bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-Validation Without Doing Cross-Validation in Genome-Enabled Prediction
Authors: Gianola Daniel , Schön Chris-Carolin 
Published: August 2016

AbstractCross-validation of methods is an essential component of genome-enabled prediction of complex traits. We develop formulae for computing the predictions that would be obtained when one or several cases are removed in the training process, to become members of testing sets, but by running the model using all observations only once. Prediction methods to which the developments apply include least squares, best linear unbiased prediction (BLUP) of markers, or genomic BLUP, reproducing kernels Hilbert spaces regression with single or multiple kernel matrices, and any member of a suite of linear regression methods known as “Bayesian alphabet.” The approach used for Bayesian models is based on importance sampling of posterior draws. Proof of concept is provided by applying the formulae to a wheat data set representing 599 inbred lines genotyped for 1279 markers, and the target trait was grain yield. The data set was used to evaluate predictive mean-squared error, impact of alternative layouts on maximum likelihood estimates of regularization parameters, model complexity, and residual degrees of freedom stemming from various strengths of regularization, as well as two forms of importance sampling. Our results will facilitate carrying out extensive cross-validation without model retraining for most machines employed in genome-assisted prediction of quantitative traits.
Genome Evolution in Three Species of CactophilicDrosophila
Authors: Sanchez-Flores Alejandro , Peñaloza Fernando , Carpinteyro-Ponce Javier , Nazario-Yepiz Nestor , Abreu-Goodger Cei , Machado Carlos A , Markow Therese Ann 
Published: August 2016

AbstractWe report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa. These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.
Genome-Wide Association Studies with a Genomic Relationship Matrix: A Case Study with Wheat and Arabidopsis
Authors: Gianola Daniel , Fariello Maria I , Naya Hugo , Schön Chris-Carolin 
Published: August 2016

Abstract
Standard genome-wide association studies (GWAS) scan for relationships between each of p molecular markers and a continuously distributed target trait. Typically, a marker-based matrix of genomic similarities among individuals (G) is constructed, to account more properly for the covariance structure in the linear regression model used. We show that the generalized least-squares estimator of the regression of phenotype on one or on m markers is invariant with respect to whether or not the marker(s) tested is(are) used for building G, provided variance components are unaffected by exclusion of such marker(s) from G. The result is arrived at by using a matrix expression such that one can find many inverses of genomic relationship, or of phenotypic covariance matrices, stemming from removing markers tested as fixed, but carrying out a single inversion. When eigenvectors of the genomic relationship matrix are used as regressors with fixed regression coefficients, e.g., to account for population stratification, their removal from G does matter. Removal of eigenvectors from G can have a noticeable effect on estimates of genomic and residual variances, so caution is needed. Concepts were illustrated using genomic data on 599 wheat inbred lines, with grain yield as target trait, and on close to 200 Arabidopsis thaliana accessions.
A Forward Genetic Screen and Whole Genome Sequencing Identify Deflagellation Defective Mutants inChlamydomonas, Including Assignment of ADF1 as a TRP Channel
Authors: Hilton Laura K , Meili Fabian , Buckoll Paul D , Rodriguez-Pike Julie C , Choutka Courtney P , Kirschner Jaime A , Warner Freda , Lethan Mette , Garces Fabian A , Qi Jingnan , Quarmby Lynne M 
Published: August 2016

AbstractWith rare exception, ciliated cells entering mitosis lose their cilia, thereby freeing basal bodies to serve as centrosomes in the formation of high-fidelity mitotic spindles. Cilia can be lost by shedding or disassembly, but either way, it appears that the final release may be via a coordinated severing of the nine axonemal outer doublet microtubules linking the basal body to the ciliary transition zone. Little is known about the mechanism or regulation of this important process. The stress-induced deflagellation response of Chlamydomonas provides a basis to identifying key players in axonemal severing. In an earlier screen we uncovered multiple alleles for each of three deflagellation genes, ADF1, FA1, and FA2. Products of the two FA genes localize to the site of axonemal severing and encode a scaffolding protein and a member of the NIMA-related family of ciliary-cell cycle kinases. The identity of the ADF1 gene remained elusive. Here, we report a new screen using a mutagenesis that yields point mutations in Chlamydomonas, an enhanced screening methodology, and whole genome sequencing. We isolated numerous new alleles of the three known genes, and one or two alleles each of at least four new genes. We identify ADF1 as a TRP ion channel, which we suggest may reside at the flagellar transition zone.
Komponen Kebutuhan Hidup Dalam Regulasi Upah Minimum Perspektif Maqa>s}id Al-Shari>’Ah
Authors: Fadilah Adin 
Published: August 2016

