bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchical reverberation mapping
Authors: Brewer Brendon J. , Elliott Tom M. 
Published: January 2014

Abstract
Reverberation mapping (RM) is an important technique in studies of active galactic nuclei (AGN). The key idea of RM is to measure the time lag τ between variations in the continuum emission from the accretion disc and subsequent response of the broad-line region (BLR). The measurement of τ is typically used to estimate the physical size of the BLR and is combined with other measurements to estimate the black hole mass MBH. A major difficulty with RM campaigns is the large amount of data needed to measure τ. Recently, Fine et al. introduced a new approach to RM where the BLR light curve is sparsely sampled, but this is counteracted by observing a large sample of AGN, rather than a single system. The results are combined to infer properties of the sample of AGN. In this Letter, we implement this method using a hierarchical Bayesian model and contrast this with the results from the previous stacked cross-correlation technique. We find that our inferences are more precise and allow for more straightforward interpretation than the stacked cross-correlation results.
A successful search for hidden Barbarians in the Watsonia asteroid family
Authors: Cellino A. , Bagnulo S. , Tanga P. , Novaković B. , Delbò M. 
Published: January 2014

Abstract
Barbarians, so named after the prototype of this class (234) Barbara, are a rare class of asteroids exhibiting anomalous polarimetric properties. Their very distinctive feature is that they show negative polarization at relatively large phase angles, where all ‘normal’ asteroids show positive polarization. The origin of the Barbarian phenomenon is unclear, but it seems to be correlated with the presence of anomalous abundances of spinel, a mineral usually associated with the so-called calcium–aluminium-rich inclusions (CAIs) on meteorites. Since CAIs are samples of the oldest solid matter identified in our Solar system, Barbarians are very interesting targets for investigations. Inspired by the fact that some of the few known Barbarians are members of, or very close to, the dynamical family of Watsonia, we have checked whether this family is a major repository of Barbarians, in order to obtain some hints about their possible collisional origin. We have measured the linear polarization of a sample of nine asteroids which are members of the Watsonia family within the phase-angle range 17°–21°. We found that seven of them exhibit the peculiar Barbarian polarization signature, and we conclude that the Watsonia family is a repository of Barbarian asteroids. The new Barbarians identified in our analysis will be important to confirm the possible link between the Barbarian phenomenon and the presence of spinel on the surface.
Dicer-related helicase 3 forms an obligate dimer for recognizing 22G-RNA
Authors: Fitzgerald Megan E. , Vela Adriana , Pyle Anna Marie 
Published: January 2014

Abstract
Dicer is a specialized nuclease that produces RNA molecules of specific lengths for use in gene silencing pathways. Dicer relies on the correct measurement of RNA target duplexes to generate products of specific lengths. It is thought that Dicer uses its multidomain architecture to calibrate RNA product length. However, this measurement model is derived from structural information from a protozoan Dicer, and does not account for the helicase domain present in higher organisms. The Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) is an ortholog of the Dicer and RIG-I family of double-strand RNA activated ATPases essential for secondary siRNA production. We find that DRH-3 specifies 22 bp RNAs by dimerization of the helicase domain, a process mediated by ATPase activity and the N-terminal domain. This mechanism for RNA length discrimination by a Dicer family protein suggests an alternative model for RNA length measurement by Dicer, with implications for recognition of siRNA and miRNA targets.
How and where to look for tRNAs in Metazoan mitochondrial genomes, and what you might find when you get there
Authors: Morrison David A. 
Published: January 2014

