Miracle-dz/UniFAR-FTUs huggingface dataset:
Over-exploitation of an alluvial aquifer in Gujarat, India

Abstract Over-exploitation of an alluvial aquifer in India has occurred since tubewells were drilled into deeper aquifers. Field information concerning-the fall in both the water table and the piezometric heads in the deeper aquifers has been examined and a numerical model has been developed to represent a heavily exploited area. Predictions using the model suggest that the annual declines in the water table and the piezometric heads are accelerating as the water table moves into a zone having a lower specific yield. Careful monitoring of the movement of the water table is proposed.
A revision of the “African Non-Spiny” Clade of Solanum L. (Solanum sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Lyciosolanum Bitter, Macronesiotes Bitter, and Quadrangulare Bitter: Solanaceae)

Abstract The African Non-Spiny (ANS) clade contains 14 species of mostly large canopy lianas or scandent shrubs confined to Madagascar (10) and continental Africa (4, with with one species reaching the southern Arabian peninsula). Members of the clade were previously classified in sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Macronesiotes Bitter and Quadrangulare Bitter, and were throught to be related to a variety of New World groups. The group is an early-branching lineage of non-spiny solanums and characters shared with other vining New World solanums are homoplastic. The 14 species of the group occupy a wide range of habitats, from wet forests in western Africa to savanna and dry forests of southern Madagascar and dune habitats in South Africa. Many members of the group are highly variable morphologically, and habit can vary between shrub and canopy vine in a single locality. We here review the taxonomic history, morphology, potential relationships and ecology of these species; we provide keys for their identification, descriptions, full synonymy (including designations of lectotypes and neotypes) and nomenclatural notes. Illustrations, distribution maps and preliminary conservation assessments are provided for all species.
Spatial distribution of δD-δ18O values of surface and shallow groundwaters from Japan, south Korea and east China

Spatial distribution of δD and δ18O values of surface water and shallow groundwaters from Japan, south Korea and east China was mapped with contours of 10 and 1‰ intervals for δD and δ18O, respectively, on the basis of the data base including more than 600 analyses made in the present and previous studies. The δD and δ18O values generally decrease with increasing the latitude. There is a systematic decrease in δD and δ18O values with contours of close intervals from the coast toward inland of southwestern Japan along the stream of the Kuroshio, a warm current in the Pacific Ocean. The δD and δ18O lows are observed in mountainous inland of central and northern Japan and east China. The trends are comparable with those observed previously for the North American continent. The map will provide fundamental information for the studies of geochemical processes such as hydrology, water-rock interaction, and precipitation of authigenic minerals in which meteoric water is involved.
glacial-interglacial Co2 change : the iron hypothesis

Several explanations for the 200 to 280 ppm glacial/interglacial change in atmospheric CO2 concentrations deal with variations in southern ocean phytoplankton productivity and the related use or nonuse of major plant nutrients. An hypothesis is presented herein in which arguments are made that new productivity in today's southern ocean (7.4 × 1013g yr−1) is limited by iron deficiency, and hence the phytoplankton are unable to take advantage of the excess surface nitrate/phosphate that, if used, could result in total southern ocean new production of 2−3 × 1015 g C yr−1. As a consequence of Fe-limited new productivity, Holocene interglacial CO2 levels (preindustrial) are as high as they were during the last interglacial (≈ 280 ppm). In contrast, atmospheric dust Fe supplies were 50 times higher during the last glacial maximum (LGM). Because of this Fe enrichment, phytoplankton growth may have been greatly enhanced, larger amounts of upwelled nutrients may have been used, and the resulting stimulation of new productivity may have contributed to the LGM drawdown of atmospheric CO2 to levels of less than 200 ppm. Background information and arguments in support of this hypothesis are presented.
Slab–mantle flow interaction: influence on subduction dynamics and duration

