Miracle-dz/UniFAR-FTUs huggingface dataset:
Progress toward heterologous expression of active G‐protein‐coupled receptors in Saccharomyces cerevisiae: Linking cellular stress response with translocation and trafficking

High‐level expression of mammalian G‐protein‐coupled receptors (GPCRs) is a necessary step toward biophysical characterization and high‐resolution structure determination. Even though many heterologous expression systems have been used to express mammalian GPCRs at high levels, many receptors are improperly trafficked or are inactive in these systems. En route to engineering a robust microbial host for GPCR expression, we have investigated the expression of 12 GPCRs in the yeast Saccharomyces cerevisiae, where all receptors are expressed at the mg/L scale. However, only the human adenosine A2a (hA2aR) receptor is active for ligand‐binding and located primarily at the plasma membrane, whereas other tested GPCRs are mainly retained within the cell. Selective receptors associate with BiP, an ER‐resident chaperone, and activated the unfolded protein response (UPR) pathway, which suggests that a pool of receptors may be folded incorrectly. Leader sequence cleavage of the expressed receptors was complete for the hA2aR, as expected, and partially cleaved for hA2bR, hCCR5R, and hD2LR. Ligand‐binding assays conducted on the adenosine family (hA1R, hA2aR, hA2bR, and hA3R) of receptors show that hA2aR and hA2bR, the only adenosine receptors that demonstrate leader sequence processing, display activity. Taken together, these studies point to translocation as a critical limiting step in the production of active mammalian GPCRs in S. cerevisiae.
Mining geographic knowledge using location aware topic model

Most online activities are associated with geographical locations. For example, people write personal blogs about interesting places they have ever been to; read news about important local events; and search the web to find delicious restaurants. Mining geographical knowledge from these online activities can greatly benefit lots of web applications. In this paper, we propose a Location Aware Topic Model (LATM), a probabilistic graphical model, to explicitly model the relationships between locations and words. Experiments on several data sets, including news and blogs, showed satisfactory results.
Simulation of spatiotemporal dynamics of water fluxes in Germany under climate change

In most of Europe, an increase in average annual surface temperature of 0·8 °C is observed, and a further increase is projected. Precipitation tends to increase in northern Europe and decrease in southern Europe, with variable trends in central Europe. The climate scenarios for Germany suggest an increase in precipitation in western Germany and a decrease in eastern Germany, and a shift of precipitation from summer to winter. When investigating the effects of climate change, impacts on water resources are among the main concerns. In this study, the first German‐wide impact assessment of water fluxes dynamics under climate change is presented in a spatially and temporally distributed manner using the state‐of‐the‐art regional climate model, Statistical Regional (STAR) model and the semi‐distributed process‐based eco‐hydrological model, soil and water integrated model (SWIM). All large river basins in Germany (lower Rhine, upper Danube, Elbe, Weser and Ems) are included. A special focus of the study was on data availability, homogeneity of data sets, related uncertainty propagation in the model results and scenario‐related uncertainty. After the model calibration and validation (efficiency from 0·6 to 0·9 in 80% of cases) the water flow components were simulated at the hydrotope level, and the spatial distributions were compared with those in the Hydrological Atlas of Germany. The actual evapotransipration is likely to increase in most parts of Germany, while total runoff generation may decrease in south and east regions. The results for the second scenario period 2051–2060 show that water discharge in all six rivers would be 8–30% lower in summer and autumn compared with the reference period, and the strongest decline is expected for the Saale, Danube and Neckar. Higher winter flow is expected in all of these rivers, and the increase is most significant for the Ems (about 18%). However, the uncertainty of impacts, especially in winter and for high water flows, remains high. Copyright © 2010 John Wiley & Sons, Ltd.
Postnatal Development of Entorhinodentate Projection of the Reeler Mutant Mouse

We anterogradely labeled entorhinodentate axons by the injection of biotin dextran amine into the entorhinal cortex of adult wildtype and reeler mice to clarify whether the course and terminal endings of the reeler entorhinal projection are normal or not. We found that in the reeler mouse, biotin dextran amine-labeled entorhinodentate fibers arising from the entorhinal cortex curved around the hippocampal fissure instead of crossing it, whereas in the wildtype mouse, they crossed the fissure as a perforant pathway. Next, we examined carbocyanine dye (DiI) labeling of the immature entorhinodentate projection and the developmental changes of the hippocampal fissure during early postnatal days based on the laminin and glial fibrillary acidic protein (GFAP) immunohistochemistry. Injection of DiI into the entorhinal area of the wildtype and reeler mice at postnatal day 1 resulted in anterograde labeling of pioneer axons passing through the hippocampal fissure. However, follower axons could not penetrate through the hippocampal fissure in reeler mice, whereas in the normal controls, many DiI-labeled axons continued to pass through the fissure. GFAP immunohistochemistry demonstrated that GFAP-immunopositive astrocytes were abundant along the hippocampal fissure both in the wildtype and reeler mice at birth. In the wildtype mouse, GFAP-positive neurons nearby the fissure were decreasing in number during the early postnatal days, whereas in the reeler mouse, many GFAP-positive astrocytes were continuing to accumulate there. This barrier made of astrocytes in the reeler mouse may obstruct the ingrowth of the follower axons arising from the entorhinal cortex through the hippocampal fissure, resulting in the abnormal course of the entorhinodentate axons in this mutant.
Comparison of fixed- and moving-vessel flow measurements with an aDp in a large river

