Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorus and ammonium concentrations in surface runoff from grasslands fertilized with broiler litter.

Application of broiler (Gallus gallus domesticus) litter to grasslands can increase ammonium (NH4-N) and dissolved reactive phosphorus (DRP) concentrations in surface runoff, but it is not known for how long after a broiler litter application that these concentrations remain elevated. This long-term study was conducted to measure NH4-N and DRP in surface runoff from grasslands fertilized with broiler litter. Six 0.75-ha, fescue (Festuca arundinacea Schreb.-)bermudagrass [Cynodon dactylon (L.) Pers. ] paddocks received broiler litter applications in the spring and fall of 1995-1996 and only inorganic fertilizer N in the spring of 1997-1998. Surface runoff from each paddock was measured and analyzed for NH4-N and DRP. Broiler litter increased flow-weighted NH4-N and DRP concentrations from background values of 0.5 and 0.4 mg L(-1), respectively, to values > 18 mg L(-1) in a runoff event that took place immediately after the third application. Ammonium concentrations decreased rapidly after an application and were not strongly related to time after application or runoff volume. In contrast, DRP concentrations tended to decrease more slowly, reaching values near 1 mg L(-1) by 19 mo after the last application. Dissolved reactive P concentrations decreased linearly with the natural logarithm of days after application (p<0.03), and increased linearly with the natural logarithm of runoff volume (p<0.0001).
Amplifiers of selection

When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement—that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two.
Analisis Performa Algoritma K-NN Dan C4.5 Pada Klasifikasi Data Penduduk Miskin

Status kemiskinan penduduk di Kecamatan Bantul diklasifikasikan melalui 11 aspek. Jumlah nilai dari keseluruhan aspek akan menentukan kelas kemiskinan diantaranya kelas miskin, sangat miskin dan rawan miskin. Klasifikasi dengan model tersebut membuat hasil pengelompokan kurang akurat sehingga perlu dicoba klasifikasi dengan model yang lain. Analisis performa klasifikasi data penduduk miskin pada penelitian ini dikerjakan menggunakan metode klasifikasi K-NN dan C4.5. Kedua algoritma klasifikasi akan dibandingkan performanya melalui uji akurasi, precision dan recall.Hasil analisis perbandingan performa algoritma K-NN dengan parameter setting k=1 memiliki performa yang paling baik dibandingkan dengan nilai k=10, 100, 1000 maupun algoritma C4.5. Hasil nilai Accuracy sebesar 94,71%, precision sebesar 84,96% dan recall sebesar 83,6%.
Infantile Digital Fibroma/Fibromatosis: A Clinicopathologic and Immunohistochemical Study of 69 Tumors From 57 Patients With Long-term Follow-up

The clinicopathologic and immunohistochemical features of 69 pediatric examples of infantile digital fibroma/fibromatosis (IDF) were analyzed. Thirty males, 26 females, and 1 child (sex unstated) ranging from newborn to 120 months of age (median, 12 mo) manifested 74 lesions (5 identified in follow-up) involving the toe or finger (n=71) and the hand or foot (n=3). Tumors ranged in size from 3 to 35 (median, 10) mm. All but 4 study members presented with a solitary lesion. Metachronous IDFs developed in 7 patients within 17 to 82 months. Microscopically, a cytologically bland, fibroproliferative lesion was observed forming a dome-shaped/polypoid nodule directly beneath the epidermis and invading dermal adnexa. Mitotic figures per 20 high-powered fields ranged from 0 to 7 (median, 1). Paranuclear cytoplasmic inclusions were identified in 57 tumors. Tumor cells immunohistochemically expressed calponin (11 of 11 tumors), desmin (9/9), α-smooth muscle actin (11/11), CD99 (11/11), CD117 (6/8), heavy caldesmon (2/11 and scattered cytoplasmic inclusions in 4 tumors), CD10 (1/9), nuclear β-catenin (2/11), and CD34 (1/11), but not muscle actin (HUC1-1), keratins, estrogen/progesterone receptor proteins, or activated caspase-3. Twenty-eight of 38 patients (74%) experienced recurrent/persistent disease (single in 22; multiple in 6) (median, 4 mo after surgery). One recurrent tumor spontaneously regressed and the size of another remained unchanged for almost 17 years before reexcision. All 23 patients with >5 years follow-up are currently disease free (median disease-free interval, 23 y). Minor postoperative functional/cosmetic complaints were reported in 47%. No patient with adequate clinical data developed the digitocutaneous dysplasia syndrome or a conventional fibromatosis, or relayed a family history of IDF/conventional fibromatosis. Our results indicate that IDF is a unique myofibroblastic process separable from conventional fibromatoses and from histologic mimics. Conservative excision or observation after biopsy (with additional surgery employed as necessary) are recommended treatment options.
Saccharomyces cerevisiae Expresses Three Phospholipid Hydroperoxide Glutathione Peroxidases*

