIS Aqua/Terra Level 1B data and MODIS/OMI dust products in the Middle East

Dust storms have a major impact on air quality, economic loss, and human health over large regions of the Middle East. Because of the broad extent of dust storms and also political–security issues in this region, satellite data are an important source of dust detection and mapping. The aim of this study was to compare and evaluate the performance of five main dust detection algorithms, including Ackerman, Miller, normalized difference dust index (NDDI), Roskovensky and Liou, and thermal-infrared dust index (TDI), using MODIS Level 1B and also MODIS Deep Blue AOD and OMI AI products in two dust events originating from Iraq and Saudi Arabia. Overall, results showed that the performance of the algorithms varied from event to event and it was not possible to use the published dust/no-dust thresholds for the algorithms tested in the study area. The MODIS AOD and OMI AI products were very effective for initial dust detection and the AOD and AI images correlated highly with the dust images at provincial scale (p-value <0.001), but the application of these products was limited at local scale due to their poor spatial resolution. Results also indicated that algorithms based on MODIS thermal infrared (TIR) bands or a combination of TIR and reflectance bands were better indicators of dust than reflectance-based ones. Among the TIR- based algorithms, TDI performed the best over water surfaces and dust sources, and accounted for approximately 93% and 90% of variations in the AOD and OMI AI data.
The Contribution of Tidal Fluvial Habitats in the Columbia River Estuary to the Recovery of Diverse Salmon ESUs

Abstract : The 2008 Biological Opinion on Operation of the Federal Columbia River Power System established estuary restoration goals for ten-year survival improvements of 9% for ocean-type and 6% for stream-type ESUs. To support these goals, a qualitative assessment process (Columbia River Estuary Recovery Plan Module) was devised to identify limiting factors and to prioritize estuary restoration actions based on their presumed survival benefits. The method ranks the potential benefits of various restoration projects based on published results and professional judgments about their relative effectiveness. Empirical estimates of survival benefits are unavailable, however, and the actual contributions of single or cumulative estuary actions to the survival goals in the Biological Opinion are unknown. Today scores of wetland restoration projects have been undertaken in the estuary as a method to recover at-risk salmon populations throughout the Columbia River basin, based in part on the latest information about the estuary s role as a productive nursery ground for juvenile salmon (Bottom et al. 2005; 2008; 2011; Roegner et al. 2008; 2010; 2012; Johnson et al. 2011). Recent genetic data collected in the estuary have shown evidence of important stock-specific differences in estuarine habitat use (Bottom et al. 2008; Teel et al. 2009) that have not been considered in the selection or design of restoration projects. Moreover, the population response to estuary restoration remains poorly understood because Research, Monitoring, and Evaluation (RME) programs have focused exclusively on the performance of estuarine-rearing juveniles rather than their ultimate contribution to adult returns.
Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution

The process by which some eukaryotic organelles, for example the endomembrane system, evolved without endosymbiotic input remains poorly understood. This problem largely arises because many major cellular systems predate the last common eukaryotic ancestor (LCEA) and thus do not provide examples of organellogenesis in progress. A model is emerging whereby gene duplication and divergence of multiple “specificity-” or “identity-” encoding proteins for the various endomembranous organelles produced the diversity of nonendosymbiotically derived cellular compartments present in modern eukaryotes. To address this possibility, we analyzed three molecular components of the endocytic membrane-trafficking machinery. Phylogenetic analyses of the endocytic syntaxins, Rab 5, and the β-adaptins each reveal a pattern of ancestral, undifferentiated endocytic homologues in the LCEA. Subsequently, these undifferentiated progenitors independently duplicated in widely divergent lineages, convergently producing components with similar endocytic roles, e.g., β1 and β2-adaptin. In contrast, β3, β4, and all other adaptin complex subunits, as well as paralogues of the syntaxins and Rabs specific for the other membrane-trafficking organelles, all evolved before the LCEA. Thus, the process giving rise to the differentiated organelles of the endocytic system appears to have been interrupted by the major speciation event that produced the extant eukaryotic lineages. These results suggest that although many endocytic components evolved before the LCEA, other major features evolved independently and convergently after diversification into the primary eukaryotic supergroups. This finding provides an example of a basic cellular system that was simpler in the LCEA than in many extant eukaryotes and yields insight into nonendosymbiotic organelle evolution.
Stimulators of AMP‐activated kinase (AMPK) inhibit seawater‐ but not cAMP‐induced oocyte maturation in a marine worm: Implications for interactions between cAMP and AMPK signaling

