bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data
Authors: Chiba Kenichi , Shiraishi Yuichi , Nagata Yasunobu , Yoshida Kenichi , Imoto Seiya , Ogawa Seishi , Miyano Satoru 
Published: September 2014

Abstract
Summary: Somatic internal tandem duplications (ITDs) are known to play important roles in cancer pathogenesis. Although recent advances in high-throughput sequencing technologies have enabled genome-wide detection of various types of genomic mutations, including single nucleotide variants, indels and structural variations, only a few studies have focused on ITDs. We have developed an analytical tool called ‘Genomon ITDetector’ for genome-wide detection of somatic ITDs. After evaluating the sensitivity and precision of the proposed approach using synthetic data, we have demonstrated that it can successfully detect not only common ITDs involving FLT3, but also a number of ITDs affecting other putative driver genes in acute myeloid leukemia exome sequencing data.
Availability and implementaion: Genomon ITDetector is freely available at https://github.com/ken0-1n/Genomon-ITDetector
Contact: kchiba@hgc.jp or yshira@hgc.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Investigating the recent decline in gadoid stocks in the west of
Scotland shelf ecosystem using a foodweb model
Authors: Alexander Karen A. , Heymans Johanna J. , Magill Shona , Tomczak Maciej T. , Holmes Steven J. , Wilding Thomas A. 
Published: September 2014

Abstract
Abundance and biomass of cod, haddock, and whiting in the waters off of the west coast of Scotland (wcoS) have undergone large changes in recent years, most notably a recent decline. These three species contribute a considerable part of Scottish demersal landings from this area and as such it is important to understand why these stocks are behaving the way they are. A number of explanations for the decline have been proposed, including: seal predation, pressure from Nephrops trawls, and fishing pressure more generally. We used an ecosystem model of the wcoS continental shelf (&lt;200 m depth) to investigate whether these proposed explanations for declining gadoid stocks are feasible. Results suggest that the rise in the grey seal population over recent years has not led to the decline in gadoid stocks; there is insufficient bycatch by the Nephrops fleet to have a large impact on gadoid stocks; however, fishing, as a key driver of the west of Scotland shelf ecosystem, has impacted stocks and by decreasing fishing levels to maximum sustainable yield cod biomass may increase slightly though not returning to previous levels. Although this means we are little further forward in understanding the cause of recent gadoid declines in the area, the development of this model has enabled us to further our knowledge and understanding of aspects of trophic structure and the impacts of fishing on the wcoS.
The Jehol Biota, an Early Cretaceous terrestrial Lagerstätte: new discoveries and implications
Authors: Zhou Zhonghe 
Published: September 2014

AbstractThe study of the Early Cretaceous terrestrial Jehol Biota, which provides a rare window for reconstruction of a Lower Cretaceous terrestrial ecosystem, is reviewed with a focus on some of the latest progress. A newly proposed definition of the biota based on paleoecology and taphonomy is accepted. Although the Jehol fossils are mainly preserved in two types of sedimentary rocks, there are various types of preservation with a complex mechanism that remains to be understood. New discoveries of significant taxa from the Jehol Biota, with an updated introduction of its diversity, confirm that the Jehol Biota represents one of the most diversified biotas of the Mesozoic. The evolutionary significance of major biological groups (e.g. dinosaurs, birds, mammals, pterosaurs, insects, and plants) is discussed mainly in the light of recent discoveries, and some of the most remarkable aspects of the biota are highlighted. The global and local geological, paleogeographic, and paleoenvironmental background of the Jehol Biota have contributed to the unique composition, evolution, and preservation of the biota, demonstrating widespread faunal exchanges between Asia and other continents caused by the presence of the Eurasia–North American continental mass and its link to South America, and confirming northeastern China as the origin and diversification center for a variety of Cretaceous biological groups. Although some progress has been made on the reconstruction of the paleotemperature at the time of the Jehol Biota, much more work is needed to confirm a possible link between the remarkable diversity of the biota and the cold intervals during the Early Cretaceous. Finally, future directions for the study of the Jehol Biota are proposed that highlight the great potential of more comprehensive and multidisciplinary studies to further our understanding of the biological and geological implications of the Jehol Lagerstätte.
Broad 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor Herbicide Tolerance in Soybean with an Optimized Enzyme and Expression Cassette
Authors: Siehl Daniel L. , Tao Yumin , Albert Henrik , Dong Yuxia , Heckert Matthew , Madrigal Alfredo , Lincoln-Cabatu Brishette , Lu Jian , Fenwick Tamara , Bermudez Ericka , Sandoval Marian , Horn Caroline , Green Jerry M. , Hale Theresa , Pagano Peggy , Clark Jenna , Udranszky Ingrid A. , Rizzo Nancy , Bourett Timothy , Howard Richard J. , Johnson David H. , Vogt Mark , Akinsola Goke , Castle Linda A. 
Published: September 2014

