bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Novel Strong and Ubiquitous Promoter/Enhancer in the SilkwormBombyx mori
Authors: Tsubota Takuya , Uchino Keiro , Suzuki Takao K , Tanaka Hiromitsu , Kayukawa Takumi , Shinoda Tetsuro , Sezutsu Hideki 
Published: May 2014

AbstractTransgenic techniques offer a valuable tool for determining gene functions. Although various promoters are available for use in gene overexpression, gene knockdown, and identification of transgenic individuals, there is nevertheless a lack of versatile promoters for such studies, and this dearth acts as a bottleneck, especially with regard to nonmodel organisms. Here, we succeeded in identifying a novel strong and ubiquitous promoter/enhancer in the silkworm. We identified a unique silkworm strain whose reporter gene showed strong and ubiquitous expression during the establishment of enhancer trap strains. In this strain, the transposon was inserted into the 5′UTR of hsp90, a housekeeping gene that is abundantly expressed in a range of tissues. To determine whether the promoter/enhancer of hsp90 could be used to induce strong gene expression, a 2.9-kb upstream genomic fragment of hsp90 was isolated (hsp90P2.9k), and its transcriptional activation activity was examined. Strikingly, hsp90P2.9k induced strong gene expression in silkworm cell cultures and also strongly induced gene expression in various tissues and developmental stages of the silkworm. hsp90P2.9k also exhibited significant promoter/enhancer activity in Sf9, a cell culture from the armyworm, suggesting that this fragment might possibly be used as a gene expression tool in other Lepidoptera. We further found that 2.0 kb of hsp90P2.9k is sufficient for the induction of strong gene expression. We believe that this element will be of value for a range of studies such as targeted gene overexpression, gene knockdown and marker gene expression, not only in the silkworm but also in other insect species.
Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
Authors: Burton Joshua N , Liachko Ivan , Dunham Maitreya J , Shendure Jay 
Published: May 2014

Abstract
Microbial communities consist of mixed populations of organisms, including unknown species in unknown abundances. These communities are often studied through metagenomic shotgun sequencing, but standard library construction methods remove long-range contiguity information; thus, shotgun sequencing and de novo assembly of a metagenome typically yield a collection of contigs that cannot readily be grouped by species. Methods for generating chromatin-level contact probability maps, e.g., as generated by the Hi-C method, provide a signal of contiguity that is completely intracellular and contains both intrachromosomal and interchromosomal information. Here, we demonstrate how this signal can be exploited to reconstruct the individual genomes of microbial species present within a mixed sample. We apply this approach to two synthetic metagenome samples, successfully clustering the genome content of fungal, bacterial, and archaeal species with more than 99% agreement with published reference genomes. We also show that the Hi-C signal can secondarily be used to create scaffolded genome assemblies of individual eukaryotic species present within the microbial community, with higher levels of contiguity than some of the species’ published reference genomes.
Genetic Control of Maize Shoot Apical Meristem Architecture
Authors: Thompson Addie M , Crants James , Schnable Patrick S , Yu Jianming , Timmermans Marja C P , Springer Nathan M , Scanlon Michael J , Muehlbauer Gary J 
Published: May 2014

AbstractThe shoot apical meristem contains a pool of undifferentiated stem cells and generates all above-ground organs of the plant. During vegetative growth, cells differentiate from the meristem to initiate leaves while the pool of meristematic cells is preserved; this balance is determined in part by genetic regulatory mechanisms. To assess vegetative meristem growth and genetic control in Zea mays, we investigated its morphology at multiple time points and identified three stages of growth. We measured meristem height, width, plastochron internode length, and associated traits from 86 individuals of the intermated B73 × Mo17 recombinant inbred line population. For meristem height-related traits, the parents exhibited markedly different phenotypes, with B73 being very tall, Mo17 short, and the population distributed between. In the outer cell layer, differences appeared to be related to number of cells rather than cell size. In contrast, B73 and Mo17 were similar in meristem width traits and plastochron internode length, with transgressive segregation in the population. Multiple loci (6−9 for each trait) were mapped, indicating meristem architecture is controlled by many regions; none of these coincided with previously described mutants impacting meristem development. Major loci for height and width explaining 16% and 19% of the variation were identified on chromosomes 5 and 8, respectively. Significant loci for related traits frequently coincided, whereas those for unrelated traits did not overlap. With the use of three near-isogenic lines, a locus explaining 16% of the parental variation in meristem height was validated. Published expression data were leveraged to identify candidate genes in significant regions.
Genome-Wide Estimation of Linkage Disequilibrium from Population-Level High-Throughput Sequencing Data
Authors: Maruki Takahiro , Lynch Michael 
Published: May 2014

