bluuebunny/crossref_metadata_2025_split huggingface dataset:
TET‐catalyzed oxidation of intragenic 5‐methylcytosine regulates CTCF‐dependent alternative splicing
Authors: Marina Ryan J , Sturgill David , Bailly Marc A , Thenoz Morgan , Varma Garima , Prigge Maria F , Nanan Kyster K , Shukla Sanjeev , Haque Nazmul , Oberdoerffer Shalini 
Published: December 2015

AbstractIntragenic 5‐methylcytosine and CTCF mediate opposing effects on pre‐mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5‐methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF‐binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF‐mediated alternative splicing through conversion of 5‐methylcytosine to its oxidation derivatives. 5‐hydroxymethylcytosine and 5‐carboxylcytosine are enriched at an intragenic CTCF‐binding sites in the CD45 model gene and are associated with alternative exon inclusion. Reduced TET levels culminate in increased 5‐methylcytosine, resulting in CTCF eviction and exon exclusion. In vitro analyses establish the oxidation derivatives are not sufficient to stimulate splicing, but efficiently promote CTCF association. We further show genomewide that reciprocal exchange of 5‐hydroxymethylcytosine and 5‐methylcytosine at downstream CTCF‐binding sites is a general feature of alternative splicing in naïve and activated CD4+ T cells. These findings significantly expand our current concept of the pre‐mRNA “splicing code” to include dynamic intragenic DNA methylation catalyzed by the TET proteins.
Eradicating tumor drug resistance at its YAP‐biomechanical roots
Authors: Zanconato Francesca , Piccolo Stefano 
Published: December 2015

Treatment with BRAF kinase inhibitors leads to rapid resistance and tumor regression in BRAF V600E mutant melanoma patients. However, the underlying mechanism of the developed tumor resistance is not fully clear. In this issue of The EMBO Journal, Kim and colleagues show that melanoma cells acquire resistance to BRAF inhibitors by changing cell shape, modifying their cytoskeleton and, in turn, activating the YAP/TAZ mechanotransduction pathway (Kim et al, ).
Gemcitabine-Based Chemoradiation in the Treatment of Locally Advanced Head and Neck Cancer: Systematic Review of Literature and Meta-Analysis
Authors: Vanderveken Olivier M. , Szturz Petr , Specenier Pol , Merlano Marco C. , Benasso Marco , Van Gestel Dirk , Wouters Kristien , Van Laer Carl , Van den Weyngaert Danielle , Peeters Marc , Vermorken Jan 
Published: December 2015

Abstract

Background.
Platinum-based concurrent chemoradiation (CCRT) improves locoregional control and overall survival of locoregionally advanced (LA) squamous cell carcinoma of the head and neck (SCCHN) when compared to radiotherapy alone, but this approach is hampered by significant toxicity. Therefore, alternative ways to enhance the radiation effects are worth investigating. Gemcitabine (2′,2′-difluorodeoxycytidine), in addition to its activity against a variety of solid tumors, including SCCHN, is one of the most potent radiosensitizers, and it has an overall favorable safety profile. In this paper, the clinical experience with gemcitabine-based chemoradiation in the treatment of patients with LA-SCCHN is reviewed.

Methods.
We conducted a review of the literature on the clinical experience with radiotherapy combined with either single-agent gemcitabine or gemcitabine/cisplatin-based polychemotherapy for the treatment of patients with LA-SCCHN. We also searched abstracts in databases of major international oncology meetings from the last 20 years. A meta-analysis was performed to calculate pooled proportions with 95% confidence intervals (CIs) for complete response rate and grade 3–4 acute mucositis rate.

Results.
A total of 13 papers were eligible for the literature review. For schedules using a gemcitabine dose intensity (DI) below 50 mg/m2 per week, the complete response rate was 86% (95% CI, 74%–93%) with grade 3–4 acute mucositis rate of 38% (95% CI, 27%–50%) and acceptable late toxicity. In one of the studies employing such low DIs, survival data were provided showing a 3-year overall survival of 50%. Compared with DI ≥50 mg/m2 per week, there was no difference in the complete response rate (71%; 95% CI, 55%–83%; p = .087) but a significantly higher (p &lt; .001) grade 3–4 acute mucositis rate of 74% (95% CI, 62%–83%), often leading to treatment interruptions (survival data provided in 8 studies; 3-year overall survival, 27%–63%). Late toxicity comprising mainly dysphagia was generally underreported, whereas information about xerostomia and skin fibrosis was scarce.