Abstract
With an optimized expression cassette consisting of the soybean (Glycine max) native promoter modified for enhanced expression driving a chimeric gene coding for the soybean native amino-terminal 86 amino acids fused to an insensitive shuffled variant of maize (Zea mays) 4-hydroxyphenylpyruvate dioxygenase (HPPD), we achieved field tolerance in transgenic soybean plants to the HPPD-inhibiting herbicides mesotrione, isoxaflutole, and tembotrione. Directed evolution of maize HPPD was accomplished by progressively incorporating amino acids from naturally occurring diversity and novel substitutions identified by saturation mutagenesis, combined at random through shuffling. Localization of heterologously expressed HPPD mimicked that of the native enzyme, which was shown to be dually targeted to chloroplasts and the cytosol. Analysis of the native soybean HPPD gene revealed two transcription start sites, leading to transcripts encoding two HPPD polypeptides. The N-terminal region of the longer encoded peptide directs proteins to the chloroplast, while the short form remains in the cytosol. In contrast, maize HPPD was found almost exclusively in chloroplasts. Evolved HPPD enzymes showed insensitivity to five inhibitor herbicides. In 2013 field trials, transgenic soybean events made with optimized promoter and HPPD variant expression cassettes were tested with three herbicides and showed tolerance to four times the labeled rates of mesotrione and isoxaflutole and two times the labeled rates of tembotrione.
Genome-Wide Study ofKNOXRegulatory Network Reveals Brassinosteroid Catabolic Genes Important for Shoot Meristem Function in Rice
Authors: Tsuda Katsutoshi , Kurata Nori , Ohyanagi Hajime , Hake Sarah 
Published: September 2014

AbstractIn flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in establishment and maintenance of the shoot apical meristem (SAM), from which aerial organs such as leaves, stems, and flowers initiate. We report that a rice (Oryza sativa) KNOX gene Oryza sativa homeobox1 (OSH1) represses the brassinosteroid (BR) phytohormone pathway through activation of BR catabolism genes. Inducible overexpression of OSH1 caused BR insensitivity, whereas loss of function showed a BR-overproduction phenotype. Genome-wide identification of loci bound and regulated by OSH1 revealed hormonal and transcriptional regulation as the major function of OSH1. Among these targets, BR catabolism genes CYP734A2, CYP734A4, and CYP734A6 were rapidly upregulated by OSH1 induction. Furthermore, RNA interference knockdown plants of CYP734A genes arrested growth of the SAM and mimicked some osh1 phenotypes. Thus, we suggest that local control of BR levels by KNOX genes is a key regulatory step in SAM function.
Clinical and biochemical consequences of an intragenic growth hormone receptor (GHR) deletion in a large Chinese pedigree
Authors: Klammt Jürgen , Shen Shuixian , Kiess Wieland , Kratzsch Jürgen , Stobbe Heike , Vogel Mandy , Luo Feihong , Pfäffle Roland 
Published: September 2014

SummaryObjectiveGrowth hormone insensitivity (GHI) may be caused by failure of GH receptor function. Some patients bearing specific GHR mutations differ from classical GHI individuals by extremely elevated GH‐binding protein (GHBP) serum concentrations. We investigated clinical, genetic and biochemical characteristics of a severely growth‐retarded Chinese boy with classical Laron syndrome manifestations.Patients and measurementsDNA and mRNA from blood cells of the patient and 11 family members were investigated for GHR mutations. Basal GH, GHBP, IGF‐1 and IGFBP‐3 concentrations were determined in serum samples. The impact of the aberrant mRNA on GHR protein expression and secretion was analysed in vitro by transfection studies in HEK293 cells.ResultsThe proband and seven relatives had excessively elevated GHBP serum concentration. Basal GH in these individuals was significantly greater compared with family members with normal GHBP. The GHBP increase originated from a novel GHR intragenic deletion comprising parts of exon and intron 8 that caused exon 8 skipping from the GHR mRNA transcript. Transfection studies revealed that the predicted loss of plasma membrane anchorage results in direct secretion of the mutant GHR.ConclusionsThe partial GHR deletion causes excessively elevated GHBP serum concentrations regardless of the state of zygosity of the mutation. The increase in GHBP is associated with significantly elevated basal GH levels. Clinically, only homozygous carriers exhibit classical GHI manifestations. The truncated GHR protein resulting from exon 8 skipping is directly secreted out of the cell.
Alkali dissolution behaviour of sea–island‐type polyethylene terephthalate ultramicrofibre knitted fabrics
Authors: Kim Hyun Sung , Shin Eun Suk , Lee Jung Jin 
Published: September 2014