AbstractThe ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to be problematic because they often vary in number (genes missing or duplicated) and also in the secondary structure of the transcribed tRNAs (T or D arms missing). I have performed a series of comparative analyses of the tRNA genes of a broad range of Metazoan mitogenomes in order to address this issue. I conclude that no single computer program is necessarily capable of finding all of the tRNA genes in any given mitogenome, and that use of both the ARWEN and DOGMA programs is sometimes necessary because they produce complementary false negatives. There are apparently a very large number of erroneous annotations in the databased mitogenome sequences, including missed genes, wrongly annotated locations, false complements, and inconsistent criteria for assigning the 5′ and 3′ boundaries; and I have listed many of these. The extent of overlap between genes is often greatly exaggerated due to inconsistent annotations, although notable overlaps involving tRNAs are apparently real. Finally, three novel hypotheses were examined and found to have support from the comparative analyses: (1) some organisms have mitogenomic locations that simultaneously code for multiple tRNAs; (2) some organisms have mitogenomic locations that simultaneously code for tRNAs and proteins (but not rRNAs); and (3) one group of nematodes has several genes that code for tRNAs lacking both the D and T arms.
The shrinking human protein coding complement: are there now fewer than 20,000 genes?
Authors: Ezkurdia Iakes , Juan David , Rodriguez Jose Manuel , Frankish Adam , Diekhans Mark , Harrow Jennifer , Vazquez Jesus , Valencia Alfonso , Tress Michael L. 
Published: January 2014

AbstractDetermining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein coding potential is the detection of cellular protein expression through peptide mass spectrometry experiments. Here we map the peptides detected in 7 large-scale proteomics studies to almost 60% of the protein coding genes in the GENCODE annotation the human genome. We find that conservation across vertebrate species and the age of the gene family are key indicators of whether a peptide will be detected in proteomics experiments. We find peptides for most highly conserved genes and for practically all genes that evolved before bilateria. At the same time there is almost no evidence of protein expression for genes that have appeared since primates, or for genes that do not have any protein-like features or cross-species conservation. We identify 19 non-protein-like features such as weak conservation, no protein features or ambiguous annotations in major databases that are indicators of low peptide detection rates. We use these features to describe a set of 2,001 genes that are potentially non-coding, and show that many of these genes behave more like non-coding genes than protein-coding genes. We detect peptides for just 3% of these genes. We suggest that many of these 2,001 genes do not code for proteins under normal circumstances and that they should not be included in the human protein coding gene catalogue. These potential non-coding genes will be revised as part of the ongoing human genome annotation effort.
Antagonistic Regulation of Growth and Immunity by the Arabidopsis Basic Helix-Loop-Helix Transcription Factor HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH INCREASED LEAF INCLINATION1 BINDING bHLH1
Authors: Malinovsky Frederikke Gro , Batoux Martine , Schwessinger Benjamin , Youn Ji Hyun , Stransfeld Lena , Win Joe , Kim Seong-Ki , Zipfel Cyril 
Published: January 2014

AbstractPlants need to finely balance resources allocated to growth and immunity to achieve optimal fitness. A tradeoff between pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and brassinosteroid (BR)-mediated growth was recently reported, but more information about the underlying mechanisms is needed. Here, we identify the basic helix-loop-helix (bHLH) transcription factor HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH IBH1 (HBI1) as a negative regulator of PTI signaling in Arabidopsis (Arabidopsis thaliana). HBI1 expression is down-regulated in response to different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs BRASSINOSTEROID ENHANCED EXPRESSION2 (BEE2) and CRYPTOCHROME-INTERACTING bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1. In contrast to its expression pattern upon PAMP treatment, HBI1 expression is enhanced by BR treatment. Also, HBI1-overexpressing plants are hyperresponsive to BR and more resistant to the BR biosynthetic inhibitor brassinazole. HBI1 is nucleus localized, and a mutation in a conserved leucine residue within the first helix of the protein interaction domain impairs its function in BR signaling. Interestingly, HBI1 interacts with several inhibitory atypical bHLHs, which likely keep HBI1 under negative control. Hence, HBI1 is a positive regulator of BR-triggered responses, and the negative effect of PTI is likely due to the antagonism between BR and PTI signaling. This study identifies a novel component involved in the complex tradeoff between innate immunity and BR-regulated growth.
Cytokinin Antagonizes Abscisic Acid-Mediated Inhibition of Cotyledon Greening by Promoting the Degradation of ABSCISIC ACID INSENSITIVE5 Protein in Arabidopsis
Authors: Guan Chunmei , Wang Xingchun , Feng Jian , Hong Sulei , Liang Yan , Ren Bo , Zuo Jianru 
Published: January 2014