The GPX1, GPX2, andGPX3 genes of Saccharomyces cerevisiaehave been reported previously to encode glutathione peroxidases (GPxs). We re-examined the sequence alignments of these proteins with GPxs from higher eukaryotes. Sequence identities, particularly with phospholipid hydroperoxide glutathione peroxidases (PHGPxs), were enhanced markedly by introduction to the yeast sequences of gaps that are characteristic of PHGPxs. PHGPx-like activity was detectable in extracts from wild-type S. cerevisiae and was diminished in extracts from gpx1Δ, gpx2Δ, andgpx3Δ deletion mutants; PHGPx activity was almost absent in a gpx1Δ/gpx2Δ/gpx3Δ triple mutant. Studies with cloned GPX1, GPX2, andGPX3 expressed heterologously in Escherichia coli confirmed that these genes encode proteins with PHGPx activity. An S. cerevisiae gpx1Δ/gpx2Δ/gpx3Δ mutant was defective for growth in medium supplemented with the oxidation-sensitive polyunsaturated fatty acid linolenate (18:3). This sensitivity to 18:3 was more marked than sensitivity to H2O2. Unlike H2O2 toxicity, delayed toxicity of 18:3 towardgpx1Δ/gpx2Δ/gpx3Δ cells was correlated with the gradual incorporation of 18:3 into S. cerevisiae membrane lipids and was suppressible with α-tocopherol, an inhibitor of lipid peroxidation. The results show that the GPX genes of S. cerevisiae, previously reported to encode GPxs, encode PHGPxs (PHGPx1, PHGPx2, and PHGPx3) and that these enzymes protect yeast against phospholipid hydroperoxides as well as nonphospholipid peroxides during oxidative stress. This is the first report of an organism that expresses PHGPx from more than one gene and produces PHGPx in the absence of a GPx.
Wave-equation migration velocity analysis by focusing diffractions and reflections

We propose a method for estimating interval velocity using the kinematic information in defocused diffractions and reflections. We extract velocity information from defocused migrated events by analyzing their residual focusing in physical space (depth and midpoint) using prestack residual migration. The results of this residual-focusing analysis are fed to a linearized inversion procedure that produces interval velocity updates. Our inversion procedure uses a wavefield-continuation operator linking perturbations of interval velocities to perturbations of migrated images, based on the principles of wave-equation migration velocity analysis introduced in recent years. We measure the accuracy of the migration velocity using a diffraction-focusing criterion instead of the criterion of flatness of migrated common-image gathers that is commonly used in migration velocity analysis. This new criterion enables us to extract velocity information from events that would be challenging to use with conventional veloci.
Human BRCA1 gene rescues the embryonic lethality of Brca1 mutant mice