Abstract
Rapidly improving sequencing technologies provide unprecedented opportunities for analyzing genome-wide patterns of polymorphisms. In particular, they have great potential for linkage-disequilibrium analyses on both global and local genetic scales, which will substantially improve our ability to derive evolutionary inferences. However, there are some difficulties with analyzing high-throughput sequencing data, including high error rates associated with base reads and complications from the random sampling of sequenced chromosomes in diploid organisms. To overcome these difficulties, we developed a maximum-likelihood estimator of linkage disequilibrium for use with error-prone sampling data. Computer simulations indicate that the estimator is nearly unbiased with a sampling variance at high coverage asymptotically approaching the value expected when all relevant information is accurately estimated. The estimator does not require phasing of haplotypes and enables the estimation of linkage disequilibrium even when all individual reads cover just single polymorphic sites.
Introduction: Islamic Law in South-East Asia
Authors: Hooker MB. 
Published: May 2014

In this paper the author confines herself to a specific set of material so as to narrow the issue. All too often this is not done and, as a consequence, argument very quickly degenerates into generalities, mostly driven by personal and/or political bias. Such is illustrated in Ahmad's discussion of Western feminist comment on Islam, Muslim women and human rights where, in quite influential books, we find a combination of inappropriate theory with no understanding of fiqh. The theory looks convincing to a Western reader because it is Western. The insidious nature of the assumptions involved is demonstrated in Ahmad's discussion of Iranian and Malaysian Muslim feminist writings in which we can find an "internalised orientalism". All that this means is that Western feminist theory has set the agenda and determines the method of argument, a position which is not acceptable.DOI: 10.15408/sdi.v10i1.636
Public Faces of Sharī’ah in Contemporary Indonesia: Towards a National Madhhab
Authors: Hooker MB. , Lindsey Tim 
Published: May 2014

The thesis of this article that all faces and expressions of shari'ah in Indonesia must be read together and that together they point to a debate about Islamic law that, while fragmented, might be said to be peculiar to Indonesia. Can they be made to amount to assonance or is dissonance the characteristic of this Madhhab Nasional Shari'ah Republik Indonesia? And if dissonance is the defining characteristic, is that necessarily a bad thing? We will suggest some answers to these questions in the conclusion to this article.DOI: 10.15408/sdi.v10i1.637
Islamic Banking in Malaysia: Past, Present and Future
Authors: Borhan Joni Tamkin 
Published: May 2014

This paper will discuss the historical development of establishment of Islamic banking in Malaysia, their operations and application of Islamic Commercial Law's principles in the Malaysian Islamic banking system. This paper will also elaborates the challenges and some issues which are being faced by Malaysian Islamic banking system and its prospects in the future.DOI: 10.15408/sdi.v10i2.630
Al-Islām wa al-Mar’ah: Qaḍīyat al-Mar’ah ‘inda al-Dārisīn bi al-Jamī’at al-Islāmīyah al-Ḥukūmīyah bi Indūnīsīyā
Authors: Jahroni Jajang 
Published: May 2014

The article's main aim is to map the development of gender discourse in IAIN throughout Indonesia. As is known, the discourse on gender only emerged and began to develop in lndonesia in the early 1990s. Yet, IAIN is not only involved in this movement but also plays a very important role in directing the movement. Many IAIN figures are influential gender activists in lndonesia.DOI: 10.15408/sdi.v10i2.632
Antara Hitam dan Putih: Penghulu pada Masa Kolonial Belanda
Authors: Fauzia Amelia 
Published: May 2014

As indicated in the title, this book describes position of the pangulu as a social phenomenon in the period of Dutch colonial administration when many social and religious changes took place. There are three main focuses of the book in describing the role of the pangulu; first, to examine their history and structure in the colonial government; second, to describe their conflicting roles as Islamic leaders and as colonial government officials; and third, to understand how pangulu interacted with Islamic reformism and the nationalist movement.DOI: 10.15408/sdi.v10i2.634
Outlines of the Strategic Plan UIN Syarif Hidayatullah Jakarta: Heading towards becoming a Research University by the Year 2007
Authors: Azra Azyumardi 
Published: May 2014