We investigate the influence of mantle flow relative to the lithosphere on subduction dynamics. We use 2D thermo‐mechanical models assuming incompressible non‐Newtonian fluid rheology. Different mantle flow velocities consistent with absolute plate motion models are tested, as well as both directions of flow, either sustaining or opposing slab dip. The effects of different inflow/outflow velocity profiles, slab strengths and upper–lower mantle viscosity contrasts are also evaluated. Slab dip deviations between models with opposite mantle flow directions range from 37° for relatively strong slabs (ηmax = 1025 Pa s) to 50° for weaker slabs (ηmax = 1024 Pa s), accounting for a significant amount of natural slab dip variability. For imposed mantle flow supporting the slab, the initial stage of slab steepening is followed by a stage of continuous slab dip decrease. This slab shallowing eventually leads to mantle wedge closure, subduction cessation and slab break‐off, possibly driving subduction flips.
A Speech Recognition-based Solution for the Automatic Detection of Mild Cognitive Impairment from Spontaneous Speech

Background: Even today the reliable diagnosis of the prodromal stages of Alzheimer’s disease (AD) remains a great challenge. Our research focuses on the earliest detectable indicators of cognitive de-cline in mild cognitive impairment (MCI). Since the presence of language impairment has been reported even in the mild stage of AD, the aim of this study is to develop a sensitive neuropsychological screening method which is based on the analysis of spontaneous speech production during performing a memory task. In the future, this can form the basis of an Internet-based interactive screening software for the recognition of MCI. Methods: Participants were 38 healthy controls and 48 clinically diagnosed MCI patients. The provoked spontaneous speech by asking the patients to recall the content of 2 short black and white films (one direct, one delayed), and by answering one question. Acoustic parameters (hesitation ratio, speech tempo, length and number of silent and filled pauses, length of utterance) were extracted from the recorded speech sig-nals, first manually (using the Praat software), and then automatically, with an automatic speech recogni-tion (ASR) based tool. First, the extracted parameters were statistically analyzed. Then we applied machine learning algorithms to see whether the MCI and the control group can be discriminated automatically based on the acoustic features. Results: The statistical analysis showed significant differences for most of the acoustic parameters (speech tempo, articulation rate, silent pause, hesitation ratio, length of utterance, pause-per-utterance ratio). The most significant differences between the two groups were found in the speech tempo in the delayed recall task, and in the number of pauses for the question-answering task. The fully automated version of the analysis process – that is, using the ASR-based features in combination with machine learning - was able to separate the two classes with an F1-score of 78.8%. Conclusion: The temporal analysis of spontaneous speech can be exploited in implementing a new, auto-matic detection-based tool for screening MCI for the community.
Unconjugated p-cresol activates macrophage macropinocytosis leading to increased LDL uptake

Patients with chronic kidney disease (CKD) and end-stage renal disease suffer from increased cardiovascular events and cardiac mortality. Prior studies have demonstrated that a portion of this enhanced risk can be attributed to the accumulation of microbiota-derived toxic metabolites, with most studies focusing on the sulfonated form of p-cresol (PCS). However, unconjugated p-cresol (uPC) itself was never assessed due to rapid and extensive first-pass metabolism that results in negligible serum concentrations of uPC. These reports thus failed to consider the host exposure to uPC prior to hepatic metabolism. In the current study, not only did we measure the effect of altering the intestinal microbiota on lipid accumulation in coronary arteries, but we also examined macrophage lipid uptake and handling pathways in response to uPC. We found that atherosclerosis-prone mice fed a high-fat diet exhibited significantly higher coronary artery lipid deposits upon receiving fecal material from CKD mice. Furthermore, treatment with uPC increased total cholesterol, triglycerides, and hepatic and aortic fatty deposits in non-CKD mice. Studies employing an in vitro macrophage model demonstrated that uPC exposure increased apoptosis whereas PCS did not. Additionally, uPC exhibited higher potency than PCS to stimulate LDL uptake and only uPC induced endocytosis- and pinocytosis-related genes. Pharmacological inhibition of varying cholesterol influx and efflux systems indicated that uPC increased macrophage LDL uptake by activating macropinocytosis. Overall, these findings indicate that uPC itself had a distinct effect on macrophage biology that might have contributed to increased cardiovascular risk in patients with CKD.
Enhanced CD8 T Cell Responses through GITR-Mediated Costimulation Resolve Chronic Viral Infection

