PENGARUH CAMPURAN ABU AMPAS KAYU PADA TANAH DESA COT SEUNONG DENGAN PENGUJIAN CALIFORNIA BEARING RATIO

Tanah yang tersedia di alam sering tidak dapat langsung digunakan karena secara alamiah tanah memiliki sifat-sifat fisis dan mekanis tertentu yang terbatas. Oleh karena itu diperlukan penelitian tentang tanah untuk mengetahui sifat-sifatnya dengan teliti sehingga dapat menyesuaikan dengan kebutuhan konstruksi sehingga menjamin stabilitas suatu konstruksi. Penelitian ini bertujuan untuk mengetahui pengaruh penambahan abu ampas kayu yang digunakan sebagai bahan stabilisasi terhadap nilai CBR (California Bearing Ratio). Tanah yang digunakan dalam penelitian ini berasal dari Desa Cot Seunong Kecamatan Montasik Kabupaten Aceh Besar. Abu ampas kayu yang diperoleh diambil dari sisa-sisa limbah perabot pembuatan kayu yang berada di daerah Desa Kajhu Aceh Besar. Tanah tersebut menurut klasifikasi AASHTO tergolong A-7-6 (tanah berlempung). Menurut USCS tanah Desa Cot Seunong termasuk golongan tanah lempung tak organik dengan plastisitas tinggi yang disimbolkan CH (Clay High) dengan indeks plastisitasnya adalah 33,69%. Persentase penambahan abu ampas kayu yaitu 0%, 5%, 10%, 15% dan 20% terhadap berat kering tanah. Hasil pengujian Standart Proctor tanpa campuran didapat nilai OMC (Optimim Moisture Content) 23,60% dengan berat isi kering maksimum (?dmax) 1,595 gr/cm3. Hasil pengujian CBR memperlihatkan bahwa nilai CBR pada persentase 0% sebesar 1,67%, pada persentase 5% sebesar 2,45%, pada persentase 10% sebesar 2,62%, pada persentase 15% sebesar 2,73%, dan pada persentase 20% sebesar 3,03%. Nilai CBR tertinggi terdapat pada persentase 20% dengan nilai CBR 3,03%, dengan demikian penggunaan abu ampas kayu pada tanah lempung Desa Cot Seunong sangat efektif karena semakin banyak campuran abu ampas kayu yang mengisi pori-pori kosong pada tanah, sehingga tanah menjadi padat dan dapat meningkatkan daya dukung tanah menjadi lebih baik.Banda Ace

AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts

An increasing number of eukaryotic and prokaryotic genes are being found to have natural antisense transcripts (NATs). There is also growing evidence to suggest that antisense transcription could play a key role in many human diseases. Consequently, there have been several recent attempts to set up computational procedures aimed at identifying novel NATs. Our group has developed the AntiHunter program for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, the program requires a genomic sequence plus an associated list of transcript names and coordinates of the genomic region. After masking the repeated regions, the program carries out a BLASTN search of this sequence in the selected EST database, reporting via email the EST entries that reveal an antisense transcript according to the user-supplied list. Here, we present the newly developed version 2.0 of the AntiHunter tool. Several improvements have been added to this version of the program in order to increase its ability to detect a larger number of antisense ESTs. As a result, AntiHunter can now detect, on average, >45% more antisense ESTs with little or no increase in the percentage of the false positives. We also raised the maximum query size to 3 Mb (previously 1 Mb). Moreover, we found that a reasonable trade-off between the program search sensitivity and the maximum allowed size of the input-query sequence could be obtained by querying the database with the MEGABLAST program, rather than by using the BLAST one. We now offer this new opportunity to users, i.e. if choosing the MEGABLAST option, users can input a query sequence up to 30 Mb long, thus considerably improving the possibility to analyze longer query regions. The AntiHunter tool is freely available at

A Smad3 transgenic reporter reveals TGF-beta control of zebrafish spinal cord development

