DaMiRseq—an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification

Abstract Summary RNA-Seq is becoming the technique of choice for high-throughput transcriptome profiling, which, besides class comparison for differential expression, promises to be an effective and powerful tool for biomarker discovery. However, a systematic analysis of high-dimensional genomic data is a demanding task for such a purpose. DaMiRseq offers an organized, flexible and convenient framework to remove noise and bias, select the most informative features and perform accurate classification. Availability and implementation DaMiRseq is developed for the R environment (R ≥ 3.4) and is released under GPL (≥2) License. The package runs on Windows, Linux and Macintosh operating systems and is freely available to non-commercial users at the Bioconductor open-source, open-development software project repository (https://bioconductor.org/packages/DaMiRseq/). In compliance with Bioconductor standards, the authors ensure stable package maintenance through software and documentation updates. Supplementary information Supplementary data are available at Bioinformatics online

CALLIMACO E L'EGITTO. TESTI E INTERPRETAZIONI

My Ph.D. dissertation, entitled Callimachus and Egypt. Texts and interpretations, combines philology and history of classical scholarship. In the second half of the XIX century, the relationship between Callimachus and Egypt was investigated by a critical current, the so called current of the \u201cEgyptianizers\u201d, whose contributions the dissertation considers in details. R. Merkelbach, L. Koenen, P. Bing and W.H. Mineur tried to prove that the Ptolemaic king intended to explain to his Greek subjects his role of Pharaoh, urging Callimachus to translate some aspects of pharaonic kingship in his works. A second \u201cgeneration\u201d of \u201cEgyptianizers\u201d, represented by D. Selden and above all by S. Stephens, expanded the scope of similar affirmations. They saw in the members of the Ptolemaic courts and in Callimachus a clear interest, not only for pharaonic kingship, but also for Egyptian realia. Therefore they maintained that some Callimachean works should be read taking into account two points of view, Greek and Egyptian (\u201cseeing double\u201d). The opponents of this critical current (G. Zanker, G. Weber, M. Asper and R. Hunter) objected that, under Ptolemy II and Ptolemy III, the Greeks created a sort of \u201capartheid\u201d towards the Egyptians. By examinig Callimachean works, they reduced the importance of explicit mentions of aegyptiaca, which, in any case, are very few. Then, my dissertation deals with three still open issues: the look of the city of Alexandria in the third century, the worship of the Ptolemaic king, the sibling wedding between Ptolemy II and Arsinoe II. I analyse the presence of pharaonic kingship in Hymn to Delos, the work more frequently read under an \u201cEgyptianizing\u201d perspective. I devote a chapter to the potential Callimachean sources concerning Egypt, namely Hecataeus of Abdera and Manetho. Hecataeus of Abdera, author of Aigyptiaka, also wrote a work About the Hyperboreans, which Callimachus used for his Hymn to Delos and, maybe, for fr. inc. lib. Aet. 186 Pf. (=fr. 97 Massimilla), for which I suggest an emendation at line 2. In the second part of the dissertation, I offer text and commentary of Callimachean passages in which aegyptiaca are mentioned: four epigrams (epp. XXXVII Pf.=17 G.-P., XLIX Pf.=27 G.P., LV Pf.=16 G.P., LVII Pf.=18 G.-P.) in which we find references to Isis and Serapis, whose cult is object of a closer examination. Then, I analyse some frr. incertae sedis, which are especially interesting because very little studied until now. In particular, I suggest a collocation or I discuss the attribution to Callimachus: fr. 655 concerning the Persea tree, fr. 715 concerning Anubi\u2019s dromos in Heliopolis, the Ious afixis quoted by Suida, fr. 811 inc. auct. concerning an alleged De Iside et Osiride, some mirabilia referable to Egypt. In conclusion, I remark that Egyptianizers\u2018 assumptions, though fascinating and stimulating, nonetheless have weak basis: Egypt appears in Callimachus in an erratic way and always subjected to an interpretatio Graeca, although the poet spended almost his entire life in Alexandria. Nonetheless in his court poems Callimachus probably made allusions to pharaonic kingship, acknowledging impulses that came to him from the Ptolemaic court. In appendix, because of its only partial connection to Egypt, I analyse the aition Busiris-Phalaris (frr. 44-47 Pf.+SH. 252=frr. 51-54 Massimilla), of which I offer text and commentary, with considerations about the figure of Busiris in Callimachus