What is meant by the term Research University? Essentially, a Research university is a university based upon a research tradition. The implications are broad, being that the university must have the capabilities and facilities to support the strengthening of this research tradition. In realizing these aspirations, there is a need to identify how prepared the university is to begin developments in the areas of academic, financial and administrative, institutional, and student affairs. This is necessary to obtain an objective evaluation of the actual capacity of the institution in the above four areas.DOI: 10.15408/sdi.v10i2.635
Mapping Radical Islam in Indonesia
Authors: Jamhari Jamhari 
Published: May 2014

This paper focuses on the emergence of groups that, according to their followers, want to apply Islamic teachings comprehensively (kaffah) and wholeheartedly. These groups have been variously described as fundamentalist, extremist, radical, and militant. Of course, they do not apply these labels to themselves. The labeling of certain groups has resulted in them gaining negative or pejorative images. It is important to note that the label "fundamentalism" initially applied to Christian-Protestant groups, actually has a neutral meaning. It refers to groups that attempt to return to their basic religious foundations.DOI: 10.15408/sdi.v10i3.622
Sha’ā’ir Qirā’ah Rawātib al-Ḥaddād fī Indūnīsīyā: Dirāsah Tamhīdīyah
Authors: Abdillah Aam 
Published: May 2014

This article aims to provide a picture of the traditions of one of the ratib developed by the tariqah followers, namely ratlb al-Haddad, which is often linked to one of the authors and Sufi from Hadrami, Sayyid 'Abd Allah ibn 'Alwt al-Hnddad. In the Indonesian Muslim community, the tradition of rending ratib al-Haddad is believed to have its roots in the tenchings of 'Alawiyyah order. In several regions, such as Bekasi, West Jvan and in the Betawi community, for example, the reading of ratibib al-Haddad has become a tradition that is passed down from one generation to the next, and which is included on various occasions, such as major Islamic days of remembrance, and other religions celebrations.DOI: 10.15408/sdi.v10i3.626
Sufism and the "Modern" in Islam
Authors: Wahid Din 
Published: May 2014

At a time when the popular imagination outside the Muslim world has been captured by images of Muslim "fundamentalists" terrorising the "West" and when predominantly Muslim countries themselves are under a variety of political pressures to express solidarity with narrowly legalistic lslam, it is timely to reappraise the actual variety of Islamic religiosity active in the lives of ordinary Muslims. Considerable effort is now being made by scholars, governments and private risk assessment agencies, to identify the social spaces occupied by intolerant, exclusivist expressions of Islam deriving from narrowly legalistic understandings of Islam. However, less energy is being directed towards identifying the contemporary modalities of liberal, non-exclusiuist modes of lslamic religiosity.DOI: 10.15408/sdi.v10i3.628
The Fragmentation of Religious Authority: Islamic Print Media in Early 20th Century Indonesia
Authors: Burhanudin Jajat 
Published: May 2014

Aside from the scarcity of historical sources, it is not the intention of this article to determine when the pesantren -or pesantren like institutions, namely surau in West Sumatra and dayah in Aceh- began to exist. Here, the main concern is that in the nineteenth century the pesantrens were established as the educational institutions of Indonesian Muslims. Dutch statistical sources from this period recorded that there were about fifteen thousands (15,000) pesantrens in Java and Madura, and about twenty-three thousand (23,000) santris (the students of pesantren) (van den Berg 1886: 518-9).DOI: 10.15408/sdi.v11i1.652
On the Genesis of Intellectual Crossroads: Early Fragmentation in the Formation of Modern Indonesian Intelligentsia
Authors: Latif Yudi 
Published: May 2014

This article is an inter-textual analysis of the early colonial and capitalist driven implantation of a western education system and its subsequent influence on the way of thought of the East Indies new elite. Such a feature will be juxtaposed with the impacts of the deepening penetration of colonialism and capitalism on the continuity and discontinuity of historical Islam.DOI: 10.15408/sdi.v11i1.653
In Search of Principles of Good Governance: Lesson Learned from a Series of Workshops on "Islamic Western Dialogues on Governance Values"
Authors: Ropi Ismatu 
Published: May 2014