<p><strong>Abstract: </strong>The provisions of minimum wage in Indonesia have been changing four times in the last few decades in line with the changes in the components of life needs referred. In fact, there are many life needs that previously were considered as trivial but they have now become important and should be referred to in setting the minimum wage. In Islam there are five sectors of human needs as established in the discourse of <em>maqa&gt;s}id al-shari&gt;'ah</em>. Each sector is ranked into three levels, namely <em>d}aru&gt;ri&gt;yah</em>, <em>h}a&gt;ji&gt;yah</em>, and<em> tah}si&gt;ni&gt;yah</em>. This study examines how the components of life needs have been referred by the regulation of the minimum wage from the viewpoint of <em>maqa&gt;s}id al-shari&gt;'ah</em>. This study came to the conclusion that the development of life needs used as guidelines in determining minimum wage levels has met the demands of life needs as intended by <em>maqa&gt;s}id al-shari&gt;’ah</em>. Most of the components of decent living (KHL) occupy levels of <em>d}aru&gt;ri&gt;yah</em> and <em>h}a&gt;ji&gt;yah</em>, and very few are classified as <em>tah}si&gt;ni&gt;yah</em>. The enhancement of quantity and quality of the components proven the attention to the level of life needs sequentially from <em>d}aru&gt;ri&gt;yah</em> level, the <em>h}a&gt;ji&gt;yah</em>, then the <em>tah}si&gt;ni&gt;yah</em> level. These changes indicate the change of law in accordance with the demands of the circumstances.</p><strong>Abstrak: </strong>Komponen kebutuhan hidup yang dijadikan acuan dalam penetapan upah minimum di Indonesia telah mengalami perubahan sebanyak 4 kali. Perubahan ini terjadi karena menyesuaikan perkembangan kebutuhan dahulu dianggap sepele namun kini menjadi penting. Dalam Islam ada 5 unsur pokok kebutuhan manusia yang harus dipenuhi atau yang dikenal dengan istilah <em>maqa&gt;s}id al-shari&gt;’ah</em>. Kelima unsur pokok <em>maqa&gt;s}id al-shari&gt;’ah</em> ini terbagi mejadi 3 kategori yakni <em>d}aru&gt;ri&gt;yah</em>, <em>h}a&gt;ji&gt;yah</em>, dan <em>tah}si&gt;ni&gt;yah</em>. Penelitian ini mengkaji bagaimana komponen kebutuhan hidup dalam regulasi upah minimum perspektif <em>maqa&gt;s}id al-shari&gt;’ah</em>. Penelitian ini memberi kesimpulan bahwa perkembangan kebutuhan hidup yang dijadikan pedoman dalam penentuan upah minimum telah memperhatikan tingkatan kebutuhan hidup. Sebagian besar komponen KHL ada pada wilayah <em>d}aru&gt;ri&gt;yah</em> dan <em>h}a&gt;ji&gt;yah,</em> sedikit sekali yang tergolong <em>tah}si&gt;ni&gt;yah</em>. Penambahan kuota komponen serta peningkatan kualitas komponen menjadi bukti bahwa adanya perhatian terhadap tingkatan kebutuhan dimulai dari yang <em>d}aru&gt;ri&gt;yah</em> dulu baru kemudian yang <em>h}a&gt;ji&gt;yah</em> baru disusul yang <em>tah}si&gt;ni&gt;yah</em>. Perubahan ini menunjukkan adanya perubahan hukum sesuai dengan perkembangan situasi.
Pembiayaan Bagi hasil Sektor Usaha Mikro di BMT Hasanah Ponorogo
Authors: Dewi Arlinta Prasetian 
Published: August 2016