A comparison of three-dimensional flow velocity measurements, made with an acoustic Doppler profiler (aDp) from fixed and moving vessels at cross sections of the Parana River, Argentina, was performed. The purpose was to design a rapid and reliable procedure for quantifying the velocity field, and related parameters such as bed shear velocity and the identification of secondary circulations, in large rivers using an aDp. The fixed-vessel measurements were performed over a period of 10 min at three vertical profiles along two of the sections. These data were then compared with the results of ten moving-vessel repeat transects made at each of the sections, and which intersected the fixed-vessel sampling locations, using a number of different aDp setup configurations. From the velocity profiles obtained with both fixed- and moving-vessel measurements, total bed shear velocity values were computed by applying the law-of-the-wall. The results indicate there can be significant differences between velocities obtained using the moving-vessel method and fixed-vessel measurements averaged over 10 min. These differences in horizontal velocity can be significantly reduced by averaging five, or more, moving-vessel transects, with corresponding shear velocities calculated from five-transect averages showing differences ranging between 10 and 15%, dependent on the aDp configuration. Location of the at-a-point vertical velocity profile in relation to large-scale bed roughness may also be an influential factor, and ideally the bed morphology should be quantified together with the aDp-derived velocities. When using the aDp to identify secondary flow cells, it was found that although one cross-section transect can provide a reasonable overall picture, an average of five cross sections is necessary to resolve the finer details of flow. The implications for applications that use moving-vessel techniques for measurement and analysis of three-dimensional flow structures, including secondary flows, are highlighted.
A Comparative Study of Divergence Cleaning Methods of Magnetic Field in the Solar Coronal Numerical Simulation

This paper presents a comparative study of divergence cleaning methods of magnetic field in the solar coronal three-dimensional numerical simulation. For such purpose, the diffusive method, projection method, generalized Lagrange multiplier method and constrained-transport method are used. All these methods are combined with a finite-volume scheme based on a six-component grid system in spherical coordinates. In order to see the performance between the four divergence cleaning methods, solar coronal numerical simulation for Carrington rotation 2056 has been studied. Numerical results show that the average relative divergence error is around $10^{-4.5}$ for the constrained-transport method, while about $10^{-3.1}- 10^{-3.6}$ for the other three methods. Although there exist some differences in the average relative divergence errors for the four employed methods, our tests show they can all produce basic structured solar wind.
Thematic proto-roles and argument selection

As a novel attack on the perennially vexing questions of the theoretical status of thematic roles and the inventory of possible roles, this paper defends a strategy of basing accounts of roles on more unified domains of linguistic data than have been used in the past to motivate roles, addressing in particular the problem of ARGUMENT SELECTION (principles determining which roles are associated with which grammatical relations). It is concluded that the best theory for describing this domain is not a traditional system of discrete roles (Agent, Patient, Source, etc.) but a theory in which the only roles are two cluster-concepts called PROTO-AGENT and PROTO-PATIENT, each characterized by a set of verbal entailments: an argument of a verb may bear either of the two proto-roles (or both) to varying degrees, according to the number of entailments of each kind the verb gives it. Both fine-grained and coarse-grained classes of verbal arguments (corresponding to traditional thematic roles and other classes as well) follow automatically, as do desired 'role hierarchies'. By examining occurrences of the 'same' verb with different argument configurations—e.g. two forms of psych predicates and object-oblique alternations as in the familiar spray/load class—it can also be argued that proto-roles act as defaults in the learning of lexical meanings. Are proto-role categories manifested elsewhere in language or as cognitive categories? If so, they might be a means of making grammar acquisition easier for the child, they might explain certain other typological and acquisitional observations, and they may lead to an account of contrasts between unaccusative and unergative intransitive verbs that does not rely on deriving unaccusatives from underlying direct objects.
Paleoclimate of the Southern Adriatic Sea region during the ‘Medieval Climate Anomaly’ reflected by organic walled dinoflagellate cysts