Cambios paleoambientales desde el Pleistoceno tardío hasta el Holoceno medio basados en el registro de diatomeas en la Salina del Bebedero (San Luis, Argentina)

This study analyzes the environmental changes that occurred in the western sector of the San Luis province (Argentina) during the Late Pleistocene to Middle Holocene period (approximately 12,600 to 3,600 years BP). The information provided by diatoms as paleobiological indicators is used for this analysis. We examined the lower 5 meters of the 10-meter-long SBIII core, which was recovered from the endorheic and hypersaline shallow lake known as Salina del Bebedero (33°20’S-66°45’W, 380 m a.s.l.). The observed peaks of relative abundance of the planktonic diatom Cyclotella choctawhatcheeana suggest episodes of substantial water supply to the shallow lake from the Andes mountains via the Desaguadero river. These episodes were interspersed with periods of low water levels, resulting in very shallow to marsh environments characterized by the presence of epiphytic and benthic diatoms. Furthermore, we discuss and integrate the inferred paleoenvironmental information obtained from the diatom records, along with data from other proxies such as pollen and sedimentology. This integration aims to enhance the previously developed paleoenvironmental model for the region, covering the period between approximately 12,600 and 3,600 years BP. Overall, this research significantly contributes to the understanding of diatom assemblages in hypersaline lacustrine systems of the eastern Andes throughout the studied period, revealing the importance of certain taxa as indicators of wetter conditions during the early Holocene and in more recent stages within this timeframe. Additionally, this study aims to expand our existing knowledge of diatoms biodiversity in this province.Este trabajo aporta herramientas de análisis para la comprensión de los cambios ambientales ocurridos en el sector occidental de la provincia de San Luis (Argentina) entre el periodo del Pleistoceno tardío y el Holoceno medio (ca. 12.600 a ca. 3.600 años AP), utilizando la información provista por diatomeas, como indicadores paleobiológicos. Se analizó la mitad inferior del testigo SBIII (10 a 5 m) obtenido en la cuenca endorreica salino-lacustre Salina del Bebedero (33° 20′ S; 66° 45′ O; 380 (m s.n.m.). Los picos de mayor abundancia relativa de la especie planctónica Cyclotella choctawhatcheeana sugieren episodios de gran aporte de agua a la laguna, procedente de la Cordillera de los Andes a través del río Desaguadero. Estos episodios estuvieron intercalados por periodos con bajos niveles lacustres (ambientes someros o palustres) caracterizados por la presencia de diatomeas epifíticas y bentónicas y se identificaron intervalos donde no se encontraron diatomeas. También discutimos y articulamos la información paleoambiental inferida para el período comprendido entre ca. 12.600 y 3.600 años AP, a partir de los registros de diatomeas, con la información disponible de otros proxies (polen y sedimentología), con el fin de mejorar el modelo paleoambiental generado previamente para la región. Este trabajo amplía el conocimiento de ensambles de diatomeas en sistemas lacustres hipersalinos de los Andes orientales durante el periodo estudiado, revelando la importancia de algunos taxones como indicadores de condiciones más húmedas durante el inicio del Holoceno y en etapas más recientes dentro de este periodo y, además, este estudio, profundiza los conocimientos existentes sobre la biodiversidad diatomológica en esta provincia

EFEKTIVITAS PENERAPAN SISTEM INFORMASI MANAJEMEN PADA BIDANG KEUANGAN

Untuk dapat mengaplikasikan system informasi manajemen yang efektif , maka sumber daya manusia perlu mendapat perhatian yang serius.Bidang Keuangan mengurus tentang Keuangan. Dimana dalam Bidang Keuangan mengurus tentang keluar masuknya dana operasional kantor,merencanakan, memantau, dan memutuskan hal yang berkaitan dengan keuangan kantor Dalam aktivitas tersebut, menggunakan media Sistem Informasi Manajemen yang bertujuan untuk mengefektifkan pekerjaan yang ada.Maka dari itu penelitian ini dilakukan untuk mengetahui Bagaimana penerapan system informasi manajemen

Microfabricated and multilayered PLGA structure for the development of co-cultured in vitro liver models