Chronic infections are characterized by the inability to eliminate the persisting pathogen and often associated with functional impairment of virus-specific T-cell responses. Costimulation through Glucocorticoid-induced TNFR-related protein (GITR) can increase survival and function of effector T cells. Here, we report that constitutive expression of GITR-ligand (GITRL) confers protection against chronic lymphocytic choriomeningitis virus (LCMV) infection, accelerating recovery without increasing pathology. Rapid viral clearance in GITRL transgenic mice coincided with increased numbers of poly-functional, virus-specific effector CD8+ T cells that expressed more T-bet and reduced levels of the rheostat marker PD-1. GITR triggering also boosted the helper function of virus-specific CD4 T cells already early in the infection, as was evidenced by increased IL-2 and IFNγ production, and more expression of CD40L and T-bet. Importantly, CD4-depletion experiments revealed that the expanded pool of virus-specific effector CD8 T cells and the ensuing viral clearance in LCMV-infected GITRL tg mice was entirely dependent on CD4 T cells. We found no major differences for NK cell and regulatory T cell responses, whereas the humoral response to the virus was increased in GITRL tg mice, but only in the late phase of the infection when the virus was almost eradicated. Based on these findings, we conclude that enhanced GITR-triggering mediates its protective, anti-viral effect on the CD8 T cell compartment by boosting CD4 T cell help. As such, increasing costimulation through GITR may be an attractive strategy to increase anti-viral CTL responses without exacerbating pathology, in particular to persistent viruses such as HIV and HCV.
Attenuation Characteristics of Peak Ground Motions in the 1995 Hyogo-ken Nanbu Earthquake

The peak horizontal acceleration and velocity of observed records from the 1995 Hyogo-ken Nanbu earthquake are compared with those predicted from empirical attenuation relations that were derived to be applicable to near-source areas. We found that the observed peak values matched well the empirical attenuation relations. The observed peak vertical accelerations were about half the peak horizontal accelerations when less than 100 cm/s/s. But, the observed peak vertical accelerations tended to be more than half the horizontal ones beyond 100 cm/s/s, and at some sites on soft soil, the peak vertical accelerations were greater than the peak horizontal accelerations. On the other hand, most of the observed peak vertical velocities were about 40% of the peak horizontal velocities independent of the peak amplitudes. At Port Island in Kobe City, remarkable non-linear behavior of soft soil was observed in the vertical array records. The high-frequency shear waves decreased due to liquefaction and the peak horizontal accelerations decayed at the surface. On the contrary, vertical ground motion was amplified by the strong contrast of P-wave velocity in the surface soils. This fact may be one of the causes for greater peak vertical acceleration than peak horizontal acceleration.
Larger depth of field for optical imaging methods

The depth of field for optical imaging system is restricted according to its structure parameters. It is obviously when optical microscopy is used, which depth of field is very small and it is lesser with larger amplification ratio. In the paper, three main methods to extend the depth of field will be shown, and their merits and shortcomings will be analyzed. The first method is to use optical mask. It is easy to achieve satisfied results with calculation simulation, but it is difficult to produce this mask if it is complicated. The second method is to use image processing. Many images can be obtained with scanning of imaging system in the direction of depth. Using image processing method, the information of each image will be extracted, then to compose a new image with them. It is a hard work to capture these scanning images. And it is difficult to achieve real time image. The last method is to combine the method of optical mask and image processing. The larger depth of field for optical imaging methods can extend the image range that can be used in the field of optical microscopy and scanning image system.
Design and Development of Novel 2-(Morpholinyl)-N-substituted Phenylquinazolin-4-amines as Selective COX-II Inhibitor