Abstract
In higher plants, seed germination is followed by postgerminative growth. One of the key developmental events during postgerminative growth is cotyledon greening, which enables a seedling to establish photosynthetic capacity. The plant phytohormone abscisic acid (ABA) plays a vital role by inhibiting seed germination and postgerminative growth in response to dynamically changing internal and environmental cues. It has been shown that ABSCISIC ACID INSENSITIVE5 (ABI5), a basic leucine zipper transcription factor, is an important factor in the regulation of the ABA-mediated inhibitory effect on seed germination and postgerminative growth. Conversely, the phytohormone cytokinin has been proposed to promote seed germination by antagonizing the ABA-mediated inhibitory effect. However, the underpinning molecular mechanism of cytokinin-repressed ABA signaling is largely unknown. Here, we show that cytokinin specifically antagonizes ABA-mediated inhibition of cotyledon greening with minimal effects on seed germination in Arabidopsis (Arabidopsis thaliana). We found that the cytokinin-antagonized ABA effect is dependent on a functional cytokinin signaling pathway, mainly involved in the cytokinin receptor gene CYTOKININ RESPONSE1/ARABIDOPSIS HISTIDINE KINASE4, downstream histidine phosphotransfer protein genes AHP2, AHP3, and AHP5, and a type B response regulator gene, ARR12, which genetically acts upstream of ABI5 to regulate cotyledon greening. Cytokinin has no apparent effect on the transcription of ABI5. However, cytokinin efficiently promotes the proteasomal degradation of ABI5 in a cytokinin signaling-dependent manner. These results define a genetic pathway through which cytokinin specifically induces the degradation of ABI5 protein, thereby antagonizing ABA-mediated inhibition of postgerminative growth.
Cutaneous lymphoma in Japan: A nationwide study of 1733 patients
Authors: Hamada Toshihisa , Iwatsuki Keiji 
Published: January 2014

AbstractTypes of cutaneous lymphoma (CL) and their incidences may vary among geographic areas or ethnic groups. The present study aimed to investigate the incidences of various CL in Japan, using epidemiological data from a nationwide registration system for CL. Between 2007 and 2011, 1733 new patients with CL were registered from over 600 dermatological institutes in Japan. The 1733 patients registered included 1485 (85.7%) patients with mature T‐ and natural killer (NK)‐cell neoplasms, 224 (12.9%) with B‐cell neoplasms and 24 (1.4%) with blastic plasmacytoid dendritic cell neoplasm. Mycosis fungoides (MF) is the most common CL subtype in the present study (750 patients, 43.3%). The proportion of MF patients with early‐stage disease was 73%, similar to that of previous studies from other cohorts. The incidence rates of adult T‐cell leukemia/lymphoma and extranodal NK/T‐cell lymphoma, nasal type were 16.7% and 2.0%, respectively, which may account for the higher incidence of mature T‐ and NK‐cell neoplasms in Japan, as compared with that in the USA and Europe. A male predominance was observed in most types of CL, except for several CL subtypes such as subcutaneous panniculitis‐like T‐cell lymphoma.
Immunological milieu in mycosis fungoides and Sézary syndrome
Authors: Miyagaki Tomomitsu , Sugaya Makoto 
Published: January 2014

AbstractTumor genesis and development are driven by a combination of intrinsic events such as oncogene activation and tumor‐suppressor gene inactivation, and extrinsic events that are dependent on the interaction with the stroma. Different types of growth factors, cytokines and chemokines secreted by the surrounding stromal cells are thought to play key roles in solid tumor progression. Accumulating evidence indicates that the immunological milieu plays an essential role in tumor development, not only in solid tumors, but also in hematopoietic malignancies. Understanding the interactions between tumor cells and microenvironment in mycosis fungoides (MF) and Sézary syndrome (SS) could provide a basis for the development of new treatments for these diseases that are sometimes resistant to current therapies. This article focuses on the wide variety of cell types and immunological milieus, affecting the characteristic features of MF and SS, such as skin‐homing of tumor cells, T‐helper type 2‐dominant tumor microenvironment, accumulation of dermal dendritic cells, epidermal hyperplasia, angiogenesis and pruritus.
Depsipeptide and roxithromycin induce apoptosis of lymphoma cells by blocking extracellular signal‐regulated kinase activation
Authors: Morimura Sohshi , Sugaya Makoto , Kai Hiromichi , Miyagaki Tomomitsu , Asano Yoshihide , Tada Yayoi , Kadono Takafumi , Murakami Takashi , Sato Sinichi 
Published: January 2014

