3,552 research outputs found
Gene Expression Commons: an open platform for absolute gene expression profiling.
Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000) of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/) which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples
Persistent anti-brane singularities
Anti-D-branes inserted in warped throat geometries (supported by fluxes that
carry D-brane charges) develop unphysical singularities. It has been argued
that these singularities could be resolved when one goes beyond the linearized
approximation or includes the effects of brane polarization. In this paper we
consider anti-D6 branes, whose singularities have been shown to exist at the
full non-linear level, and demonstrate that there is no D8 brane polarization
that can resolve the singularity. We comment on the potential implications of
this result for the resolution of anti-D3 brane singularities in the
Klebanov-Strassler geometry.Comment: 16 pages; v2: comments added, version to appear in JHE
Analisis Strategi Pengelolaan Ekosistem Terumbu Karang Berbasis Resiliensi (Studi Kasus di Teluk Doreri, Kabupaten Manokwari)
Pengelolaan terumbu karang berbasis resiliensi merupakan paradigma baru dan
telah menjadi konsep kunci untuk mendukung kemampuan sistem terumbu karang
dalam menghadapi tekanan lokal dan dampak perubahan iklim. Pengelolaan berbasis
resiliensi mencakup dua aspek penting, yaitu penilaian potensi resiliensi secara spasial
dan perencanaan atau strategi pengelolaan yang sesuai dengan kondisi resiliensi
sistem terumbu karang. Sejauh ini penelitian-penelitian untuk menentukan indikatorindikator
penilaian resiliensi telah mengalami kemajuan yang berarti, namun masih
terbatas dalam kerangka kerja untuk merumuskan strategi pengelolaan berdasarkan
kondisi resiliensi ekosistem terumbu karang. Penelitian ini mengkombinasikan
pendekatan-pendekatan yang berbeda dalam penilaian resiliensi ekosistem terumbu
karang, yaitu penilaian potensi rezime/status terumbu karang, penilaian potensi
resiliensi dan penilaian potensi tekanan/stres dalam satu kerangka kerja (framework)
untuk menentukan tindakan dan strategi pengelolaan ekosistem terumbu karang di
kawasan Teluk Doreri, Kabupaten Manokwari.
Tujuan penelitian ini adalah: 1) menganalisis status dan potensi rezim-rezim
terumbu yang ada di ekosistem terumbu karang; 2) menganalisis potensi resiliensi
ekologi terumbu karang; 3) menganalisis potensi tekanan aktivitas manusia terhadap
terumbu karang; 4) memodelkan skenario perubahan tekanan terhadap resiliensi dan
status terumbu karang; 5) merumuskan strategi pengelolaan yang mendukung
resiliensi dan keberlanjutan ekosistem terumbu karang. Penelitian ini akan
berkontribusi dalam mengisi kekosongan basis data terumbu karang, menyediakan
informasi tentang kondisi terkini resiliensi ekosistem terumbu karang, serta
berkontribusi dalam penyempurnaan kerangka kerja yang mengakomodir aspek
penilaian resiliensi dalam perencanaan pengelolaan terumbu karang.
Penelitian ini menerapkan metode deskriptif dengan observasi lapangan, studi
dokumentasi, studi pustaka dan pemodelan statistik sebagai sumber datanya. Variabelvariabel
yang digunakan dikelompokkan dalam 3 kelompok variabel, yaitu variabel
proses, variabel tekanan dan variabel habitat bentik. Data dikumpulkan dengan
menerapkan pendekatan lapangan (observasi dan wawancara), analisis laboratorium
dan analisis spasial. Potensi rezim terumbu karang dinilai dengan menerapkan statistik
deskriptif (mean±SE), analisis PSI (phase shift index), korelasi PCA, hierarchical
cluster, dan K-means cluster. Pola spasial perubahan terumbu karang diperoleh
melalui pemrosesan citra satelit Landsat multisensor dan multitemporal. Analisis
potensi resiliensi relatif dan potensi tekanan mengikuti metode perhitungan menurut
Maynard et al. (2015) yang meliputi proses kompilasi, normalisasi, pengaturan skala satu arah, perhitungan nilai rata-rata, perhitungan nilai potensi relatif dan penentuan
ranking lokasi/site. Penentuan tindakan pengelolaan dilakukan melalui kueri nilai
potensi resiliensi dan tekanan terhadap kriteria pengelolaan. Analisis persepsi
masyarakat dilakukan melalui penerapan metode tabulasi yang didahului proses
editing dan coding. Metode hybrid A’WOT diterapkan untuk analisis prioritas strategi
pengelolaan ekosistem terumbu karang.