In the Indonesia context, issues of good governance have also been an unflagging national agenda. Despite recognition of the importance of good governance, public discourse on this issue has not gained as much attention as it should within this newly democratic country. Following the downfall of the New Order government in 1998,Indonesia has faced the task of rebuilding a social and political system responsive to the changing expectations of the Indonesian people, embodied in the new animating spirit popularly known as Reformasi. This paradigm of reform refers to the wish to see democratic ideals permeate the lives of all Indonesians.DOI: 10.15408/sdi.v11i1.657
Mafhūm Ahl al-Sunnah wa al-Jamā’ah ‘Inda Jam’īyah Nahḍah al-‘Ulamā’
Authors: Hasan Mohammad Tolchah 
Published: May 2014

this article deals with one of the basic pillars of traditionalist Islam in Indoneisa, ahlussunah waljama'ah (Ar. ahl al-sunnah wa al-jama'ah, meaning people of the sunnah and the [orthodox] community). it was first advocated in Indonesia by the leading 'ulama of the pesantrens, and then appeared as a key religious principle for Nahdlatul Ulama (NU), an institution of 'ulama in Indonesia established in 1926.DOI: 10.15408/sdi.v12i1.648
Literal Translation, Sacred Scripture and Kitab Malay
Authors: Riddell Peter G. 
Published: May 2014

The study of Malay dialects was a specialist concern during the period of Dutch colonization of Indonesia and British colonization of the Malay peninsular. In recent times, the Malaysian National Language Council, the Dewan Bahasa dan Pustaka, and its Indonesian counterpart, the Pusat Pembinaan dan Pengembangan Bahasa (PPPB), have devoted considerable resources to the study of Malay dialectology. Such dialect studies have necessarily had a geographical focus, by way of descriptive grammars of Malay dialects spoken in particular areas. Examples are the studies of Pontianak Malay (Kamal et. al' 1986) and Palembang Malay (Aliana et. al. 1987) published by the PPPB.DOI: 10.15408/sdi.v9i1.672
Uṣūl al-Madhāhib al-Ṣūfīyah al-Muḥaddathah bi Indūnīsīyā: Mulāhaẓat ‘alā Kitāb Itḥāf al-Dhākī li al-Shaykh Ibrāhīm al-Kurānī
Authors: Fathurahman Oman 
Published: May 2014

The present article is a philological study of one of the most important works of lbrahim al-Kurani, written in Malay-Indonesian context, that is Ithaf al-Zaki bi Sharh al-Tuhfah al-Mursalah Ila Ruh al- Nabi. Looking at the title, one can see that Ithaf al-Zaki -two of the manuscripts of which were found in the library of Dar al-Kutub al-Misriyyah, Cairo- is a commentary of the Tuhfah al-Mursalah Ila Ruh al-Nabi of al-Burhanpuri. As is mentioned above, this particular work of al-Burhanpuri had raise controversy not only among the Malay-Indonesian Muslim scholars, but also in the Muslim world in general.DOI: 10.15408/sdi.v9i1.676
Al-Shaykh Muḥammad Zain Shukrī: Imtidād al-Turāth al-Fikrī li ‘Ulamā’ Fālimbānj fī al-Qarn al-‘Ishrīn al-Mīlādī
Authors: Zulkifli Zulkifli 
Published: May 2014

This present article, which was written to try to fill the gap, discusses a figure, namely K.H.M. Zen Syukri, who was one of the productive and influential religious scholars in Palembang at the beginning of the 20th century. Issues such as his biography and religious thoughts, his activities and roles in the spheres of education, dakwah (missionary) and in that of socio-politics are discussed. But more specifically, the article is concerned with the role of K.H.M. Zen Syukri in the development of the Sammaniyyah Order in South Sumatera.DOI: 10.15408/sdi.v9i1.677
Teologi Reformis, Rasional dan Neo-Modern dalam Konteks Pertarungan Wacana Teologi Islam di Indonesia
Authors: Hara Abubakar Eby 
Published: May 2014