Previous studies have shown that elevations in intraoocytic cAMP prevent mammalian oocytes from maturing, whereas cAMP degradation allows these oocytes to begin maturation, as evidenced by the onset of oocyte nuclear disassembly (=“germinal vesicle breakdown”, GVBD). Moreover, such cAMP degradation not only reduces cAMP levels but also generates AMP, which in turn can stimulate AMP‐activated kinase (AMPK), a well‐documented inducer of GVBD in mice. Alternatively, in some marine invertebrates, intraoocytic cAMP triggers, rather than blocks, GVBD, and whether AMPK up‐ or downregulates maturation in these species has not been tested. Thus, AMPK was monitored in the nemertean worm Cerebratulus during GVBD stimulated by seawater (SW) or cAMP elevators. In oocytes lacking surrounding follicle cells, AMPK activity was initially elevated in immature oocytes but subsequently reduced during SW‐ or cAMP‐induced GVBD, given that the catalytic α‐subunit of AMPK in maturing oocytes displayed a decreased stimulatory phosphorylation at T172 and an increased inhibitory phosphorylation at S485/491. Accordingly, AMPK‐mediated phosphorylation of acetyl‐CoA carboxylase, a known target of active AMPK, also declined during maturation. Moreover, treatments with either ice‐cold calcium‐free seawater (CaFSW) or AMPK agonists dissolved in SW maintained AMPK activity and inhibited GVBD. Conversely, adding cAMP elevators to CaFSW‐ or SW‐solutions of AMPK activators restored GVBD while promoting S485/491 phosphorylation and AMPK deactivation. Collectively, such findings not only demonstrate for the first time that intraoocytic AMPK can block GVBD in the absence of surrounding follicle cells, but these results also provide evidence for a novel GVBD‐regulating mechanism involving AMPK deactivation by cAMP‐mediated S485/491 phosphorylation. Mol. Reprod. Dev. 77: 497–510, 2010. © 2010 Wiley‐Liss, Inc.
IL-2 reverses established type 1 diabetes in NOD mice by a local effect on pancreatic regulatory T cells

Regulatory T cells (T reg cells) play a major role in controlling the pathogenic autoimmune process in type 1 diabetes (T1D). Interleukin 2 (IL-2), a cytokine which promotes T reg cell survival and function, may thus have therapeutic efficacy in T1D. We show that 5 d of low-dose IL-2 administration starting at the time of T1D onset can reverse established disease in NOD (nonobese diabetic) mice, with long-lasting effects. Low-dose IL-2 increases the number of T reg cells in the pancreas and induces expression of T reg cell–associated proteins including Foxp3, CD25, CTLA-4, ICOS (inducible T cell costimulator), and GITR (glucocorticoid-induced TNF receptor) in these cells. Treatment also suppresses interferon γ production by pancreas-infiltrating T cells. Transcriptome analyses show that low-dose IL-2 exerts much greater influence on gene expression of T reg cells than effector T cells (T eff cells), suggesting that nonspecific activation of pathogenic T eff cells is less likely. We provide the first preclinical data showing that low-dose IL-2 can reverse established T1D, suggesting that this treatment merits evaluation in patients with T1D.
Fin-Width Dependence of Ionizing Radiation-Induced Subthreshold-Swing Degradation in 100-nm-Gate-Length FinFETs