Hasil menunjukkan bahwa rata-rata persentase karang hidup di Teluk Doreri
46,75%, dimana tergolong cukup baik, namun demikian ada potensi perkembangan
rezim abiotik dan alga yang diperkuat dengan pola spasial tren pengurangan tutupan
karang hidup yang cukup tajam dalam kurun waktu 15 tahun terakhir. Potensi resiliensi
ekosistem terumbu karang umumnya masih cukup baik berdasarkan indikator-indikator
proses resiliensi, namun terdapat kelemahan pada aspek indikator biomassa dan
kehadiran kelompok fungsional ikan herbivora. Hampir 50% lokasi yang disurvei
menghadapi potensi tekanan atau stress yang tinggi, bahkan 70% lokasi mengalami
tekanan tinggi khusus dalam bentuk tekanan penangkapan. Hasil queri terhadap
kriteria-kriteria penentuan area target dan tindakan pengelolaan menunjukkan bahwa
pengelolaan perikanan dan penegakan hukum adalah prioritas yang utama, disamping
juga pemantauan pemutihan karang (bleaching) dan dukungan pemulihan. Prioritas
strategi utama adalah meningkatkan keterpaduan antar sektor dan stakeholder dalam
pengelolaan terumbu karang, membangun perilaku dan partisipasi aktif masyakat
dalam pelestarian dan pengelolaan ekosistem terumbu karang, dan meningkatkan
pemantauan kondisi terumbu karang dan efektifitas penegakan hukum. Berdasarkan
hasil disarankan program pemantauan jangka panjang juga perlu dilakukan untuk
memperoleh tren indikator-indikator proses resiliensi dan tantangan resiliensi.
Disamping itu perlu upaya untuk meningkatkan kesadaran, pemahaman, serta
dukungan dan partisipasi masyarakat dalam pengelolaan ekosistem terumbu karang
mulai dari proses perencanaan sampai pengawasan dan evaluasi
Comprehensive methylome map of lineage commitment from haematopoietic progenitors.