To obtain insight into the character and forcing of southern Italian climate change during the ‘Medieval Climate Anomaly’ (c. ad 900–1200), marine sediments deposited between ad 990 and 1200 from the Gulf of Taranto have been analyzed for their dinoflagellate cyst content with a 3.5 yr resolution. The reconstructed sea surface temperature (SST) appears to be lower than today. We observe a clear 11.4 yr cyclicity in the reconstructed SST series. Furthermore, there is a good matching between SST and global 14C anomalies. This suggests that solar activity might have had an important influence on the local climate during Medieval time. Short-term fluctuations in accumulation rates of aerobic degradation resistant species that react sensitively on the trophic state of the upper waters and/or are characteristic for river plume waters indicate that the trophic state of the upper waters is closely linked to river discharge, which in turn is strongly related to precipitation in Italy. We reconstruct low river discharge/precipitations in the Adriatic area synchronous to widespread drought events in other nearby subtropical regions. We attribute this to NAO and ENSO related large-scale ocean–atmosphere circulation shifts during the Medieval period. Furthermore, we suggest that eruptions of southern Italian volcanoes might have influenced the local upper water nutrient conditions as well.
Characterising Faults in Aspect-Oriented Programs: Towards Filling the Gap Between Theory and Practice

Since the proposal of Aspect-Oriented Programming, several candidate fault taxonomies for aspect-oriented (AO) software have been proposed. Such taxonomies, however, generally rely on language features, hence still requiring practical evaluation based on realistic implementation scenarios. The current lack of available AO systems for evaluation as well as historical data are the two major obstacles for this kind of study. This paper quantifies, documents and classifies faults uncovered in several releases of three AO systems, all from different application domains. Our empirical analysis naturally led us to revisit and refine a previously defined fault taxonomy. We identified particular fault types that stood out amongst the categories defined in the taxonomy. Besides this, we illustrate recurring faulty scenarios extracted from the analysed systems. We believe such scenarios should be considered for the establishment of testing strategies along the software development process.
Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 104 in A. schaeriana and 6.26 x 103 in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.
Snow cover and snowmelt of an extensive High Arctic wetland: spatial and temporal seasonal patterns

Abstract This study examined the end-of-winter snow storage, its distribution and the spatial and temporal melt patterns of a large, low gradient wetland at Polar Bear Pass, Bathurst Island, Nunavut, Canada. The project utilized a combination of field observations and a physically-based snowmelt model. Topography and wind were the major controls on snow distribution in the region, and snow was routinely scoured from the hilltop regions and deposited into hillslopes and valleys. Timing and duration of snowmelt at Polar Bear Pass were similar in 2008 and 2009. The snowmelt was initiated by an increase in air temperature and net radiation receipt. Inter-annual variability in spatial snowmelt patterns was evident at Polar Bear Pass and was attributed to a non-uniform snow cover distribution and local microclimate conditions. In situ field studies and modelling remain important in High Arctic regions for assessing wetland water budgets and runoff, in addition to model parameterization and validation of satellite imagery. Editor Z.W. Kundzewicz Citation Assini, J. and Young, K.L. , 2012. Snow cover and snowmelt of an extensive High Arctic wetland: spatial and temporal seasonal patterns. Hydrological Sciences Journal, 57 (4), 738–755.
Influence of the discontinuation of a school-based, supervised fluoride mouthrinsing programme on the prevalence of dental caries.

OBJECTIVE Since 1984 a weekly supervised fluoride mouthrinsing programme has been implemented for schoolchildren in Hisayama, Japan. Consequently, four years after the start of the programme the DMFT index for 12.5-year-old schoolchildren in Hisayama decreased to a value of less than 3.0. However, since 1992 it has increased. The purpose of this study was to investigate the causes of this increasing prevalence of dental caries since 1992. PARTICIPANTS One hundred and one schoolchildren aged 12 years in 1994 were selected. This age group showed the highest increase in the prevalence of dental caries in that year. OUTCOME MEASURES Children who had discontinued the use of fluoride mouthrinse for one year or more were identified by means of a confidential questionnaire. Oral examination was carried out, by three examiners, under a suitable artificial light using a mirror and an explorer. RESULTS The DMFT and DMFS indices of the continuous mouthrinsing (CM) group were significantly lower than those of the discontinuous mouthrinsing (DM) group (P < 0.001). Significant differences between the CM and DM groups were also observed in the DMFT rates for premolars (P < 0.05) and for the first molar (P < 0.001). CONCLUSIONS The continuation of fluoride mouthrinsing for children of school age was important in achieving the advantages of the programme in Hisayama.
Clustering by Plasma Lipoprotein Profile Reveals Two Distinct Subgroups with Positive Lipid Response to Fenofibrate Therapy