The dependence of the subthreshold-swing (SS) degradation on fin width is reported for irradiated 100-nm-gate- length, fully depleted n -channel FinFETs. The wider the fin is, the greater the radiation-induced SS degradation. The higher tolerance to radiation-induced charge for the narrower FinFETs is attributed to the additional lateral gate control over the body potential. The irradiation and room temperature annealing results suggest that the SS increase for wider FinFETs is due primarily to nonuniform trapped charge in the buried oxide (BOX). The subthreshold characteristics of FinFETs with two fins are more likely to exhibit a nonuniform subthreshold slope (NUSS), resulting from fin-to-fin variability, than FinFETs with 20 fins, where the corresponding Id -V gs curve is the composite of the 20 individual Id-V gs curves.
Mixing in numerical models of mantle convection incorporating plate kinematics

The process by which subducted lithosphere is mixed by mantle convection is investigated in numerical calculations. The results show that the observed isotopic heterogeneity of mantle sources and their ancient (1-2 b.y.) apparent ages are consistent with convective mixing. Passive tracers, which are introduced below "trenches," are efficiently dispersed, but nonetheless, heterogeneities in tracer density with a large range of length scales are observed to persist for 40 or more transit times (one transit time is the time to travel the fluid depth with the boundary velocity). In particular, there is a strong tendency to form high-density folds of the tracer strings, which persist much longer than simple shearing indicates. The folds persist because there is a strong tendency for material that enters the flow at the margins of cells to be transferred to adjacent cells, where it is "unmixed. " When the simulations are scaled to the whole mantle, the tight clumps (folds) of tracers are shown to persist for up to 1-2 b . y. There is also a tendency for large-scale convection cells to remain isolated from recycled material for 1-2 b.y. These results are consistent with the significant chemical heterogeneity of the mantle as revealed by isotopic studies of oceanic basalts. Despite the spatial heterogeneity in tracer density, the average time tracers remain in the box from subduction at trenches to sampling at ridges (i.e., the residence time) is well constrained and within 20% of the mean residence time expected from an analytic model in which tracers are assumed to be sampled randomly. Model ages of the mantle that explicitly incorporate increased convection rates in the past and assume random sampling of heterogeneities bracket the - 2 b.y. apparent Pb-Pb and Rb-Sr isochrons of midocean ridge basalts and oceanic island basalts. The conclusion of persistent spatial heterogeneity is different from the conclusions drawn from other studies. The different conclusions result, primarily, from our emphasis on the details of spatial variations as opposed to some average of the mixing, from a difference in flow unsteadiness, and from the different ways tracers have been introduced into the flow.
Gravity survey in the central ranges, Honshu, Japan

An extensive gravity survey was carried out from 1978 through 1980 in the area of the Central Ranges (Japan Alps), Honshu, which consist of the three largest mountain ranges in Japan (Hida, Akaishi, and Kiso). The Central Ranges area of 40, 000km2 has provided about 3, 700 gravity data including 2, 214 newly measured data, from which a Bouguer anomaly map was drawn. Bouguer and terrain corrections were made with a topographic data file of 230×280m2 grid at a distance of up to 80km from any measuring point, taking the earth's sphericity into account. A value of 2.64g/cm3 was used for the average density of surface features, and this was derived from the observed gravity data using a newly proposed least-squares method. The possible errors involved in the analysis were critically evaluated. The newly drawn anomaly map has an overall accuracy of 5mgal (=5×10-5m·sec-2). The Central Ranges area is known as a broad zone of strong negative anomaly, which has now been resolved into two parts, one along the axis of the Hida mountain range and the other along the northern Fossa Magna. Bouguer anomaly and topography are correlated negatively in the Hida range, marginally in the Akaishi range and positively in the Kiso range, suggesting that the correlation becomes progressively negative with increasing massiveness of mountain structure. The Central Ranges are bounded by the Itoigawa-Shizuoka Tectonic Line to the east and by the Atera fault to the southwest across which the regional Bouguer anomaly pattern changes sharply. The Atera fault is a firstclass active fault along which a narrow but very clear Bouguer low is observed that may be attributable to fault gouge material.