Conclusion.
This review highlights the radiosensitizing potential of gemcitabine and suggests that even very low dosages (less than 50 mg/m2 per week) provide a sufficient therapeutic ratio and therefore should be further investigated. Refinements in radiation schemes, including intensity-modulated radiation therapy, in combination with low-dose gemcitabine and targeted agents, such as cetuximab, are currently being investigated.
DEMOKRASI DI INDONESIA Antara Pembatasan dan Kebebasan Beragama
Authors: Hafsin Abu 
Published: December 2015

<p>Democracy has been understood differently. Law no.1/PNPS/1965 which<br />is previously recognized as protection of religious followers is recognized as<br />limitation that denied principle of democracy recently. The polemic of religious<br />freedom ended with proposal of judicial review on law no.1/PNPS/1965 proposed</p><p>by some group of societies. This proposal, finally, is rejected by prime<br />court. This rejection can be corrected since UUD 1945 follows an expressive<br />relativism on religious freedom. Because of the existence of ambiguous words<br />in such law, revision is really needed so that there will be a clear explanation<br />related to who has the authority to determine whether certain religious teaching<br />is wrong or not. It is important to solve the problematic matters faced by government and certain religious groups.</p><p><strong>Keywords</strong> : demokrasi, relativisme</p>
Makna Ritual Dalam Risalah Tarekat Qodiriyah Naqysabandiyah
Authors: Hidayat R Aris 
Published: December 2015

Philological study to religious manuscripts is quite interesting because it<br />is considered as a way to maintain a very highly-valued cultural heritage. And<br />this research is a kind of such effort. This study examines the Risalah Qadiriyah<br />Naqsyabandiyah, an Islamic Javanese manuscript, which is preserved in the<br />National Library of Republic of Indonesia. Using philological and historical<br />methods, this research is to edit the manuscript and to analyze its messages.<br />In additions, this study is aimed to give significant contributions not only to<br />the Ministry of Religious Affairs of Republic Indonesia but also to public in<br />general.<br />The result of the study says that according to the Risalah Qadiriyyah<br />Naqsyabandiyyah in the midst of the nineteenth century, there was a group<br />of people practicing the teachings of the Tarekat Qadiriyah Naqsyabandiyah.<br />Their wirid, however, was different from either the Tarekat Qadiriyyah or the<br />Tarekat Naqsyabandiyah. The fact obviously shows that Islam in Java, according<br />to the manuscript had a nuance of mysticism and syncretism.<br /><br /><br />
Problems of Under Age Marriage
Authors: Mawardi Marmiati 
Published: December 2015

<p><em>Th</em><em>e industrial development in Wonoayu district contributes to economic growth in society. On the other hand, there is a shift of norms because of open information access that affects sexual intercourse among teenagers. This results in an early marriage because the girls have already been pregnant. This research uses a qualitative approach in order to investigate the influential factors, causes, motives and impact of the early marriage, and how society’s view on early marriage in Wonoayu district. The contributing factors of early marriages are sexual intercourse and pre-marital pregnancy. The motives of early marriage are; religiously legal marriage, reducing economic burden of parent, and preserving social reputation of their parents. Meanwhile the impact of legally formal marriage is to avoid sin and to protect the children’s status legally. Economically, the family in general is not ready to get married, and psychologically they are not mature yet, because they still have strong ego and are not independent.</em></p>
Moral Value in Lyrics of Dangdut Compesed by Rhoma Irama
Authors: Mustolehudin Mustolehudin 
Published: December 2015

<p><em>Mora</em><em>l values undoubtedly play a significant role in human life. These values are not only in religious texts (such as Qur’an, Hadits, Old Testament, Bible, Book of Psalms) but also in literatures. One of the examples is lyrics of Rhoma Irama’s song from 1970s to 1980s. This is a library research using a content analysis approach. Meanwhile, this research utilizes semiotic and hermeneutic methods. The findings show that the lyrics of Rhoma Irama’s song during 1970-1980 contained some moral values which could be implemented in personal life, family, society and religious life. The important values contained in such songs are amanah (trustful), as-siddiq (truth, honesty), al-‘adl (justice), al-rahmah (love), al-ukhuwah (brotherhood) and tasamuh (tolerance). The aforementioned values refer to two Islamic primary sources that are relevant to all times, in the past, present and future.</em></p>
Women Behind Terrorists (Religiousity, Self Adaptation and Husband-Wife Relationship within Suspected Terrorists Family in Pekalongan)
Authors: Maghfur Maghfur , Muniroh Siti Mumun 
Published: December 2015