AbstractDepsipeptide (FK228), a histone deacetylase inhibitor, was recently approved for use in cutaneous T‐cell lymphoma. Roxithromycin (RXM) is a macrolide antibiotic that can induce apoptosis of some T‐cell lines. In this study, we investigated whether combination of FK228 and RXM had a synergistic inhibitory effect on cell survival of various lymphoma cells and which signaling pathway was affected by the drugs in the presence or absence of chemokines, which were reported to inhibit apoptosis of some tumor cells. FK228 and RXM additively decreased the number of HUT‐78, Ki‐JK and EL‐4 lymphoma cells at doses over 50 nmol/L and 50 μmol/L, respectively. These drugs inhibited phosphorylation of Akt and extracellular signal‐regulated kinase (ERK) of EL‐4 cells in a dose‐dependent manner. Significant association between ERK phosphorylation and cell number or annexin V+ cells suggested that the ERK pathway may be critical for survival of EL‐4 cells. Combination of 10 or 50 nmol/L of FK228 and 10 μmol/L of RXM decreased cell number of HUT78 and EL‐4 compared to a single use of each drug. Our in vitro study suggested that combination of FK228 and RXM may be helpful for enhancing tumor killing effects. Although further study is necessary, this combination may be applicable to patients with cutaneous T‐cell lymphoma in the future.
Epstein–Barr virus‐associated T/natural killer‐cell lymphomas in the elderly: The first consensus meeting in Kofu 2013
Authors: Hamada Toshihisa , Nakamura Shigeo , Ko Young‐Hyeh , Yoshino Tadashi , Ohshima Koichi , Matsuzawa Takamitsu , Miura Keiko , Takahashi Toshifumi , Nomura Hisashi , Hoshino Tomomi , Suzuki Daisuke , Shimada Shinji , Iwatsuki Keiji 
Published: January 2014

AbstractFrom a clinicopathological conference on nine elderly patients with Epstein–Barr virus (EBV)‐associated T/natural killer (NK)‐cell lymphoma, we have addressed the patients' backgrounds, clinical manifestations, histopathological findings, cytogenesis, complications and prognoses. Among these elderly patients (>65 years old), seven patients had extranodal NK/T‐cell lymphoma, nasal type (ENKL) with an NK‐cell phenotype, and two patients had EBV+ T‐cell lymphomas or lymphoproliferative disorders (LPD) with cutaneous lesions mimicking pityriasis lichenoides et varioliformis acuta (PLEVA) or hydroa vacciniforme (HV). No patients had a previous episode of EBV‐related symptoms such as infectious mononucleosis, chronic active EBV infection, HV or hypersensitivity to mosquito bites. Elderly patients with ENKL may show the centroblastoid variant. EBV+CD8+CD56+/− lymphocytes may be responsible for the development of PLEVA or HV‐like cutaneous lesions in the elderly.
Meeting report on the possible proposal of an extranodal primary cutaneous variant in the lymphoma type of adult T‐cell leukemia‐lymphoma
Authors: Tsukasaki Kunihiro , Imaizumi Yositaka , Tokura Yoshiki , Ohshima Kouichi , Kawai Kazuhiro , Utsunomiya Atae , Amano Masahiro , Watanabe Toshiki , Nakamura Shigeo , Iwatsuki Keiji , Kamihira Shimeru , Yamaguchi Kazunari , Shimoyama Masanori 
Published: January 2014