Summary: Half of all familial breast cancers are due to mutation in the BRCA1 gene. However, despite its importance, attempts to model BRCA1‐induced disease in the mouse have been disappointing. Heterozygous Brca1 knockout mice do not develop mammary tumors and homozygous knockout mice die during embryogenesis from ill‐defined causes. Sequence analysis has shown that the coding region, genomic organization, and regulatory sequences of the human and mouse genes are not well conserved. This has raised the question of whether the mouse can serve as an effective model for functional analysis of the human BRCA1 gene. To address this question we have introduced a bacterial artificial chromosome containing the human BRCA1 gene into the germline of Brca1 knockout mice. Surprisingly, we have found that the embryonic lethality of Brca1 knockout mice is rescued by the human transgene. We also show that expression of human BRCA1 transgene mirrors the endogenous murine gene. Our “humanized” transgenic mice can serve as a model system for functional analyses of the human BRCA1 gene. genesis 29:72–77, 2001. Published 2001 Wiley‐Liss, Inc.
Single amino acid change alters the ability to specify male or female organ identity

The molecular mechanisms underlying the developmental processes that shape living organisms provide a basis to understand the evolution of biological complexity. Gene duplication allows biological functions to become separated, leading to increased complexity through subfunctionalization. Recently, the relative contributions to morphological evolution of changes to the regulatory and/or coding regions of duplicated genes have been the subject of debate. Duplication generated multiple copies of the MADS-box transcription factor genes that play essential roles in specifying organ identity in the flower, making this evolutionary novelty a good model to investigate the nature of the changes necessary to drive subfunctionalization. Here, we show that naturally occurring variation at a single amino acid in a MADS-box transcription factor switches its ability to specify male and female reproductive organs by altering its repertoire of protein–protein interactions. However, these different developmental fates are only manifest because of an underlying variation in the expression pattern of interacting proteins. This shows that the morphological outcomes of changes to protein sequence and gene expression must be interpreted in the context of the wider regulatory network. It also suggests an explanation for the surprisingly widespread duplications of some of the floral transcription factors.
Time Series modelling for solar irradiance estimation in northeast Brazil

In this work we used time series modelling for generating synthetic sets of hourly solar irradiance for the city of Petrolina located in the northeastern region of Brazil. The models were obtained for each month and were based on 20 years of satellite data. For each month, four time series structures were investigated: auto regressive, auto regressive integrated, auto regressive moving average and auto regressive integrated moving average. We compare the 48 obtained models by comparing the the mean of the synthetic series with the data set means. Another comparison made to validate the time series model was the square error between the data histogram and the synthetic series histogram. Results show that the different model structures generate the best fitting synthetic data for the studied city. This work describes the process of pre-filtering of the data for finally obtaining the monthly models. It also presents the generated synthetic series for hourly solar irradiation. The process described in this work might be used in the planning phase of a solar farm by generating stochastic data for solar irradiance estimation.
Purification and characterization of hydrolytic haloalkane dehalogenase from Xanthobacter autotrophicus GJ10

A new enzyme, haloalkane dehalogenase, was isolated from the 1,2-dichloroethane-utilizing bacterium Xanthobacter autotrophicus GJ10. The purified enzyme catalyzed the hydrolytic dehalogenation of n-halogenated C1 to C4 alkanes, including chlorinated, brominated, and iodinated compounds. The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane. The enzyme followed Michaelis-Menten kinetics, and the Km for 1,2-dichloroethane was 1.1 mM. Maximum activity was found at pH 8.2 and 37 degrees C. Thiol reagents such as p-chloromercuribenzoate and iodoacetamide rapidly inhibited the enzyme. The protein consists of a single polypeptide chain of a molecular weight of 36,000, and its amino acid composition and N-terminal sequence are given.
Spinning Disk Reactor Technique for the Synthesis of Nanometric Sulfur TiO2Core–Shell Powder for Lithium Batteries

