ChIP-AP – An Integrated ChIP-Seq Analysis Pipeline

ChIP-Seq is a technique used to analyse protein-DNA interactions. The protein-DNA complex is pulled down using a protein antibody, after which sequencing and analysis of the bound DNA fragments is performed. A key bioinformatics analysis step is “peak” calling - identifying regions of enrichment. Benchmarking studies have consistently shown that no optimal peak caller exists. Peak callers have distinct selectivity and specificity characteristics which are often not additive and seldom completely overlap in many scenarios. In the absence of a universal peak caller, we rationalized one ought to utilize multiple peak-callers to 1) gauge peak confidence as determined through detection by multiple algorithms, and 2) more thoroughly survey the protein-bound landscape by capturing peaks not detected by individual peak callers owing to algorithmic limitations and biases. We therefore developed an integrated ChIP-Seq Analysis Pipeline (ChIP-AP) which performs all analysis steps from raw fastq files to final result, and utilizes four commonly used peak callers to more thoroughly and comprehensively analyse datasets. Results are integrated and presented in a single file enabling users to apply selectivity and sensitivity thresholds to select the consensus peak set, the union peak set, or any sub-set in-between to more confidently and comprehensively explore the protein-bound landscape. (https://github.com/JSuryatenggara/ChIP-AP).

Demand Response Programs Management in an Energy Community with Diversity of Appliances

This paper shows the behaviour of a Demand Response program designed to be implemented in Energy Communities, where they take advantage of photovoltaic production. The primary objective is to manage both photovoltaic overproduction and village consumption efficiently. The DR program focuses on looking for consecutive periods that exceed a target peak set by the aggregator after analysing the consumption of the given energy community. The case study includes three villages, where participants are expected to be members of a community. The results are that participants will see a reduction in costs and electricity consumption.

Melting temperature versus crystallinity: new way for identification and analysis of multiple endotherms of poly(ethylene terephthalate)

Poly(ethylene terephthalate) (PET) materials with different molecular weights were isothermally crystallized from melt by systematically varying the temperature and duration of the treatment performed in the differential scanning calorimeter (DSC). Multiple endotherm peaks were observed on the subsequent heating thermograms that were separated from each other on the basis of their melting temperature versus crystallization temperature and melting temperature versus crystallinity function. By this new approach five sub-peak sets were identified and then comprehensively characterised. Wide-Angle X-Ray Diffraction (WAXD) analyses revealed that the identified sub-peak sets do not differ in crystalline forms. By analysing the crystallinity and the melting temperature of the sub-peak sets as a function of crystallization time, crystallization temperature and intrinsic viscosity, it was concluded that below the crystallization temperature of 460 K the sub-peak sets that were formed during primary or secondary crystallization transform partially or completely to a third sub-peak set during the heating run of the measurement, while above this temperature, the sub-peak set formed during primary crystallization gradually transforms to a more stable structure, with higher melting temperature. These formations and transformations are described with mathematically defined parameters as well.

Shuffle-Compatible Permutation Statistics II: The Exterior Peak Set

This paper is a continuation of the work "Shuffle-compatible permutation statistics" by Gessel and Zhuang (but can be read independently from the latter). We study the shuffle-compatibility of permutation statistics — a concept introduced by Gessel and Zhuang, although various instances of it have appeared throughout the literature before. We prove that (as Gessel and Zhuang have conjectured) the exterior peak set statistic (Epk) is shuffle-compatible. We furthermore introduce the concept of an "LR-shuffle-compatible" statistic, which is stronger than shuffle-compatibility. We prove that Epk and a few other statistics are LR-shuffle-compatible. Furthermore, we connect these concepts with the quasisymmetric functions, in particular the dendriform structure on them.

Glacial and Postglacial History of the White Cloud Peaks-Boulder Mountains, Idaho, U.S.A.

ABSTRACT Glacial and glaciofluvial deposits are mapped and differentiated to develop new local, relative-age (RD) stratigraphies for the North Fork of the Big Lost River, Slate Creek and Pole Creek drainages in the White Cloud Peaks and Boulder Mountains, Idaho. This stratigraphic model expands the areal extent of the "Idaho glacial model". Volcanic ash samples collected from the study area are petrographically characterized and correlated, on the basis of mineralogy and glass geochemistry, to reference samples of identified Cascade Range tephras. Four distinct tephras are recognized including; Mount St. Helens-Set S (13,600-13,300 yr BP), Glacier Peak-Set B (11,250 yr BP), Mount Mazama (6600 yr BP) and Mount St. Helens-Set Ye (4350 yr BP). A core of lake sediments containing two tephra units was obtained from a site called "Pole Creek kettle". Pollen and sediment analyses indicate three intervals of late Pleistocene and Holocene climatic change. Cool and wet climatic conditions prevailed in the region shortly before and immediately following the deposition of the Glacier Peak-Set B ash (11,250 yr BP). Climatic warming occurred from approximately 10,500 to 6600 yr BP after which warm, dry conditions prevailed. Sediment accumulation in the kettle ceased by 4350 yr BP. The presence of Glacier Peak-Set B tephra in the base of the Pole Creek kettle core provides a minimum age of 11,250 yr BP for the retreat of valley glaciers from their Late Wisconsinan maximum position. A radiocarbon date of 8450 + 85 yr BP (SI-5181), and the presence of Mount Mazama ash (6600 yr BP) up-core support the Glacier Peak-Set B identification.