Epigenetic modifications must underlie lineage-specific differentiation as terminally differentiated cells express tissue-specific genes, but their DNA sequence is unchanged. Haematopoiesis provides a well-defined model to study epigenetic modifications during cell-fate decisions, as multipotent progenitors (MPPs) differentiate into progressively restricted myeloid or lymphoid progenitors. Although DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 hypomorphs, a comprehensive DNA methylation map of haematopoietic progenitors, or of any multipotent/oligopotent lineage, does not exist. Here we examined 4.6 million CpG sites throughout the genome for MPPs, common lymphoid progenitors (CLPs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and thymocyte progenitors (DN1, DN2, DN3). Marked epigenetic plasticity accompanied both lymphoid and myeloid restriction. Myeloid commitment involved less global DNA methylation than lymphoid commitment, supported functionally by myeloid skewing of progenitors following treatment with a DNA methyltransferase inhibitor. Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands. Many examples of genes and pathways not previously known to be involved in choice between lymphoid/myeloid differentiation have been identified, such as Arl4c and Jdp2. Several transcription factors, including Meis1, were methylated and silenced during differentiation, indicating a role in maintaining an undifferentiated state. Additionally, epigenetic modification of modifiers of the epigenome seems to be important in haematopoietic differentiation. Our results directly demonstrate that modulation of DNA methylation occurs during lineage-specific differentiation and defines a comprehensive map of the methylation and transcriptional changes that accompany myeloid versus lymphoid fate decisions
D-brane potentials in the warped resolved conifold and natural inflation
In this paper we obtain a model of Natural Inflation from string theory with
a Planckian decay constant. We investigate D-brane dynamics in the background
of the warped resolved conifold (WRC) throat approximation of Type IIB string
compactifications on Calabi-Yau manifolds. When we glue the throat to a compact
bulk Calabi-Yau, we generate a D-brane potential which is a solution to the
Laplace equation on the resolved conifold. We can exactly solve this equation,
including dependence on the angular coordinates. The solutions are valid down
to the tip of the resolved conifold, which is not the case for the more
commonly used deformed conifold. This allows us to exploit the effect of the
warping, which is strongest at the tip. We inflate near the tip using an
angular coordinate of a D5-brane in the WRC which has a discrete shift
symmetry, and feels a cosine potential, giving us a model of Natural Inflation,
from which it is possible to get a Planckian decay constant whilst maintaining
control over the backreaction. This is because the decay constant for a wrapped
brane contains powers of the warp factor, and so can be made large, while the
wrapping parameter can be kept small enough so that backreaction is under
control.Comment: 41 pages, 3 appendices, 1 figure, PDFLaTex; various clarifications
added along with a new appendix on b-axions and wrapped D5 branes;version
matches the one published in JHE
Higher Spin Black Holes from CFT
Higher spin gravity in three dimensions has explicit black holes solutions,
carrying higher spin charge. We compute the free energy of a charged black hole
from the holographic dual, a 2d CFT with extended conformal symmetry, and find
exact agreement with the bulk thermodynamics. In the CFT, higher spin
corrections to the free energy can be calculated at high temperature from
correlation functions of W-algebra currents.Comment: 24 pages; v2 reference adde
Il-qawwa tal-kelma : ir-retorika politika
Il-kelma. Il-qawwa tal-kelma. B’kelma nista’ niġbdek jew nimbuttak. B’kelma nista’ nqanqal il-folla, inkella nnaffarha. Il-qawwa tal-kelma hija tali li biha nista’ ngħarrax rewwixta billi noħroġ lin-nies fit-toroq, inkella nista’ nsensel kunsens u nħeġġeġ biex dak li jkun jagħraf il-ħtieġa tal-kompromess. Tiskanta kemm għemejjel u emozzjonijiet jirriżultaw mill-kelma. Il-politiku jaf sewwa l-qawwa tal-kelma għax lilha juża bħala għodda biex iwassal il-messaġġ tiegħu. B’politiku m’aħniex nifhmu biss dawk il-ftit li jirnexxilhom jiksbu siġġu fil-Parlament Malti jew Ewropew, imma wkoll dawk li jinsabu jipparteċipaw fil-ħajja demokratika ta’ pajjiżna. Jiġuna f’moħħna r-rappreżentanti tal-imsieħba soċjali bħalma huma t-trade unions u l-għaqdiet tal-impjegati, il-movimenti tas-soċjetà ċivili, il-Knisja u l-bqija. Dawn l-esponenti lkoll jiddependu u, fl-istess waqt, jinqdew bil-kelma biex jasserixxu rwieħhom fil-ħajja pubblika. Biha jridu jikkomunikaw, jipperswadu, jikkonsultaw, jinnegozjaw, jiddibattu, jikkonflinġu, jirraġunaw, inkella jbellgħulna r-ross bil-labra jekk mhux ukoll jgħodduna ta’ Ġaħan.peer-reviewe