Sulfur/lithium battery performances are strictly related to the morphology and nanostructure of sulfur particles. In this work, a comparison of the morphological characteristics and electrochemical properties of electrodes based on colloidal sulfur (CS) obtained by means of traditional chemical precipitation from aqueous solution and via spinning disk reactor (SDR) has been performed. In particular, through the SDR technique and by using different fluid dynamic conditions, it was possible to obtain monodisperse and nanometricsulfurparticles with higher electrochemical performances when used as the cathodic active material in lithium batteries. Moreover, a method to produce core–shell nanoparticles with sulfur and titanium dioxide, starting from a colloidal sulfur (S8) solution and produced by SDR, has been performed, obtaining good electrochemical results. In particular, the nanometric sulfur powder produced by the SDR technique showed a capacity higher than CS after 100 cycles, even if the capacity decreased rapidly in both cases. Instead, considering the core–shell S–TiO2 material, the nanostructured electrode allowed a wide use of active material and a reduced capacity decay during cycling. Specifically, the material showed an initial capacity of 1395 mAh/g, i.e., representing 83% of the theoretical value, which decreased during operation up to 450 mAh/g after about 30 cycles. Then, the material capacity remained unchanged and no substantial loss of capacity was recorded up to 100th cycle.
Challenges for Capillary Self-Assembly of Microsystems

Within the currently rising trend of heterogeneous microsystem integration and packaging, capillary self-assembly emerges as an innovative technique to enhance, complement and eventually replace pick-and-place assembly. Vast literature and experimental data support such claim. Still, the technique needs to overcome some important limitations in order to fully express its potential and earn wide industrial recognition. In this paper, we review and illustrate what are in our opinion the challenges ahead for making part-to-substrate capillary self-assembly reliable and seriously competitive with long-established assembly techniques. After setting self-assembly methods in the context of microsystem assembly and integration technologies, we focus on the standard embodiment of capillary self-assembly, and we describe in details the main, often novel technological steps required for its effective and reproducible performance. This preludes to an outline of what are presently, in our view, the major failure modes affecting the overall yield of the capillary self-assembly technique. Consequently, we propose solutions to face and overcome these challenges, which need to be met to foster the success of this technique.
Evaluating the SPICE rating scale with regard to the internal consistency of capability measures

The international SPICE (Software Process Improvement and Capability dEtermination) project mounted a series of trials to validate the emerging international standard ISO/IEC 15504 against the goals and requirements defined at the start of the project and to verify the consistency and usability of its component parts. This study aims to evaluate the SPICE rating scale with regard to the internal consistency (reliability) of capability measures. For this purpose, this study analyzed 691 process instances assessed during the Phase 2 SPICE Trials (between September 1996 and June 1998). Our findings indicate that the current four-category rating scale gave a higher internal consistency of capability level than two- or three-category rating scales. Since the current version of ISO/IEC 15504, due to become an International Standard scheduled for publication (Part 2) in 2003, still uses the four-category rating scale, the results in this article are still valid for the current version. Copyright © 2004 John Wiley & Sons, Ltd.
Apply Market Mechanism to Agent-Based Grid Resource Management

In this paper, we apply market mechanism and agent to build grid resource management, where grid resource consumers and providers can buy and sell computing resource based on an underlying economic architecture. All market participants in the grid environment including computing resources and services can be represented as agents. Market participant is registered with a Grid Market Manager. A grid market participant can be a service agent that provides the actual grid service to the other market participants. Grid market participants communicate with each other by communication space that is an implementation of tuple space. In this paper, Grid agent model description is given. Then, the structure of Grid Market is described in detail. The design and implementation of agent oriented and market oriented grid resource management are presented in this paper.
Long noncoding RNA CASC2 predicts the prognosis of glioma patients and functions as a suppressor for gliomas by suppressing Wnt/β-catenin signaling pathway