Background: A novel series of 2-(Morpholin-4-yl)-N-phenylquinazolin-4-amine derivatives were synthesized and confirmed with spectral and elemental techniques. Methods: The compounds were tested for analgesic and anti-inflammatory activity by various pain models in rodents whereas the selectivity towards COX-2 receptor is determined by in vitro assay. Results: Screening results of compounds exhibited comparable biological activity with that of standard compound Indomethacin used for study. Compound 5d was found to be significantly potent with respect to its anti-inflammatory and analgesic activity with substantial COX-II selectivity. Conclusion: In silico analysis by molecular docking and 3D-QSAR studies justifies activity profile of compound 5d, suggesting that it may have potential for further evaluation and development as lead molecule for therapy in pain management.
Screening of NO Inhibitor Release Activity from Soft Coral Extracts Origin Palu Bay, Central Sulawesi, Indonesia

Background: As a marine organism, soft corals can be utilized to be various bioactive substances, especially terpenoids and steroids. The soft corals family which produces bioactive generally come from clavulariidae, alcyoniidae, nephtheidae and xeniidae family. Objective: To investigate the bioactivity of Nitric Oxide (NO) inhibitor release from soft coral crude extracts of Sinularia sp. (SCA), Nephthea sp. (SCB), Sarcophyton sp. (SCC), Sarcophyton sp. (SCD), Sinularia sp. (SCE) and Sinularia sp. (SCF). Materials and Methods: Soft coral is collected from Palu Bay (Central Sulawesi). NO inhibitory release activity measured according to the Griess reaction. Soft corals sample macerated with 1:2 (w/v). Then, Soft coral extracts with the best NO Inhibitor activity partitioned with Dichloromethane, Ethyl acetate, and n-butanol. The bioactive of all crude extracts were identified by GC-MS to find compounds with anti-inflammatory potential. Results: Sarcophyton sp. (SCC) and Sinularia sp. (SCF) are able to inhibit NO concentrations of 0.22 ± 0.04 and 0.20 ± 0.04 μM at 20 mg/mL, respectively. The chemical constituents determined and showed the potential as anti-inflammatory in the crude of Sinularia sp. (SCA) were Octacosane (3.25%). In Nephthea sp. , (SCB) were Cyclohexene, 6-ethenyl-6-methyl-1-(1-methylethyl)-3-(1-methylethylidene)-,(S)- (0.55%); Azulene, 1,2,3,4,5,6,7,8-octahydro-1,4-dimethyl-7-(1-methylethylidene)-, (1S-cis)- (0.53%); and 1,7,7-Trimethyl-2-vinylbicyclo[2.2. 1]hept-2-ene (4.72%). In Sarcophyton sp, (SCC) were Eicosane (0.12%); Nonacosane (10.7%); 14(β)-Pregnane (0.87%); Octacosane 6.39%); and Tricosane (1.53%). In Sarcophyton sp. (SCD) were 14(β)-Pregnane (2.69%); and Octadecane (27.43%). In crude of Sinularia sp. (SCE) were Oleic Acid (0.63%); 7,10-Hexadecadienoic acid, methyl ester (0.54%); 14(β)-Pregnane (1.07%); 5,8,11,14-Eicosatetraenoic acid, ethyl ester, (all-Z)- (4.60%); Octacosane (7.75%); and 1,2-Benzisothiazole, 3-(hexahydro-1H-azepin-1-yl)-, 1,1-dioxide (1.23%). In the crude of Sinularia sp. , (SCF) were Oxirane, decyl- (1.38%); Nonacosane (0.57%); Cyclohexanol, 5-methyl-2-(1-methylethenyl)- (0.61%); 14B-Pregnane (0.76%); and Tetratriacontane (1.02%). Conclusion: The extract of Sarcophyton sp. (SCC) and Sinularia sp. (SCF) showed the best NO inhibitory release activity. This study is making soft corals from Central Sulawesi, Indonesia can become a potential organism in the discovery and development of bioactive substances anti-inflammatory.
Identification and removal of ribosomal RNA sequences from metatranscriptomes

Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications. Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge. net/. Contact: rschmied@sciences.sdsu. edu; rschmied@sciences.sdsu. edu Supplementary information: Supplementary data are available at Bioinformatics online.
iMotifs: an integrated sequence motif visualization and analysis environment

