26,924 research outputs found
MANAJEMEN KEPALA SEKOLAH DALAM PENINGKATAN PROFESIONALITAS GURU PENDIDIKAN AGAMA ISLAM MAN 3 SLEMAN YOGYAKARTA
AbstractIn the context of regional autonomy and decentralization of education the succeed also failure of education in schools is  techer as educator, principals, and supervisors, because these figures are the keys that determine and mobilize various other school components and dimensions. To achieve the expected goals, it takes an organization in which there is organization cooperationor ganizational cooperation. This research is included in the field research namely: this research is carried out in a certain environment to carry out observations and data collection needed. The research was conducted by researchers at MAN 3 Sleman Yogyakarta, this research method uses descriptive qualitative research. In terms of its nature, this research is descriptive in nature, that is, research that aims to systematically and accurately describe the facts and characteristics of a particular field. The results of the study of the headmaster of the school have applied management in the improvement of the professionalism of PAI MAN 3 S teachers in Yogyakarta, this is evident that the teachers of MAN 3 Sleman have extensive mastery as evidenced by the standardization of certification. And have very personal competencies so that they can communicate very well with other staff.Keywords: Management, Professionalism, Principal AbstrakDalam konteks otonomi daerah dan desentralisasi pendidikan, keberhasilan juga kegagalan pendidikan di sekolah adalah techer sebagai pendidik, kepala sekolah, dan pengawas, karena angka ini merupakan kunci yang menentukan dan memobilisasi berbagai komponen dan dimensi sekolah lainnya. Untuk mencapai tujuan yang diharapkan, dibutuhkan sebuah organisasi di mana ada organisasi kooperasiatau kerjasama ganizational. Penelitian ini termasuk dalam penelitian lapangan yaitu: penelitian ini dilakukan di lingkungan tertentu untuk melaksanakan pengamatan dan pengumpulan data yang diperlukan. Penelitian ini dilakukan oleh peneliti di MAN 3 Sleman Yogyakarta, metode penelitian ini menggunakan penelitian kualitatif deskriptif. Dalam hal sifatnya, penelitian ini adalah deskriptif di alam, yaitu, penelitian yang bertujuan untuk secara sistematis dan akurat menggambarkan fakta dan karakteristik dari bidang tertentu. Hasil kajian kepala sekolah telah menerapkan manajemen dalam peningkatan profesionalisme para guru PAI MAN 3 S di Yogyakarta, hal ini terbukti bahwa para guru dari MAN 3 Sleman memiliki penguasaan luas yang dibuktikan dengan standardisasi sertifikasi. Dan memiliki kompetensi yang sangat pribadi sehingga mereka dapat berkomunikasi dengan baik dengan staf lain.Kata Kunci: Manajemen, Profesionalisme, Kepala Sekola
Improving dbNSFP
IMPROVING dbNSFP
Mingyao Lu, B.S.
Advisory Professor: Xiaoming Liu, Ph.D.
The analysis and interpretation of DNA variation are very important for the Whole Exome studies (WES). Genome research has focused on single nucleotide variants (SNVs). Since indels are as important as SNVs, especially indels in coding regions are often candidates of disease-causing variants, thus, it is necessary to expand the focus to include indel mutations.
The goal of my project is to provide an automatic annotation pipeline to the WES based disease studies project by extending the dbNSFP with a tool for automated indel annotation and deleteriousness prediction. The current sequencing results typically include both SNVs and indels. Although there have been many available tools to integrate functional prediction/annotations for SNV effects, there are no such tools for indels to my knowledge. Therefore, the aim of this thesis was to add deleteriousness prediction scores to indel annotation based on gene models, including CADD, SIFT, and PROVEAN. All those scores can be calculated on-the-fly after installing resources locally. A Docker implementing the indel annotation and deleteriousness prediction has been developed and ready to be deployed from the cloud
Fundamental Bounds and Approaches to Sequence Reconstruction from Nanopore Sequencers
Nanopore sequencers are emerging as promising new platforms for
high-throughput sequencing. As with other technologies, sequencer errors pose a
major challenge for their effective use. In this paper, we present a novel
information theoretic analysis of the impact of insertion-deletion (indel)
errors in nanopore sequencers. In particular, we consider the following
problems: (i) for given indel error characteristics and rate, what is the
probability of accurate reconstruction as a function of sequence length; (ii)
what is the number of `typical' sequences within the distortion bound induced
by indel errors; (iii) using replicated extrusion (the process of passing a DNA
strand through the nanopore), what is the number of replicas needed to reduce
the distortion bound so that only one typical sequence exists within the
distortion bound.
