GeneCodis 4: Expanding the modular enrichment analysis to regulatory elements

ABSTRACTGeneCodis is a web-based tool for functional enrichment analysis that allows researchers to integrate different sources of annotations. It extracts sets of significant concurrent annotations and assigns a statistical score to evaluate those that are significantly enriched in the input list. Since its first release in 2007, it has been widely employed to analyze lists of genes in order to interpret the underlying biological mechanisms. Here we present GeneCodis 4, a new release that expands the functional analysis provided by the application, to accept regulatory elements, including lists of, transcription factors, CpG sites and miRNAs. It also incorporates new annotation databases and improved interactive visualizations functionalities to explore results. GeneCodis 4 is freely available at https://genecodis.genyo.es.

Analysing the effects of access to tractor service on technical efficiency of small-scale maize farmers in Mpumalanga province

The Purpose of the study was to analyse the effects of access to tractor service on technical efficiency among small-scale maize farmers following the implementation of Masibuyele Emasimini programme in Mpumalanga Province. Data collection was carried out in the districts of Mpumalanga province and these are: Ehlanzeni, Nkangala and Gert Sibande. Purposive sampling technique was used in identifying the three districts. A total of 101 small-scale maize farmers were purposively selected from the districts and used for the study. The study concluded that small-scale maize farmers do have access to tractor service rendered by the Masibuyele Emasimini programme, with 73% of farmers in Ehlanzeni and 60% in both Nkangala and Gert Sibande district that have access to the service, compared to 27% and 40% without access. Results indicate that there are socio-economic factors influencing small-scale maize farmers’ access to tractor service, for example, irrigation, inter alia. The Cobb-Douglas model found access to tractor service to be negative and insignificant in both Ehlanzeni and Nkangala district. The variable was however positive (although insignificant) in Gert Sibande. The study recommends that modern irrigation systems (preferably, sprinkler) should be provided as part of the programmes’ input list to contribute towards efficient maize production.

Parallel Counting Sort: A Modified of Counting Sort Algorithm

Sorting is one of a classic problem in computer engineer. One well-known sorting algorithm is a Counting Sort algorithm. Counting Sort had one problem, it can’t sort a positive and negative number in the same input list. Then, Modified Counting Sort created to solve that’s problem. The algorithm will split the numbers before the sorting process begin. This paper will tell another modification of this algorithm. The algorithm called Parallel Counting Sort. Parallel Counting Sort able to increase the execution time about 70% from Modified Counting Sort, especially in a big dataset (around 1000 and 10.000 numbers).

GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation

The GenSensor Suite consists of four web tools for elucidating relationships among genes and proteins. GenPath results show which biochemical, regulatory, or other gene set categories are over- or under-represented in an input list compared to a background list. All common gene sets are available for searching in GenPath, plus some specialized sets. Users can add custom background lists. GenInteract builds an interaction gene list from a single gene input and then analyzes this in GenPath. GenPubMed uses a PubMed query to identify a list of PubMed IDs, from which a gene list is extracted and queried in GenPath. GenViewer allows the user to query one gene set against another in GenPath. GenPath results are presented with relevant P- and q-values in an uncluttered, fully linked, and integrated table. Users can easily copy this table and paste it directly into a spreadsheet or document.

Perfect trees and bit-reversal permutations

One well known algorithm is the Fast Fourier Transform (FFT). An efficient iterative version of the FFT algorithm performs as a first step a bit-reversal permutation of the input list. The bit-reversal permutation swaps elements whose indices have binary representations that are the reverse of each other. Using an amortized approach, this operation can be made to run in linear time on a random-access machine. An intriguing question is whether a linear-time implementation is also feasible on a pointer machine, that is, in a purely functional setting. We show that the answer to this question is in the affirmative. In deriving a solution, we employ several advanced programming language concepts such as nested datatypes, associated fold and unfold operators, rank-2 types and polymorphic recursion.

Implicit and Explicit Forgetting: When is Gist Remembered?

Recognition (YES/NO) and stem completion (cued: complete with a word from the list; and uncued: complete with the first word that comes to mind) were tested following either semantic or non-semantic processing of a categorized input list. Item/instance information was tested by contrasting target items from the input list with new items that were categorically related to them; gist/categorical information was tested by comparing target items semantically related to the input items with unrelated new items. For both recognition and stem completion, regardless of initial processing condition, item information decayed rapidly over a period of one week. Gist information was maintained over the same period when initial processing was semantic but only in the cued condition for completion. These results are discussed in terms of dual process theory, which postulates activation/integration of a representation as primarily relevant to implicit item information and elaboration of a representation as mainly relevant to semantic (i.e. categorical) information.

On the Validity of Morpheme Structure Constraints

Morpheme structure constraints (MSCs or, equivalently, morphemic constraints), i.e., constraints on underived items, pose a logical problem to any theory claiming that the first input list to the lexicon, i.e., the dictionary (DICT), may contain material which is considered ill-formed by the MSCs of the language. This problem is related to Scobbie’s (1991:1) “interaction problem”, i.e., the need to make explicit the way in which constraints, rules and representations interact. In the case of MSCs, the interaction problem can be stated as follows: how can ill-formed material be present in the DICT if the DICT contains constraints, i.e., MSCs, against ill-formed material? The Theory of Constraints and Repair Strategies (TCRS) proposed by Paradis (1988a, 1988b, 1990, 1993, this volume), along with Optimality Theory (e.g., Itô and Mester, this volume, and McCarthy, this volume) but in contrast with Declarative Phonology (e.g., Scobbie, this volume), claims explicitly that the DICT can contain material which is identified as ill-formed by post-morphemic constraints (see Paradis and Prunet 1989a:331; Bagemihl 1991:641; Paradis and El Fenne 1991, 1992, 1993; and Ulrich 1991 for other instances of underlying ill-formedness). To solve this interaction problem, Paradis (1993, this volume) suggests that phonological constraints are active in the lexicon (the component where words are morphologically derived) and the post-lexical level alone, not in the DICT. Structures of the DICT may be identified as ill-formed only when going through the lexicon. The theory of phonology which emerges from this position clearly contradicts the commonly-held view that DICT entries are constrained by MSCs.

Memorability, Word Frequency and Negative Recognition

Brown (1976) has provided an analysis of the effect of the memorability of an item on the confidence with which it is accepted or rejected in a test of recognition or recall. When the subject has no clear recollection of the inclusion of an item in an input list, he is assumed to evaluate its memorability in the context of the experiment before he decides whether to accept or reject it. If the judged memorability is high, the absence of a clear recollection is stronger evidence against the item than if it is low. A specific prediction is that memorable distractors in a recognition test will be more confidently rejected than non-memorable ones. This prediction was tested and confirmed in three experiments in which recognition was tested by 4-category rating. Except in Experiment I, items memorable to individual subjects were identified by administering a questionnaire. For example, in Experiment III forenames of immediate family were assumed to have high memorability. This experiment also included word frequency as a variable. Low-frequency distractors were rejected significantly more firmly than high-frequency distractors: extraction of memorable names enhanced this effect. The relationship of memorability to word frequency is discussed.