<em>Women and their religiosity are questioned along with the proliferation of conflict, violence, and religion-based riots which allegedly involving ‘husband’ suspected terrorists. This article discusses the religiosity of the wives, the adjustment of wives of suspected terrorists against psychological and social burden, and the patterns of marital relations of terrorist suspects in Pekalongan-Central Java. The result of this phenomenological study revealed that the religiosity of terrorist-suspects’ wives are more dominant is exclusive patterned- if it is compared to moderate or inclusive ones. In terms of adjustment, the wives are just accept the fate and tend to be indifferent to the activities of their husbands. The wives also nullifying the public’s negative perception and judgment, but some are closed to the social interaction. While the pattern of relationships that were frequently built tent to be more owner property and head-complement in characteristics. Wives are positioned as husband’s complement for all activities in the fields of social, religious and political.</em>
Estimating where and how animals travel: an optimal framework for path reconstruction from autocorrelated tracking data
Authors: Fleming C. H. , Fagan W. F. , Mueller T. , Olson K. A. , Leimgruber P. , Calabrese J. M. 
Published: December 2015

AbstractAn animal's trajectory is a fundamental object of interest in movement ecology, as it directly informs a range of topics from resource selection to energy expenditure and behavioral states. Optimally inferring the mostly unobserved movement path and its dynamics from a limited sample of telemetry observations is a key unsolved problem, however. The field of geostatistics has focused significant attention on a mathematically analogous problem that has a statistically optimal solution coined after its inventor,Krige. Kriging revolutionized geostatistics and is now the gold standard for interpolating between a limited number of autocorrelated spatial point observations. Here we translate Kriging for use with animal movement data. Our Kriging formalism encompasses previous methods to estimate animal's trajectories—the Brownian bridge and continuous‐time correlated random walk library—as special cases, informs users as to when these previous methods are appropriate, and provides a more general method when they are not. We demonstrate the capabilities of Kriging on a case study with Mongolian gazelles where, compared to the Brownian bridge, Kriging with a more optimal model was 10% more precise in interpolating locations and 500% more precise in estimating occurrence areas.
Functional diversity and trait composition of butterfly and bird communities in farmlands of central romania
Authors: Hanspach Jan , Loos Jacqueline , Dorresteijn Ine , Von wehrden Henrik , Moga Cosmin Ioan , David Alin 
Published: December 2015

AbstractCultural landscapes all over the world harbor species communities that are taxonomically and functionally diverse. In Eastern Europe, but also in many other regions of the world, the conservation of this farmland biodiversity is threatened by land use intensification and abandonment. In order to counteract the negative effects of land use change in such landscapes, a thorough understanding of the functional relationships between species and their environment is crucial. In this study, we investigated the relationship of functional traits of butterfly and bird communities and environmental conditions in 120 sites in traditional farmlands of southern Transylvania, Romania. First, we compared taxonomic diversity (i.e., Shannon diversity) with functional diversity (i.e., functional dispersion), and second, we linked species traits to environmental variables by performing RLQ analyses. Functional traits indicating reproduction, movement, and feeding behavior related with environmental variables describing heterogeneity, amount of woody vegetation, and topography at three different spatial scales. We found positive relationships between taxonomic and functional diversity, as well as strong linkages between species traits and environmental conditions for both groups. Specifically, butterfly composition was most strongly influenced by land use type and life‐history strategies. Bird composition was most strongly related to the amount of woody vegetation and nesting and foraging strategies. We conclude that maintaining the typical features of traditional farming landscapes, especially a small‐scale heterogeneity in arable land and gradients of woody vegetation cover, would be desirable in order to sustain a high functional diversity in southern Transylvania in the future.
Stent Thrombosis after Rescue Percutaneous Coronary Intervention in
Acute ST-Segment Elevation Myocardial Infarction
Authors: Thani Khalid Bin , Al-Moosa Fajer , Murad Eman , Al-Moosa Aisha , Alalawi Mohamed E. , Al-Sindi Hind 
Published: December 2015