AbstractBased on the advances in research on the clinicopathophysiology of adult T‐cell leukemia‐lymphoma (ATL), Japanese researchers collected and evaluated cases of smoldering ATL exhibiting primary cutaneous manifestation but showing poor prognosis. Macroscopic findings of skin eruptions were categorized into the patch, plaque, multipapular, nodulotumoral, erythrodermic and purpuric types, as previously reported. Pathological findings were divided into low or high grade based on epidermotropism, tumor cell size and perivascular infiltration. Eight eligible cases were evaluated among 14 collected cases. Macroscopic findings were nodulotumoral in six cases, a subcutaneous tumor in one case and plaque in one case, and the number and size were heterogeneous in each case. Pathological findings of all eight cases were T‐cell lymphoma, high‐grade type (pleomorphic, medium or large size), with prominent perivascular infiltration and scant epidermotropism. To diagnose such cases as the “lymphoma type of ATL, extranodal primary cutaneous variant”, it is essential to examine each case carefully, including cutaneous lesions at onset, lymph nodes and other organ involvement using computed tomography (CT) and/or positron emission tomography/CT, as well as the percentage of abnormal lymphocytes in peripheral blood. Based on the results of an ongoing nationwide survey on ATL, ATL with cutaneous lesions will be analyzed to investigate the incidence and prognosis of the so‐called “lymphoma type of ATL, extranodal primary cutaneous variant”.
Rhodobacter sphaeroides, a novel tumor‐targeting bacteria that emits natural near‐infrared fluorescence
Authors: Kwon Seong Young , Jiang Sheng‐Nan , Zheng Jin Hai , Choy Hyon E. , Min Jung‐Joon 
Published: January 2014

ABSTRACTSeveral optical imaging techniques have been used to monitor bacterial tropisms for cancer. Most such techniques require genetic engineering of the bacteria to express optical reporter genes. This study investigated a novel tumor‐targeting strain of bacteria, Rhodobacter sphaeroides 2.4.1 (R. sphaeroides), which naturally emits near‐infrared fluorescence, thereby facilitating the visualization of bacterial tropisms for cancer. To determine the penetration depth of bacterial fluorescence, various numbers of cells (from 108 to 1010 CFU) of R. sphaeroides and two types of Escherichia coli, which stably express green fluorescent protein (GFP) or red fluorescent protein (RFP), were injected s.c. or i.m. into mice. Bacterial tropism for cancer was determined after i.v. injection of R. sphaeroides (108 CFU) into mice implanted s.c. with eight types of tumors. The intensity of the fluorescence signal in deep tissue (muscle) from R. sphaeroides was much stronger than from E. coli‐expressing GFP or RFP. The near‐infrared fluorescence signal from R. sphaeroides was visualized clearly in all types of human or murine tumors via accumulation of bacteria. Analyses of C‐reactive protein and procalcitonin concentrations and body weights indicated that i.v. injection of R. sphaeroides does not induce serious systemic immune reactions. This study suggests that R. sphaeroides could be used as a tumor‐targeting microorganism for the selective delivery of drugs to tumor tissues without eliciting a systemic immune reaction and for visualizing tumors.
Geographic distance is more relevant than elevation to patterns of outbreeding in Ranunculus bulbosus
Authors: Matter Philippe , Kettle Chris J. , Frei Esther R. , Ghazoul Jaboury , Pluess Andrea R. 
Published: January 2014

Summary

Mountain ecosystems can exert different selection pressures on plant populations over small scales due to steep environmental gradients.

Gene flow between lower‐ and higher‐elevation plant populations could lead to the increased integration of potentially adaptive genes and thereby to outbreeding vigour under current rapid climatic changes. Alternatively, gene flow across elevation could disrupt gene complexes leading to outbreeding depression.

We explored the responses of higher (1800 m a.s.l.) and lower (1200 m a.s.l.) Ranunculus bulbosusL. populations to intra‐ and interelevational and short‐ as well as long‐distance gene flow by means of controlled crosses and assessment of the offspring's germination, growth and fitness.

Outbreeding differed between elevations of origin: higher populations were negatively affected by pollen flow from lower populations at the earliest life stages, but tended to be positively affected in terms of growth later on while gene flow across small vs. large distances had no impact on growth traits. Lower populations were not significantly affected by the elevational origin of pollen per se.

However, fitness of offspring of populations from both higher and lower elevations was jointly affected by elevational and regional origins of pollen, in which case the gene flow distance had a comparatively stronger positive impact on fitness (outbreeding vigour) than elevational origin.

Synthesis: Our results indicate that compared to gene flow at regional scales, gene flow across elevational gradients has a minor effect on R. bulbosus. The lack of outbreeding depression suggests that potentially adaptive genes might well be integrated across populations resulting in an increased resilience of R. bulbosus and potentially similar montane plant species in changing climatic conditions.