Fauzan Saleh's book, on Islamic theological discourses in Indonesia shows the dynamism of Islamic thoughts and practices in Indonesia. From Saleh's description, we may conclude that there have been efforts among Moslem theologians to reform Islamic theological thoughts so that they can cope with progress and modernity. The book focuses on three main modern theological trends: reformist, rationalist and neo-modernist discourses. The reformist was represented by two organizations: Muhammadiyah and Persatuan Islam (Persis), which attempted to purify Islamic teachings among Indonesian Moslems. For the theologians from these organizations, some practices and teachings of Islam adopted by Moslems did not reflect the true spirits of Islam, and were heavily influenced by local traditions such as Hinduism.DOI: 10.15408/sdi.v9i1.678
The Politic of Salt, not the Politics of Lipstick: Mohammad Hatta on Islam and Nationalism
Authors: Ali-Fauzi Ihsan 
Published: May 2014

This article will try to show that Hatta was consistently a religious nationalist, but one who also rejected the idea of an Islamic state. Born in a devout Muslim family, Hatta grew and had always been a devout Muslim in his entire life. But his being a devout Muslim had never been a problem for him to be an astute proponent of Indonesian nationalism. If anything, it even encouraged his nationalist stand. When Indonesia's independence was still in its early stage of preparation in the 1940s, he made it clear that he accepted Pancasila as the basis of the future state, particularly when the "Belief in God" was finally put as the first principle of this state's basis.DOI: 10.15408/sdi.v9i2.667
Irsā al-Usus al-‘Ilmīyah li al-Dirāsat al-Islāmīyah: al-Taṭawwur al-Akādīmī li al-Jāmi’at al-Islāmīyah al-Ḥukūmīyah wa al-Ma’āhid al-Islāmīyah al-Ḥukūmīyah al-‘Ulyā bi Indūnīsīyā
Authors: Jabali Fuad 
Published: May 2014

in the past, the main purpose of IAIN was "simply" as a missionary institution, responsible for the dissemination of the Islamic religion throughout the community. However, as it developed, besides remaining as an institute for propagating missionary works, IAIN has also played an increasingly bigger role as an academic institution in the arena of Islamic higher education. Due to this, the oreinetation, efforts and responsibility of IAIN have shifted noticeable into the realm of academia and knowledge building.DOI: 10.15408/sdi.v9i2.668
Gender in the Eyes of the Indonesian Muslim Organizations
Authors: Ropi Ismatu 
Published: May 2014

Needles to say that there are numerous Muslim organizations all over Indonesia, and therefore, some limitation is a necessity. The following qualifications are used to select which of them are to be included: (1) they must be well established and enjoyed a high community support, and (2) act as centers of religious values production and reproduction, especially for the surrounding community. Thus only Muslim organizations with real mass support and strong networks, as well as with real contributions in shaping the Muslims minds and attitudes, will be studied. Using the criteria, besides PERTI, NU and Muhammadiyah mentioned before, thirteen organizations are selected including PERSIS, DDI (Darul Dakwah wa lrryad), Nahdlatul Wathan, and al-Washliyah. Some of these organization are strong only outside Java sucb as PERTI in West Sumatera, al-Washliah in North Sumatera and DDI in South Sulawesi. It is only natural that the research also put great emphasis on Muslims traditions outside Java.DOI: 10.15408/sdi.v9i2.671
Fatwas on Inter-faith Marriage in Indonesia
Authors: Ali Muhamad 
Published: May 2014

This article presents a study on the fatwas (legal opinion) concerning inter faith marriage in Indonesia. The fatwas under the discussion are those issued by Nahdlatul Ulama (NU) and Majelis Ulama Indonesia (MUI) in post-Independence Indonesia. Those fatwas are of special significance, both in terms of Islamic legal discourses and -perhaps more importantly- Muslims' perceptions and attitudes towards other religious communities in Indonesia. Issued by authoritative bodies of Indonesian Islam, more in particular the NU, the fatwas could be said as presenting the voices of Indonesian Muslims in their encounters with the issues of religious tolerance and plurality.DOI: 10.15408/sdi.v9i3.658
Islam as an Ideology: The Political Thought of Tjokroaminoto
Authors: Melayu Hasnul Arifin 
Published: May 2014

There are two reasons why Tjokroaminoto maintained a cooperative attitude toward the Dutch. First, he was more inspired by the fear of government retaliation than by conviction; at that time, based on Article 111 of the ordinance of 1854, the Dutch government forbade any political association. Second, this attitude could not be separated from the political environment created by the Dutch government. A moderate attitude shown by Governor General Idenburg created a sympathetic attitude among the S.I. leaders toward the Dutch.DOI: 10.15408/sdi.v9i3.659