Main Problem:To determine the incidence of coronary stent thrombosis (ST) in patients with acute ST
segment elevation myocardial infarction (STEMI) after rescue percutaneous coronary intervention (PCI).
Methods:An observational study looking at the incidence of ST in a middle-eastern population. A total of 510
consecutive patients presented with ST-segment elevation myocardial infarction (STEMI) were enrolled and underwent
thrombolytic therapy with a total follow-up period of 2 years. Study outcomes were ST, death, re-infarction or acute
coronary syndrome requiring coronary angiography and PCI.
Results:A total of 510 patients enrolled, all diagnosed with STEMI and underwent thrombolytic therapy. Only 100
subjects underwent rescue PCI with intra-coronary stenting, including 54 patients with drug-eluting stent (DES) and 46
patients with bare metal stent (BMS). During the study period and follow-up, the overall rate of ST was 13.7%, definite
ST occurred in 6 patients (5.5%), probable ST in 8 patients (7.3%), and possible ST in one patient (0.9%), including 0.9%
acute ST, 0.9% sub-acute ST, 2.8% late ST and 8.3% very late ST. Patients with ST were likely to have prior PCI
(p=0.001), prior coronary artery bypass grafting (CABG) (p=0.002) and history of heart failure (p=0.04).
Conclusion:ST is infrequent event with major consequences in patients presenting with STEMI in the first 2 years after
stent implantation.
Molecular evolutionary relationships of <i>Euphorbia scordifolia</i> Jacq. within the genus inferred from analysis of internal transcribed spacer sequences
Authors: Al-Hemaid Fahad M.A. , Ali M. Ajmal , Lee Joongku , Kim Soo-Yong , Rahman Md. Oliur 
Published: December 2015

The present study explored molecular phylogenetic analysis of 28 species of Euphorbia L. for the identification and establishment of molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus based on the internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA). The sequence similarity search using Basic Local Alignment Search Tool (BLAST) of the ITS sequence of E. scordifolia showed the closest sequence similarity to E. supina Raf. The analysis of ITS sequence data revealed four major clades consistent with subgeneric classifications of the genus. Molecular data support placement of E. scordifolia in the subgenus Chamaesyce.Bangladesh J. Plant Taxon. 22(2): 111-118, 2015 (December)
<i>Rhododendron leigongshanense</i> (Ericaceae), a new species from China
Authors: Yang Cheng-Hua , Xie Zheng-Guo , Yu Yong-Fu , Yang Zhi-Rong 
Published: December 2015

Rhododendron leigongshanense, a new species from Leishan County, Guizhou Province, China, is described and illustrated. The new species is close to R. magniflorun W.K. Hu and R. glanduliferum Franchet, but differs by having stipitatus glands on leaf abaxial surface, corolla trumpet-shaped with 7 lobes, 7.58.0 cm long, 810 cm in diameter and calyx 7- lobed.Bangladesh J. Plant Taxon. 22(2): 119-123, 2015 (December)
<i>Stenochlaena riauensis</i> (Blechnaceae), a new fern species from Riau, Indonesia
Authors: Sofiyanti Nery , Iriani Dyah , Fitmawati Dr , Roza Andesba A. 
Published: December 2015

Stenochlaena riauensis, a new fern species from Riau, Indonesia is described and illustrated. This species can be distinguished from its most closely related species S. palustris by the position of fertile and sterile pinnae. In the new species, both fertile and sterile pinnae are located on the same frond, the lower part of lamina consisted of sterile pinnae that gradually narrower towards apex forming linear fertile pinnae.Bangladesh J. Plant Taxon. 22(2): 137-141, 2015 (December)
RESOLVED MILLIMETER-WAVELENGTH OBSERVATIONS OF DEBRIS DISKS AROUND SOLAR-TYPE STARS
Authors: Steele Amy , Hughes A. Meredith , Carpenter John , Ricarte Angelo , Andrews Sean M. , Wilner David J. , Chiang Eugene 
Published: December 2015