One of the main advantages of having an in vitro model is the possibility of reducing toxic effects of drugs on human body and evaluate their response to pharmacological treatments to improve the efficacy of a patient-specific therapy. The limitation of such in vitro model is the use of monolayer hepatocytes cultures that show some problems of protein secretion and hepatic functionality. In order to overcome these drawbacks, we present two innovative multilayer structures based on micro-stamped poly(lactic-co-glycolic acid) (PLGA) structures and hepatocytes and fibroblast co-cultures. In particular, the first model consisted of 1 up to 5 layers of PLGA seeded with the previously cited co-culture, while the second model consisted of various sandwich structures of PLGA functionalised (or not) with collagen and seeded with hepatocytes and/or fibroblasts. A mechanical analysis, contact angle and surface charge density measurements were carried out. After these preliminary tests, a metabolic analysis was performed evaluating glucose consumption and urea and albumin production over a culture period of 11 days. Results showed promising application of these in vitro liver models, in particular considering the field of cirrhotic liver treatment

ANALISA KINERJA RUAS JALAN WILLIEM ISKANDAR DENGAN ADANYA BANGUNAN McDONALD KABUPATEN DELI SERDANG

Dengan meningkatnya jumlah kendaraan di Kota Medan sehingga pergerakan lalu lintas semakin meningkat dalam menjalankan aktifitas sehari-hari yang menyebabkan tingginya arus lalu lintas dan berkurangnya kapasitas ruas jalan serta menurunnya tingkat pelayanan pada ruas jalan yang kemudian dapat menimbulkan kemacetan di ruas jalan tersebut. Untuk mengetahui dan mengidentifikasi hal-hal yang mempengaruhi tingkat pelayanan ruas jalan, apakah layak dipertahankan pada karakteristik geometrik dan perilaku lalu lintas ruas jalan yang ada sekarang ini, diperlukan sebuah analisis tingkat pelayanan dan untuk itu harus dicari penyebab permasalahan yang ada sehingga dapat diketahui faktor-faktor apa saja yang menjadi penyebab berkurangnya tingkat pelayanan pada ruas jalan saat ini. Untuk menentukan tingkat pelayanan ruas jalan metode yang digunakan adalah Manual Kapasitas Jalan Indonesia (MKJI) Februari 1997. Dengan melakukan perhitungan cara manual yaitu dengan menghitung jumlah lalu lintas kendaraan pada ruas jalan pada periode waktu.  Data yang telah didapat digunakan adalah data jam puncak, yang telah dikalikan dengan satuan mobil penumpang (smp) untuk menentukan kapasitas jalan dan didukung data-data geometrik jalan yang disurvei. Data hasil perhitungan yang didapat maka tingkat pelayanan kinerja ruas jalan berdasarkan kecepatan perjalanan rata-rata dan nilai volume dan kapasitas pada ruas Jalan Williem Iskandar adalah tingkat pelayanan E yaitu yaitu Volume lalu lintas sudah mendekati kapasitas ruas jalan, kecepatan lebih rendah dari 29,89 km/jam dan pergerakan lalu lintas kadang terhambat

Electroweak Corrections at High Energies

We present a survey of the most abundant processes at the LHC for sensitivity to electroweak corrections at \sqrt{s} = 8, 14, 33, and 100 TeV proton-proton collision energies. The processes studied are pp -> dijet, inclusive W and Z, W/Z+jets, and WW. In each case we compare the experimental uncertainty in the highest kinematic regions of interest with the relative magnitude of electroweak corrections and fixed-order \alpha_S calculations.Comment: Contribution to the Snowmass-2013 report of the QCD Working Group. 15 pages, 14 figures, 5 tables. Version 2: Added a new section 4A and updated the author list, acknowledgements, and references. Version 3: Added a new reference Ref.[36

Sequence Context Influences the Structure and Aggregation Behavior of a PolyQ Tract

Expansions of polyglutamine (polyQ) tracts in nine different proteins cause a family of neurodegenerative disorders called polyQ diseases. Because polyQ tracts are potential therapeutic targets for these pathologies there is great interest in characterizing the conformations that they adopt and in understanding how their aggregation behavior is influenced by the sequences flanking them. We used solution NMR to study at single-residue resolution a 156-residue proteolytic fragment of the androgen receptor that contains a polyQ tract associated with the disease spinobulbar muscular atrophy, also known as Kennedy disease. Our findings indicate that a Leu-rich region preceding the polyQ tract causes it to become α-helical and appears to protect the protein against aggregation, which represents a new, to our knowledge, mechanism by which sequence context can minimize the deleterious properties of these repetitive regions. Our results have implications for drug discovery for polyQ diseases because they suggest that the residues flanking these repetitive sequences may represent viable therapeutic targets