Fibrates lower triglycerides and raise HDL cholesterol in dyslipidemic patients, but show heterogeneous treatment response. We used k-means clustering to identify three representative NMR lipoprotein profiles for 775 subjects from the GOLDN population, and study the response to fenofibrate in corresponding subgroups. The subjects in each subgroup showed differences in conventional lipid characteristics and in presence/absence of cardiovascular risk factors at baseline; there were subgroups with a low, medium and high degree of dyslipidemia. Modeling analysis suggests that the difference between the subgroups with low and medium dyslipidemia is influenced mainly by hepatic uptake dysfunction, while the difference between subgroups with medium and high dyslipidemia is influenced mainly by extrahepatic lipolysis disfunction. The medium and high dyslipidemia subgroups showed a positive, yet distinct lipid response to fenofibrate treatment. When comparing our subgroups to known subgrouping methods, we identified an additional 33% of the population with favorable lipid response to fenofibrate compared to a standard baseline triglyceride cutoff method. Compared to a standard HDL cholesterol cutoff method, the addition was 18%. In conclusion, by using constructing subgroups based on representative lipoprotein profiles, we have identified two subgroups of subjects with positive lipid response to fenofibrate therapy and with different underlying disturbances in lipoprotein metabolism. The total subgroup with positive lipid response to fenofibrate is larger than subgroups identified with baseline triglyceride and HDL cholesterol cutoffs.
Nivolumab-induced vitiligo successfully treated with narrowband UVB phototherapy

Figure 1. A) Multiple asymmetric bluish-grey macules on the abdomen, with close-up view. B) Histological examination reveals an empty cavity, where presumably the needle had been inserted, surrounded by fibrous tissue. Dark pigmented granules are deposited along the lining of the cavity wall and walls of blood vessels (inset). Plain radiograph of the neck (C) and three-dimensional computed tomography (CT) of the lower trunk (D) showing numerous embedded acupuncture needles aggregated in the uterus, corresponding to the site of a myoma. E) Plain chest CT imaging reveals several needles in the right ventricle (encircled by yellow arrows) and outside the thorax (red arrows). One needle appears to reach the apex of the left ventricle from outside the thorax (blue arrow) and into the pulmonary artery ([F]; red arrow). Elementary analysis of the cutaneous biopsy specimens using energy dispersive X-ray spectrometry led to the detection of silver (G).
The Late Quaternary Flow through the Bering Strait Has Been Forced by the Southern Ocean Winds

Because North and South America are surrounded by water, they constitute together a gigantic island whose peripheral sea level is controlled by the winds east of the island, winds along the western boundary of the island, the freshwater flux, and the meridional overturning cell. This idea has been expressed in several articles where a series of analytical models show that the Bering Strait (BS) flow is controlled by the interplay of the Southern Winds (sometimes referred to as the ‘‘Subantarctic Westerlies’’), and the North Hemisphere freshwater flux. Here, the authors report a paleoceanographic analysis of proxies in the BS as well as the Southern Ocean, which clearly support the above through employment of a slowly varying time-dependent version of the coupled Sandal–Nof model. This study shows a very strong correlation between the Southern Ocean winds and the BS flow. A midHolocene weakening of the Southern Winds followed by the cession of freshwater fluxes from the melting Laurentide ice sheet strengthened the BS flow for several thousand years. Increasing the Southern Winds enhances the near surface, cross-equatorial flow from the Southern Ocean to the Northern Hemisphere. This cross-equatorialflowdecreasestheArcticoutflowintotheAtlanticdemonstratingadynamiclinkagebetween the Southern Ocean Winds and the mean flow through the BS.
Controlled electromagnetic sources for measuring electrical conductivity beneath the oceans: 1. Forward problem and model study

Exact closed-form expressions for the electromagnetic induction fields produced by vertical and horizontal current sources in the conducting ocean overlying a one-dimensional earth are derived from the Maxwell equations. Numerical methods for the evaluation of the solutions are given, including correction for the finite size of real sources. Simple models of the electrical conductivity structure of the ocean crust and lithosphere are deduced from geologic, petrologic, and laboratory data, and their electromagnetic response is modeled. Horizontal electric dipole sources produce much larger field amplitudes than their vertical counterparts for a given frequency and range, and the horizontal electric field offers superior received signal performance. Reflections of electromagnetic waves from the sea surface and thermocline must be considered for low enough frequencies or long ranges. Estimates of the ambient noise level from natural electromagnetic sources in the frequency range 0.01–10 Hz are presented. The ability of controlled sources to determine features of the conductivity of the ocean crust and upper mantle, especially low conductivity zones, is demonstrated. If the mantle conductivity is low enough, horizontal ranges of 50 km and conductivity estimates to over 20 km depth can be achieved.