<p><strong>Abstract: </strong>Financing is one of the products of the <em>Baitul Mal wat Tamwil (BMT)</em> much in demand, in the form of profit sharing and is based on Islamic principles. However, such products is in fact high risk, because the profits and losses will be shared. One of the evidence of that is that the troubled financing in BMT Hasanah currently reaches 10%, and urgently needs immediate actions to avoid deterioration. This study examined BMT Hasanah commitment to operational standards for this kind of financing. The results showed that the financing mechanism in the form of profit sharing in BMT Hasanah has several stages; namely the examination stage, the analysis stage and the stage of the disbursement of funds. Risk management cycle begins with risk identification, risk measurement and risk management. BMT Hasanah manages the risks through preventive measures, revitalizing and curative measures or takeover of collateral. To minimize risks, the BMT Hasanah implements three strategies, the strategy of the finance portfolio, the strategy of collection of receivables and the collateral strategy.</p><strong>Abstrak: </strong>Pembiayaan merupakan salah satu produk lembaga keuangan yang banyak diminati. BMT sebagai lembaga keuangan mikro yang menjalankan operasional kerjanya dengan prinsip syariah, identik dengan pembiayaan bagi hasil. Meskipun demikian, tingkat pembiayaan bagi hasil pada sebagian lembaga keuangan masih rendah. Hal ini dikarenakan pembiayaan bagi hasil masuk dalam kategori<em>high risk</em>, karena keuntungan maupun kerugian akan ditanggung oleh kedua belah pihak. Pembiayaan bermasalah di BMT Hasanah saat ini mecapai 10%, jika tidak segera diambil tindakan kemungkinan bertambah akan tinggi. Maka, penelitian memfokuskan bagaimana kesesuaian pembiayaan bagi hasil di BMT Hasanah dengan fatwa DSN MUI sekaligus manajemen resikonya terhadap pembiayaan yang bermasalah. Hasil penelitian menunjukkan bahwa, mekanisme pembiayaan bagi hasil di BMT Hasanah dibagi menjadi beberapa tahapan, tahap pemeriksaan, tahap analisa dan tahap pencairan dana. Siklus manajemen resiko diawali dengan Identifikasi resiko, pengukuran resiko dan pengelolaan resiko. Pengelolaan resiko BMT Hasanah melalui tindakan <em>prefentif, revitalisasi dan kuratif/ </em>pengambil alihan agunan. Untuk meminimalisir resiko, BMT mengelompokkan strategi kedalam tiga kelompok, yaitu: strategi penyaluran pembiayaan, strategi pengumpulan piutang dan strategi jaminan.
Pengaruh Sistem Waralaba Terhadap Retail Kecil Di Ponorogo Tinjauan Maṣlaḥah
Authors: Wulandari Siti 
Published: August 2016

<p><strong>Abstract: </strong>One of the indications of the acceleration of economic progress in Ponorogo is the rapid development of the real sectors, especially the proliferation of modern businesses using the franchise system. Therefore, small retail businesses today are facing new competitors with huge capital and reliability of modern management. This study tries to find out the impact of the franchise system invasion to the existence of small retails, and how it affects the <em>ma</em><em>ṣ</em><em>la</em><em>ḥ</em><em>ah</em> (safety) of small retails in Ponorogo. This study uses the theory of <em>maqā</em><em>ṣ</em><em>id</em> <em>al-sharīah</em> in the aspects of <em>ḥ</em><em>if</em><em>ẓ</em><em> al-māl</em> to analyze the sustainability of small retail businesses amid the proliferation of franchise businesses. <em>Ma</em><em>ṣ</em><em>lā</em><em>ḥ</em><em>ah</em> is thinking about the advantages and disadvantages on the basis of religious teachings by thinking about priorities and side with the community (<em>al-ma</em><em>ṣ</em><em>la</em><em>ḥ</em><em>ah</em> <em>al-'āmah</em>). The results of this study found out the threat of franchise trading system to the existence of small retails. Therefore, the <em>ma</em><em>ṣ</em><em>la</em><em>ḥ</em><em>ah</em> for small retail of businesses means the realization of the safety from the expansion of large investors, such as monopoly.</p><p><strong>Abstrak: </strong>Salah satu indikator meningkatnya laju perekonomian Kabupaten Ponorogo ditandai dengan pesatnya perkembangan sektor riil terutama dengan menjamurnya berbagai jenis toko-roko modern (khususnya dengan sistem waralaba) yang terus bertambah jumlahnya. Lalu bagaimana dengan para pebisnis retail kecil yang kebanyakan mereka memiliki usaha dengan modal yang tidak terlalu besar. Penelitian ini berupaya mengetahui adakah pengaruh yang terjadi akibat adanya toko-toko dengan sistem waralaba terhadap eksistensi retail kecil, serta adakah pengaruhnya terhadap kemaslahatan retail kecil yang ada di Ponorogo. Penelitian ini menggunakan teori keberlangsungan usaha yang dikaitkan dengan <em>maqāsid al-shar’īah</em> aspek kemaslahatan <em>hifz al-māl</em> untuk menguji pengaruh kemaslahatan retail kecil dengan adanya bisnis waralaba. Hasil penelitian ini menunjukan hubungan signifikan, artinya terdapat pengaruh negatif sistem waralaba terhadap eksistensi retail kecil dan juga mengganggu kemaslahatannya. <em>Maslāhah</em> menurut Abd al Wahhāb Khallāf adalah sesuatu yang dapat menarik suatu manfaat dalam suatu masyarakat, menolak bahaya, atau menghilangkan kesulitan bagi peradaban umat manusia. Kemaslahatan dari aspek <em>hifz al-māl</em> adalah terciptanya kesejahteraan dalam masyarakat dengan terjaga dari monopoli usaha, serta kesenjangan ekonomi dan taraf hidup. Dalam konteks retail kecil di Ponorogo, agar keberlangsungannya dan kemaslahatannya terjaga, harus mampu berkreasi dan berinovasi mengembangkan usahanya dalam menghadapi persaingan global.</p>
Pemahaman PNS Lulusan Pondok Pesantren Tentang Kewajiban Zakat Profesi Perspektif Sosiologi Pengetahuan
Authors: Fitriani Hanik 
Published: August 2016