Background Previous studies have demonstrated that long noncoding RNA cancer susceptibility candidate 2 (lncRNA CASC2) is frequently downregulated in several types of tumors and functions as a tumor-suppressive factor. However, the clinical significance and function of CASC2 in human glioma remain largely unknown. The purpose of this study was to identify the clinical values of CASC2, as well as investigate the potential molecular mechanisms in glioma. Methods This retrospective study first analyzed the expression levels of CASC2 using quantitative real-time polymerase chain reaction. Then, CASC2 expression levels were associated with various clinicopathologic characteristics and the survival rate of patients with glioma. Finally, the function and underlying molecular mechanisms of CASC2 in human glioma were investigated in U251 cell line. Results By quantitative real-time polymerase chain reaction analysis, our data showed that CASC2 expression was significantly downregulated in glioma tissues and cell lines (U87 and U251) compared to adjacent normal brain tissues or normal human astrocytes. Moreover, its expression negatively correlated with tumor grade in glioma patients. Furthermore, Kaplan–Meier curves with log-rank analysis revealed a close correlation between downregulated CASC2 and shorter survival time in glioma patients. In addition, Cox regression analysis indicated that CASC2 could be considered as an independent risk factor for poor prognosis. Finally, in vitro experiment demonstrated that CASC2 overexpression remarkably suppressed glioma cell proliferation, migration, and invasion through suppressing Wnt/β-catenin signaling pathway. Conclusion This study suggested that CASC2 may potentially serve as a valuable diagnostic and prognostic biomarker and a therapeutic target for glioma patients.
Trans mRNA splicing in trypanosomes : cloning and analysis of a PRP 8-homologous gene from Trypanosoma brucei provides evidence for a U 5-analogous RNP to conventional cis mRNA splicing . In analogy to cis

Institut für Biochemie, Humboldt-Universität/Charité, structure, a trans spliceosome. Only a few RNA and Monbijou-Strasse 2a, D-10117 Berlin and 1Max-Planck-Institut für protein components have been identified in trypanosomes Biochemie, Genzentrum, Am Klopferspitz 18a, D-82152 Martinsried, that are relevant for trans splicing. In particular, U2, U4 Germany and U6 snRNAs are essential co-factors (Tschudi and 2Corresponding author Ullu, 1990) and occur in the form of snRNPs in the cell
PCA – A Powerful Method for Analyze Ecological Niches

Principal Component Analysis, PCA, is a multivariate statistical technique that uses orthogonal transformation to convert a set of correlated variables into a set of orthogonal, uncorrelated axes called principal components (James & McCulloch 1990; Robertson et al., 2001; Legendre & Legendre 1998; Gotelli & Ellison 2004). Ecologists are most frequently dealing with multivariate datasets. This is especially true in field ecology, and this is why PCA is an attractive and frequently used method of data ordination in ecology. PCA enables condensation of data on a multivariate phenomenon into its main, representative features by projection of the data into a two-dimensional presentation. The two created resource axes are independent, and although they reduce the number of dimensions–i.e. the original data complexity–they maintain much of the original relationship between the variables: i.e., information or explained variance (Litvak & Hansell 1990). This is helpful in focusing attention on the main characteristics of the phenomenon under study. It is convenient that, if the first few principal components (PCs) explain a high percentage of variance, environmental variables that are not correlated with the first few PCs can be disregarded in the analysis (Toepfer et al., 1998). In addition, applying PCA has become relatively userfriendly because of the numerous programs that assist in carrying out the computational procedure with ease (Doledec et al., 2000; Guisan & Zimmerman 2000; Robertson et al., 2001; Rissler & Apodaca 2007; Marmion et al., 2009).
A unified finite-element solution from zero frequency to microwave frequencies for full-wave modeling of large-scale three-dimensional on-chip interconnect structures

It has been observed that a full-wave finite-element-based solution breaks down at low frequencies. This hinders its application to on-chip problems in which broadband modeling from DC to microwave frequencies is required. Although a static formulation and a full-wave formulation can be stitched together to solve this problem, it is cumbersome to implement both static and full-wave solvers and make transitions between these two when necessary. In this work, a unified finite-element solution from zero frequency to microwave frequencies is developed for full-wave modeling of large-scale three-dimensional on-chip interconnect structures. In this solution, a single full-wave formulation is used. No switching to a static formulation is needed at low frequencies. Numerical and experimental results demonstrate its validity.