TGF-beta (TGFβ) family mediated Smad signaling is involved in mesoderm and endoderm specification, left-right asymmetry formation and neural tube development. The TGFβ1/2/3 and Activin/Nodal signal transduction cascades culminate with activation of SMAD2 and/or SMAD3 transcription factors and their overactivation are involved in different pathologies with an inflammatory and/or uncontrolled cell proliferation basis, such as cancer and fibrosis. We have developed a transgenic zebrafish reporter line responsive to Smad3 activity. Through chemical, genetic and molecular approaches we have seen that this transgenic line consistently reproduces in vivo Smad3-mediated TGFβ signaling. Reporter fluorescence is activated in phospho-Smad3 positive cells and is responsive to both Smad3 isoforms, Smad3a and 3b. Moreover, Alk4 and Alk5 inhibitors strongly repress the reporter activity. In the CNS, Smad3 reporter activity is particularly high in the subpallium, tegumentum, cerebellar plate, medulla oblongata and the retina proliferative zone. In the spinal cord, the reporter is activated at the ventricular zone, where neuronal progenitor cells are located. Colocalization methods show in vivo that TGFβ signaling is particularly active in neuroD+ precursors. Using neuronal transgenic lines, we observed that TGFβ chemical inhibition leads to a decrease of differentiating cells and an increase of proliferation. Similarly, smad3a and 3b knock-down alter neural differentiation showing that both paralogues play a positive role in neural differentiation. EdU proliferation assay and pH3 staining confirmed that Smad3 is mainly active in post-mitotic, non-proliferating cells. In summary, we demonstrate that the Smad3 reporter line allows us to follow in vivo Smad3 transcriptional activity and that Smad3, by controlling neural differentiation, promotes the progenitor to precursor switch allowing neural progenitors to exit cell cycle and differentiate

The risk of late or advanced presentation of HIV infected patients is still high, associated factors evolve but impact on overall mortality is vanishing over calendar years: Results from the Italian MASTER Cohort

BACKGROUND: We aimed at evaluating frequency and factors associated with late presentation and advanced HIV disease and excess risk of death due to these conditions from 1985 to 2013 among naïve HIV infected patients enrolled in the Italian MASTER Cohort. METHODS: All antiretroviral naive adults with available CD4+ T cell count after diagnosis of HIV infection were included. Multivariable logistic regression analysis investigated factors associated either with late presentation or advanced HIV disease. Probabilities of survival were estimated both at year-1 and at year-5 according to the Kaplan-Meier method. Flexible parametric models were used to evaluate changes in risk of death overtime according to late presentation and advanced HIV disease. The analyses were stratified for calendar periods. RESULTS: 19,391 patients were included (54 % were late presenters and 37.6 % were advanced presenters). At multivariable analysis, the following factors were positively associated with late presentation: male gender (OR = 1.29), older age (≥55 years vs. <25 years; OR = 7.45), migration (OR = 1.54), and heterosexual risk factor for HIV acquisition (OR = 1.52) or IDU (OR = 1.27) compared to homosexual risk. Survival rates at year-5 increased steadily and reached 92.1 % for late presenters vs. 97.4 % for non-late presenters enrolled in the period 2004-2009. Using flexible parametric models we found a sustained reduction of hazard ratios over time for any cause deaths between late and non-late presenters over time. Similar results were found for advanced HIV disease. CONCLUSION: Screening polices need to be urgently implemented, particularly in most-at-risk categories for late presentation, such as migrants, older patients and those with heterosexual intercourse or IDU as risk factors for HIV acquisition. Although in recent years the impact of late presentation on survival decreased, about 10 % of patients diagnosed in more recent years remains at increased risk of death over a long-term follow-up

Importance of Different Types of Prior Knowledge in Selecting Genome‐Wide Findings for Follow‐Up

Biological plausibility and other prior information could help select genome‐wide association ( GWA ) findings for further follow‐up, but there is no consensus on which types of knowledge should be considered or how to weight them. We used experts’ opinions and empirical evidence to estimate the relative importance of 15 types of information at the single‐nucleotide polymorphism ( SNP ) and gene levels. Opinions were elicited from 10 experts using a two‐round Delphi survey. Empirical evidence was obtained by comparing the frequency of each type of characteristic in SNP s established as being associated with seven disease traits through GWA meta‐analysis and independent replication, with the corresponding frequency in a randomly selected set of SNP s. SNP and gene characteristics were retrieved using a specially developed bioinformatics tool. Both the expert and the empirical evidence rated previous association in a meta‐analysis or more than one study as conferring the highest relative probability of true association, whereas previous association in a single study ranked much lower. High relative probabilities were also observed for location in a functional protein domain, although location in a region evolutionarily conserved in vertebrates was ranked high by the data but not by the experts. Our empirical evidence did not support the importance attributed by the experts to whether the gene encodes a protein in a pathway or shows interactions relevant to the trait. Our findings provide insight into the selection and weighting of different types of knowledge in SNP or gene prioritization, and point to areas requiring further research.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96262/1/gepi21705.pd