The use of chlorhexidine in the prevention of alveolar osteitis after third molar extractions
Data sources: Cochrane Central Register of Controlled Trials (CENTRAL), Medline through PubMed, Scopus, Science Direct, ISI Web of Science, Evidence-Based Dentistry, ClinicalTrials.gov, the European Union Clinical Trials Register, the Spanish General University Board database of doctoral theses in Spain (TESEO), the Spanish National Research Council (CSIC) bibliographic databases, and the Spanish Medical Index (IME).Study selection: Randomised controlled trials (RCTs) (with or without placebo) of patients of any age or gender who underwent maxillary or mandibular third molar extractions. Studies were required to have analysed the efficacy of only chlorhexidine in any concentration, formulation or treatment regimen for preventing alveolar osteitis (AO). There was no language restriction.Data extraction and synthesis: Data extraction was carried out independently by two researchers, and a third researcher was consulted in case of disagreements. When explicit data were not stated in the text, they were calculated using data from the tables where possible. In addition, authors were contacted to obtain any necessary missing information. Datasets were assessed for heterogeneity, and meta-analysis was conducted on homogenous datasets. Publication bias was assessed through funnel plots. The research was conducted and is reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement.Results: Twenty-three studies published from 1979 to 2015, corresponding to 18 trials (16 parallel-group and two split-mouth RCTs), that reported on 2,824 third molar extractions (1,458 in experimental group and 1,366 in control group) were included. The overall relative risk (RR) was 0.53 (95% CI, 0.45-0.62; PConclusions: The use of chlorhexidine, in any formulation (rinse or gel), concentration (0.12% or 0.20%), or regimen (before, during and/or after surgery), is efficacious and effective in preventing AO in patients who have undergone third molar extraction. The findings showed that in order to prevent one case of AO, eight patients would have to be treated with chlorhexidine. Chlorhexidine gel was found to be moderately more efficacious than the rinse formulation.</p
Quantum fluctuations can promote or inhibit glass formation
The very nature of glass is somewhat mysterious: while relaxation times in
glasses are of sufficient magnitude that large-scale motion on the atomic level
is essentially as slow as it is in the crystalline state, the structure of
glass appears barely different than that of the liquid that produced it.
Quantum mechanical systems ranging from electron liquids to superfluid helium
appear to form glasses, but as yet no unifying framework exists connecting
classical and quantum regimes of vitrification. Here we develop new insights
from theory and simulation into the quantum glass transition that surprisingly
reveal distinct regions where quantum fluctuations can either promote or
inhibit glass formation.Comment: Accepted for publication in Nature Physics. 22 pages, 3 figures, 1
Tabl
Pathotypic diversity of Hyaloperonospora brassicae collected from Brassica oleracea
Downy mildew caused by Hyaloperonospora brassicae is an economically destructive disease of brassica crops in many growing regions throughout the world. Specialised pathogenicity of downy mildews from different Brassica species and closely related ornamental or wild relatives has been described from host range studies. Pathotypic variation amongst Hyaloperonospora brassicae isolates from Brassica oleracea has also been described; however, a standard set of B. oleracea lines that could enable reproducible classification of H. brassicae pathotypes was poorly developed. For this purpose, we examined the use of eight genetically refined host lines derived from our previous collaborative work on downy mildew resistance as a differential set to characterise pathotypes in the European population of H. brassicae. Interaction phenotypes for each combination of isolate and host line were assessed following drop inoculation of cotyledons and a spectrum of seven phenotypes was observed based on the level of sporulation on cotyledons and visible host responses. Two host lines were resistant or moderately resistant to the entire collection of isolates, and another was universally susceptible. Five lines showed differential responses to the H. brassicae isolates. A minimum of six pathotypes and five major effect resistance genes are proposed to explain all of the observed interaction phenotypes. The B. oleracea lines from this study can be useful for monitoring pathotype frequencies in H. brassicae populations in the same or other vegetable growing regions, and to assess the potential durability of disease control from different combinations of the predicted downy mildew resistance genes
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