Our results provide a number of important insights: (i) the maximum length of
a sequence that can be accurately reconstructed in the presence of indel and
substitution errors is relatively small; (ii) the number of typical sequences
within the distortion bound is large; and (iii) replicated extrusion is an
effective technique for unique reconstruction. In particular, we show that the
number of replicas is a slow function (logarithmic) of sequence length --
implying that through replicated extrusion, we can sequence large reads using
nanopore sequencers. Our model considers indel and substitution errors
separately. In this sense, it can be viewed as providing (tight) bounds on
reconstruction lengths and repetitions for accurate reconstruction when the two
error modes are considered in a single model.Comment: 12 pages, 5 figure
File Updates Under Random/Arbitrary Insertions And Deletions
A client/encoder edits a file, as modeled by an insertion-deletion (InDel)
process. An old copy of the file is stored remotely at a data-centre/decoder,
and is also available to the client. We consider the problem of throughput- and
computationally-efficient communication from the client to the data-centre, to
enable the server to update its copy to the newly edited file. We study two
models for the source files/edit patterns: the random pre-edit sequence
left-to-right random InDel (RPES-LtRRID) process, and the arbitrary pre-edit
sequence arbitrary InDel (APES-AID) process. In both models, we consider the
regime in which the number of insertions/deletions is a small (but constant)
fraction of the original file. For both models we prove information-theoretic
lower bounds on the best possible compression rates that enable file updates.
Conversely, our compression algorithms use dynamic programming (DP) and entropy
coding, and achieve rates that are approximately optimal.Comment: The paper is an extended version of our paper to be appeared at ITW
201
Accurate reconstruction of insertion-deletion histories by statistical phylogenetics
The Multiple Sequence Alignment (MSA) is a computational abstraction that
represents a partial summary either of indel history, or of structural
similarity. Taking the former view (indel history), it is possible to use
formal automata theory to generalize the phylogenetic likelihood framework for
finite substitution models (Dayhoff's probability matrices and Felsenstein's
pruning algorithm) to arbitrary-length sequences. In this paper, we report
results of a simulation-based benchmark of several methods for reconstruction
of indel history. The methods tested include a relatively new algorithm for
statistical marginalization of MSAs that sums over a stochastically-sampled
ensemble of the most probable evolutionary histories. For mammalian
evolutionary parameters on several different trees, the single most likely
history sampled by our algorithm appears less biased than histories
reconstructed by other MSA methods. The algorithm can also be used for
alignment-free inference, where the MSA is explicitly summed out of the
analysis. As an illustration of our method, we discuss reconstruction of the
evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with
arXiv:1103.434
Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.)
The extreme resistance to Turnip mosaic virus observed in the Chinese cabbage (Brassica rapa) line, BP8407, is monogenic and recessive. Bulked segregant analysis was carried out to identify simple sequence repeat and Indel markers linked to this recessive resistance gene, termed recessive Turnip mosaic virus resistance 02 (retr02). Mapping of PCR-specific Indel markers on 239 individuals of a BP8407 × Ji Zao Chun F 2 population, located this resistance gene to a 0.9-cM interval between two Indel markers (BrID10694 and BrID101309) and in scaffold000060 or scaffold000104 on chromosome A04 of the B. rapa genome. Eleven eukaryotic initiation factor 4E (eIF4E) and 14 eukaryotic initiation factor 4G (eIF4G) genes are predicted in the B. rapa genome. A candidate gene, Bra035393 on scaffold000104, was predicted within the mapped resistance locus. The gene encodes the eIF(iso)4E protein. Bra035393 was sequenced in BP8407 and Ji Zao Chun. A polymorphism (A/G) was found in exon 3 between BP8407 and Ji Zao Chun. This gene was analysed in four resistant and three susceptible lines. A correlation was observed between the amino acid substitution (Gly/Asp) in the eIF(iso)4E protein and resistance/susceptibility. eIF(iso)4E has been shown previously to interact with the TuMV genome-linked protein, VPg
Pair HMM based gap statistics for re-evaluation of indels in alignments with affine gap penalties: Extended Version
Although computationally aligning sequence is a crucial step in the vast
majority of comparative genomics studies our understanding of alignment biases
still needs to be improved. To infer true structural or homologous regions
computational alignments need further evaluation. It has been shown that the
accuracy of aligned positions can drop substantially in particular around gaps.
Here we focus on re-evaluation of score-based alignments with affine gap
penalty costs. We exploit their relationships with pair hidden Markov models
and develop efficient algorithms by which to identify gaps which are
significant in terms of length and multiplicity. We evaluate our statistics
with respect to the well-established structural alignments from SABmark and
find that indel reliability substantially increases with their significance in
particular in worst-case twilight zone alignments. This points out that our
statistics can reliably complement other methods which mostly focus on the
reliability of match positions.Comment: 17 pages, 7 figure
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