SNP Prioritization Using a B ayesian Probability of Association

Prioritization is the process whereby a set of possible candidate genes or SNP s is ranked so that the most promising can be taken forward into further studies. In a genome‐wide association study, prioritization is usually based on the P ‐values alone, but researchers sometimes take account of external annotation information about the SNP s such as whether the SNP lies close to a good candidate gene. Using external information in this way is inherently subjective and is often not formalized, making the analysis difficult to reproduce. Building on previous work that has identified 14 important types of external information, we present an approximate B ayesian analysis that produces an estimate of the probability of association. The calculation combines four sources of information: the genome‐wide data, SNP information derived from bioinformatics databases, empirical SNP weights, and the researchers’ subjective prior opinions. The calculation is fast enough that it can be applied to millions of SNPS and although it does rely on subjective judgments, those judgments are made explicit so that the final SNP selection can be reproduced. We show that the resulting probability of association is intuitively more appealing than the P ‐value because it is easier to interpret and it makes allowance for the power of the study. We illustrate the use of the probability of association for SNP prioritization by applying it to a meta‐analysis of kidney function genome‐wide association studies and demonstrate that SNP selection performs better using the probability of association compared with P ‐values alone.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96317/1/gepi21704.pd

Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways

BACKGROUND: SCA28 is an autosomal dominant ataxia associated with AFG3L2 gene mutations. We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated healthy controls matched for sex and age. METHODS: Gene expression was evaluated with the Affymetrix GeneChip Human Genome U133A 2.0 Arrays and data were validated by real-time PCR. RESULTS: We found 66 genes whose expression was statistically different in SCA28 LCLs, 35 of which were up-regulated and 31 down-regulated. The differentially expressed genes were clustered in five functional categories: (1) regulation of cell proliferation; (2) regulation of programmed cell death; (3) response to oxidative stress; (4) cell adhesion, and (5) chemical homeostasis. To validate these data, we performed functional experiments that proved an impaired SCA28 LCLs growth compared to controls (p\u2009<\u20090.005), an increased number of cells in the G0/G1 phase (p\u2009<\u20090.001), and an increased mortality because of apoptosis (p\u2009<\u20090.05). We also showed that respiratory chain activity and reactive oxygen species levels was not altered, although lipid peroxidation in SCA28 LCLs was increased in basal conditions (p\u2009<\u20090.05). We did not detect mitochondrial DNA large deletions. An increase of TFAM, a crucial protein for mtDNA maintenance, and of DRP1, a key regulator of mitochondrial dynamic mechanism, suggested an alteration of fission/fusion pathways. CONCLUSIONS: Whole genome expression profiling, performed on SCA28 LCLs, allowed us to identify five altered functional categories that characterize the SCA28 LCLs phenotype, the first reported in human cells to our knowledge. \ua9 2013 Mancini et al.; licensee BioMed Central Ltd

Giosuè Carducci prosatore

Questo volume su Giosuè Carducci prosatore raccoglie i contributi presentati al XVII Convegno internazionale di Letteratura italiana "Gennaro Barbarisi", tenutosi a Palazzo Feltrinelli (Gargnano del Garda) dal 29 settembre al 1° ottobre 2016. Si è trattato di una proficua occasione di incontro, di studio e di approfondimento su un tema forse poco frequentato, soprattutto in tempi recenti, ma ricco di sollecitazioni per una più articolata e storicamente fondata definizione della personalità di un autore così significativo nel panorama della cultura italiana fra Otto e primo Novecento; non soltanto sul versante della poesia (un primato sancito dal premio Nobel nel 1906) ma anche, e forse ancora di più, su quello della prosa saggistica, degli scritti di polemica, delle curatele editoriali, delle ricerche erudite, fino alle prove di alta oratoria e all'epistolografia