<p><strong>Abstract: </strong>The idea of profession alms is a relatively novelty in Indonesian Islamic societies. In Indonesia, the government officials who are graduates of boarding school really know that the Koran, Hadith, and religious textbooks, which they have learned, do not require profession alms. So they consider profession alms as an unknown duty in Islam. But in reality, the profession alms has been charged by the government to them directly deducted monthly from their salaries. This study examines the attitude of government employees who are graduates of the boarding school on the obligations of profession alms with the main question “why they finally fulfill alms profession”. The answers will be sought with the perspective of the sociology of knowledge. This perspective is used to reveal which human knowledge is most decisive for his actions. This research has resulted in findings, using the Karl Mannheim’s relationism theory, that the subordination of government employees graduated from boarding school to to pay profession alms is dominated by power relation. Here knowledge has been used as instrument of power to determine a rule that must effectively apply.</p><strong>Abstrak: </strong>Zakat profesi merupakan wacana baru yang berkembang di masyarakat. Para pegawai negeri sipil (PNS) lulusan pondok pesantren memahami bahwa kewajiban zakat profesi tidak dibahas dalam al-Qur’an, Hadith, dan literatur salaf. Dalam konteks ini, peraturan pemerintah yang menetapan kadar zakat profesi sebesar 2,5%, yang langsung dipotongkan dari gaji PNS setiap bulannya, mendapat tanggapan kontroversial dari sebagian kalangan PNS lulusan pondok pesantren karena belum menemukan dasar yang kuat. Penelitian ini akan mengkaji terkait pandangan PNS lulusan Pondok pesantren mengenai kewajiban zakat profesi, serta landasan PNS tersebut dalam menjalankan kewajiban membayar zakat profesi. Penelitian ini menghasilkan temuan, <em>Pertama,</em> PNS lulusan pondok pesantren menganggap bahwa relasionisme antara PNS lulusan pondok pesantren merupakan implementasi konsep relasionisme Karl Mannheim, buktinya bahwa pengetahuan tentang zakat profesi dimunculkan oleh pemerintah sebagai penguasa. <em>Kedua,</em> Dasar ketundukan PNS lulusan pondok pesantren tetap patuh membayar zakat profesi didominasi oleh relasi kekuasaan dan pengetahuan, pemerintah yang memiliki kekuasaan memiliki kekuatan untuk mengikat PNS sebagai masyarakat. Pengetahuan sebagai alat yang digunakan oleh kekuasaan untuk menentukan sebuah peraturan yang harus dipatuhi oleh masyarakat.<p> </p>
Pemanfaatan Social Media Network Sebagai Media Komunikasi Komunitas Pustakawan Homogen Dalam Rangka Optimalisasi Resources Sharing Koleksi Antar Perguruan Tinggi
Authors: Haryanto Haryanto 
Published: August 2016