Motivation: Short sequence motifs are an important class of models in molecular biology, used most commonly for describing transcription factor binding site specificity patterns. High-throughput methods have been recently developed for detecting regulatory factor binding sites in vivo and in vitro and consequently high-quality binding site motif data are becoming available for increasing number of organisms and regulatory factors. Development of intuitive tools for the study of sequence motifs is therefore important. iMotifs is a graphical motif analysis environment that allows visualization of annotated sequence motifs and scored motif hits in sequences. It also offers motif inference with the sensitive NestedMICA algorithm, as well as overrepresentation and pairwise motif matching capabilities. All of the analysis functionality is provided without the need to convert between file formats or learn different command line interfaces. The application includes a bundled and graphically integrated version of the NestedMICA motif inference suite that has no outside dependencies. Problems associated with local deployment of software are therefore avoided. Availability: iMotifs is licensed with the GNU Lesser General Public License v2.0 (LGPL 2.0). The software and its source is available at http://wiki.github. com/mz2/imotifs and can be run on Mac OS X Leopard (Intel/PowerPC). We also provide a cross-platform (Linux, OS X, Windows) LGPL 2.0 licensed library libxms for the Perl, Ruby, R and Objective-C programming languages for input and output of XMS formatted annotated sequence motif set files. Contact: matias.piipari@gmail.com; imotifs@googlegroups.com
Controlled attenuation parameter measured using transient elastography for the noninvasive assessment of macrovesicular steatosis in potential living liver donors

Purpose This study aimed to determine the diagnostic performance of the controlled attenuation parameter (CAP) measured using transient elastography (TE) for assessing macrovesicular steatosis (MaS) in potential living liver donors using same-day biopsy as a reference standard. Methods This retrospective study included 204 living liver donor candidates who underwent TE and liver biopsy on the same day between July 2013 and June 2014. The histologic degree of MaS was determined. The area under the receiver operating characteristic curve (AUROC) was used to evaluate the performance of CAP for diagnosing MaS of >10%, and the optimal cutoff value was identified using the maximal Youden index. Results Based on liver biopsy, 185 subjects had MaS of ≤10% and 19 had MaS of >10%. The CAP value was significantly correlated with the percentage of MaS on liver biopsy (r=0.635, P<0.001), and the median CAP value was significantly higher in subjects with MaS of >10% than in those with MaS of ≤10% (300 dB/m vs. 209 dB/m, P<0.001). The AUROC for diagnosing MaS of >10% by CAP was 0.938 (95% confidence interval, 0.896 to 0.967), and a CAP of >259 dB/m yielded a sensitivity of 84.2% and a specificity of 92.4%. Conclusion The CAP measured using TE was significantly correlated with MaS and accurately detected substantial MaS in potential living liver donors. The CAP is a promising tool for the noninvasive diagnosis of MaS and may be used to screen unsuitable living liver donor candidates.
Revised standards for reporting interventions in clinical trials of acupuncture (STRICTA) :

The Standards for Reporting Interventions in Clinical Trials of Acupuncture (STRICTA) were published in ﬁve journals in 2001 and 2002. These guidelines, in the form of a checklist and explanations for use by authors and journal editors, were designed to improve reporting of acupuncture trials, particularly the interventions, thereby facilitating their interpretation and replication. Subsequent reviews of the application and impact of STRICTA have highlighted the value of STRICTA as well as scope for improvements and revision. ©
Geomorphologic and Soil Hydraulic Parameters for Watershed Environmental Hydrology (WEHY) Model

The upscaled hydrologic conservation equations in the Watershed Environmental Hydrology (WEHY) model are capable of taking into account the effect of heterogeneity within natural watersheds. Model parameters that are capable of describing the heterogeneity of the flow domains also need to be estimated. The parameters of the WEHY model are related to the physical properties of the watershed, and they can be estimated from readily available information on topography, soils, and vegetation/land cover conditions. The fundamental assumption of the parameter estimation methodology in this study is that the heterogeneities of land characteristics over a model computational unit (MCU), representing an individual hillslope, are spatially stationary. Consequently, the parameters of the WEHY model that represent the statistical moments of point-location parameter values (such as the variance of log saturated hydraulic conductivity) do not vary over different transects of an MCU. The geomorphologic parameters that de.