ABSTRACT
The presence of debris disks around young main-sequence stars hints at the existence and structure of planetary systems. Millimeter-wavelength observations probe large grains that trace the location of planetesimal belts. The Formation and Evolution of Planetary Systems Spitzer Legacy survey of nearby young solar analogues yielded a sample of five debris disk-hosting stars with millimeter flux suitable for interferometric follow-up. We present observations with the Submillimeter Array (SMA) and the Combined Array for Research in Millimeter-wave Astronomy at ∼2″ resolution that spatially resolve the debris disks around these nearby (d ∼ 50 pc) stars. Two of the five disks (HD 377, HD 8907) are spatially resolved for the first time and one (HD 104860) is resolved at millimeter wavelengths for the first time. We combine our new observations with archival SMA and Atacama Large Millimeter/Submillimeter Array data to enable a uniform analysis of the full five-object sample. We simultaneously model the broadband photometric data and resolved millimeter visibilities to constrain the dust temperatures and disk morphologies, and perform a Markov Chain Monte Carlo analysis to fit for basic structural parameters. We find that the radii and widths of the cold outer belts exhibit properties consistent with scaled-up versions of the Solar System's Kuiper Belt. All the disks exhibit characteristic grain sizes comparable to the blowout size, and all the resolved observations of emission from large dust grains are consistent with an axisymmetric dust distribution to within the uncertainties. These results are consistent with comparable studies carried out at infrared wavelengths.
X-RAY AFTERGLOW OF SWIFT J1644+57: A COMPTON ECHO?
Authors: Cheng K. S. , Chernyshov D. O. , Dogiel V. A. , Kong Albert K. H. , Ko C. M. 
Published: December 2015

ABSTRACT

Swift, Chandra, and XMM have found a weak but nearly constant X-ray component from Swift J1644+57 that appeared at ∼500 days and was visible at least until ∼1400 days after the stellar capture, which cannot be explained by standard tidal disruption theories. We suggest that this X-ray afterglow component may result from the Thomson scattering between the primary X-rays and its surrounding plasma, i.e., a Compton echo effect. Similar phenomena have also been observed from molecular clouds in our Galactic Center, which were caused by the past activity of Srg A*. If this interpretation of Swift J1644+57 afterglow is correct, this is the first Compton Echo effect observed in the cosmological distances.
ON THE METALLICITY AND ORIGIN OF THE SMITH HIGH-VELOCITY CLOUD*
Authors: Fox Andrew J. , Lehner Nicolas , Lockman Felix J. , Wakker Bart P. , Hill Alex S. , Heitsch Fabian , Stark David V. , Barger Kathleen A. , Sembach Kenneth R. , Rahman Mubdi 
Published: December 2015

ABSTRACT
The Smith Cloud (SC) is a gaseous high-velocity cloud (HVC) in an advanced state of accretion, only 2.9 kpc below the Galactic plane and due to impact the disk in ≈27 Myr. It is unique among HVCs in having a known distance (12.4 ± 1.3 kpc) and a well-constrained 3D velocity (296 km s−1), but its origin has long remained a mystery. Here we present the first absorption-line measurements of its metallicity, using Hubble Space Telescope/COS UV spectra of three active galactic nuclei lying behind the Cloud together with Green Bank Telescope 21 cm spectra of the same directions. Using Voigt-profile fitting of the S ii
λλ1250, 1253, 1259 triplet together with ionization corrections derived from photoionization modeling, we derive the sulfur abundance in each direction; a weighted average of the three measurements gives [S/H] = −0.28 ± 0.14, or

solar metallicity. The finding that the SC is metal-enriched lends support to scenarios where it represents recycled Galactic material, rather than the remnant of a dwarf galaxy or accreting intergalactic gas. The metallicity and trajectory of the Cloud are both indicative of an origin in the outer disk. However, its large mass and prograde kinematics remain to be fully explained. If the cloud has accreted cooling gas from the corona during its fountain trajectory, as predicted in recent theoretical work, its current mass would be higher than its launch mass, alleviating the mass concern.
THE EXTENT OF POWER-LAW ENERGY SPECTRA IN COLLISIONLESS RELATIVISTIC MAGNETIC RECONNECTION IN PAIR PLASMAS
Authors: Werner G. R. , Uzdensky D. A. , Cerutti B. , Nalewajko K. , Begelman M. C. 
Published: December 2015

ABSTRACT
Using two-dimensional particle-in-cell simulations, we characterize the energy spectra of particles accelerated by relativistic magnetic reconnection (without guide field) in collisionless electron–positron plasmas, for a wide range of upstream magnetizations σ and system sizes L. The particle spectra are well-represented by a power law

, with a combination of exponential and super-exponential high-energy cutoffs, proportional to σ and L, respectively. For large L and σ, the power-law index α approaches about 1.2.