<p><strong>Abstrak</strong><strong>; </strong>Karya ilmiah ini merupakan hasil analisis yang mengulas media sosial sebagai media yang sangat efektif di jadikan sebagai media komunikasi komunitas pustakawan dari perpustakaan yang sama program studinya (homogen) antar perguruan tinggi.</p><p>Tujuan dari analisis ini adalah terciptanya komunikasi antar pustakawan homogen antar perguruan tinggi sehingga dapat saling mendukung dalam penyediaan koleksi. karena dalam dunia perpustakaan, keterbatasan koleksi dihadapi oleh hampir semua perpustakaan, sehingga diperlukan usaha seperti sharing koleksi (resources sharing), untuk itu di perlukan suatu media yang dapat dijadikan media komunikasi yang menghubungkan perpustakaan-perpustakaan tersebut. Dan media sosial tersebut adalah facebook</p><p>Dengan media sosial dapat dimungkinkan membuat komunitas-komunitas sejenis atau homogen sehingga dapat berkomunikasi secara cepat untuk sharing koleksi. Dalam memanfaatkan media sosial untuk resources sharing perpustakaan perguruan tinggi, agar efektif diperlukan beberapa hal diantaranya kesamaan komunitas jurusan / homogen, admin utama pengendali, kesepakatan resources sharing, daftar admin masing-masing perpustakaan, jasa ekspedisi, serta MoU.</p><strong><em></em></strong><strong><em>Abstract</em></strong><em>; </em><em>This paper is the result of analysis to review social media as a very effective medium in use as a medium of communication community librarians from the same library studies program (homogeneous) between universities.</em><p><em></em><em>The purpose of this analysis is the creation of a homogeneous communication between librarians between </em><em>universities</em><em> so that they can support each other </em><em>to provide</em><em> of collection. </em><em>I</em><em>n the world of libraries, collection limitations faced by almost all libraries, so that the necessary efforts such as sharing collections (resources sharing), for it is need</em><em>ed</em><em> of a </em><em>comunication </em><em>medium that can be used as a medium of communication that connect these libraries. And social media is facebook</em></p><p><em></em><em>With social media may be possible to create communities of similar or homogeneous so that they can communicate </em><em>quickly for sharing collections. In utilizing social media for sharing resources the college library, in</em><em> order to effectively take a few things in common among communities majors / homogeneous, the main admin control, resources sharing deal, admin list each library, freight forwarding services, as well as the MoU.</em></p><p> </p><p><strong> </strong></p>
Digitalisasi Katalog Pameran Dalam Pengembangan Image Repository: Studi Analisis Proses Di UPT Perpustakaan ISI Yogyakarta
Authors: Hakim Heri Abi Burachman 
Published: August 2016

<p><strong>Abstrak;</strong> Makalah ini akan mendiskripsikan proses digitalisasi katalog pameran yang dilakukan UPT Perpustakaan ISI Yogyakarta. Digitalisasi katalog pameran dilakukan dalam rangka pengembangan <em>image repository</em>. Pengembangan <em>image repository</em> merupakan upaya untuk meningkatkan aksesibilitas katalog pameran. Katalog pemeran merupakan koleksi yang mendokumentasi karya seni lengkap dengan informasi pencipta karya serta deskripsi dari karya. Melalui penulisan makalah ini penulis akan mendeskripsikan kegiatan pemilihan aplikasi, proses digitalisisi katalog pameran, penentuan format file gambar serta organisasi informasi hasil digitalisasi. Dengan penulisan makalah ini diharapkan mampu memberikan gambaran teknis terkait kegiatan digitalisasi dan pengelolaan koleksi gambar berbasis <em>image repository</em>. Dengan digitalisi katalog pameran dan mengelolanya melalui<em> image repository </em>memungkinkan memperbanyak titik akses penelusuran informasi. Selama ini katalog pameran hanya dapat ditelusurr dengan titik akses judul pameran, subjek serta kurator. Dengan pengelolaan gambar berbasis<em> image repository</em> dapat dilakukan dengan menggunakan nama pencipta karya, judul karya, judul pemeran, subjek dan kurator.</p><strong><em>Abstract;</em></strong><em> This paper will describes how to digitize exhibition catalogue that was did by ISI Yogyakarta Library, to develop image repository. The development of image repository should be done to make easy access to the catalogue. Exhibition catalogue is a collection of complete art work, including of creator and art description. This paper will also describes how to choose application, digitizing process, how to organize catalogue and ensure picture file format. Base on image repository, the catalogue should make more access point to search, including author, title, exhibition title, subject and curator. </em><p><strong> </strong></p><p><strong></strong><em><br /></em></p>