Sea–island‐type polyethylene terephthalate ultramicrofibre (0.007 denier per filament) with a single fibre diameter of ca. 800 nm has been produced over the last 4 years. Three kinds of sea–island‐type polyethylene terephthalate knitted fabric manufactured from this ultramicrofibre were alkali treated, and their dissolution behaviour was investigated. It was found that the dissolution ratio was dependent upon temperature and sodium hydroxide concentration in the alkali treatment. Practical dissolution ratios mostly reached the theoretical values after alkali treatment with 1.0% (w/w) sodium hydroxide solution at 95 °C for 40 min in all samples. Alkali dissolution of the sea component and revealing of the island component were confirmed by differential scanning calorimetry and scanning electron microscopy. Alkali dissolution behaviour could also be monitored indirectly by the cationic dye staining method. While all untreated samples exhibited high colour yield values after cationic dyeing, alkali‐treated samples showed reduced colour yield values with increasing alkali treatment time and a final levelling‐off point.
Filtration of crushed tablet suspensions has potential to reduce infection incidence in people who inject drugs
Authors: Ng Huei , Patel Rahul P. , Bruno Raimondo , Latham Roger , Wanandy Troy , McLean Stuart 
Published: September 2014

AbstractIntroduction and AimsThe medical complications of injecting preparations from crushed tablets can be severe, and most can be attributed to the injection of insoluble particles and micro‐organisms. Previously we have shown that most of the particles can be removed by filtration, but it was not known whether bacteria could also be filtered in the presence of a high particle load. This study aims to determine the feasibility of filtration to remove bacteria from injections prepared from tablets.Design and MethodsInjections were prepared from crushed slow‐release morphine tablets, in mixed bacterial suspensions of Staphylococcus aureus, Streptococcus pyogenes and Pseudomonas aeruginosa. The injection suspensions were passed through syringe filters of porosity 0.45 or 0.20 μm, or combined 0.8 then 0.2 μm, and the bacterial load was counted.ResultsBacterial concentrations in unfiltered injections were 2.5–4.3 × 106 colony forming units mL−1. Both the 0.20 and 0.45 μm filters blocked unless a prefilter (cigarette filter) was used first. The 0.2 μm filter and the combined 0.8/0.2 μm filter reduced the bacteria to the limit of detection (10 colony forming units mL−1) or below. Filtration through a 0.45 μm filter was slightly less effective.Discussion and ConclusionsUse of a 0.2 μm filter, together with other injection hygiene measures, offers the prospect of greatly reducing the medical complications of injecting crushed tablets and should be considered as a highly effective harm reduction method. It is very likely that these benefits would also apply to other illicit drug injections, although validation studies are needed. [Ng H, Patel RP, Latham R, Bruno R, Wanandy R, McLean S. Filtration of crushed tablet suspensions has potential to reduce infection incidence in people who inject drugs. Drug Alcohol Rev 2015;34:67–73]
Aggression Levels Affect Social Interaction in the Non‐Breeding Territorial Aggression of the Weakly Electric Fish, Gymnotus omarorum
Authors: Zubizarreta Lucía , Stoddard Philip K. , Silva Ana 
Published: September 2014

AbstractAnimals typically decide whether to fight or retreat from conspecifics based on their individual estimates of the costs and benefits of fighting. Theoretical models predict how contenders solve a conflict, but the evaluation processes involved in these decisions depend on multiple factors that are difficult to explore experimentally. We addressed these questions using the non‐breeding territorial aggression of Gymnotus omarorum, in which subordinates make three distinctive decisions to signal their submission during a fight: (1) interruption of their electric discharges to hide from the dominant, (2) stop attacking and retreat, and (3) emission of ‘chirps’, transient submissive electric signals. We confirmed that subordinates take into account the aggressive performance of dominants to shape their own agonistic decisions and performance. The intensity of aggression is highly correlated with an agonistic dyad, and the decision of subordinates to retreat is influenced by the attack rates of dominants. When we lowered the aggression of expected dominants with a 5‐HT1A receptor agonist, the correlation between the two contenders' aggression levels was lost and subordinates completely stopped emitting electric chirp signals. The aforementioned results contribute to the understanding of the decision‐making strategies driven by social challenge inherent to agonistic encounters.
Coeliac‐like duodenal pathology in orthotopic liver transplant patients on mycophenolic acid therapy
Authors: Cotter Maura B , AbuShanab Ahmed , Merriman Raphael , McCormick Aiden , Sheahan Kieran 
Published: September 2014

AimsDiarrhoea following orthotopic liver transplantation (OLT) is a significant clinical problem associated with mycophenolic acid (MPA). The histological injury pattern associated with MPA in the large bowel is well documented in the literature; however, that in the duodenum is less extensively documented. The aim of this study was to investigate the histological spectrum of duodenal injury specifically in symptomatic OLT patients on MPA, and to compare this with the spectrum in patients with coeliac disease and in normal controls.Methods and resultsWe reviewed our pathology database for all duodenal biopsies from patients on the OLT list over a period of 19 years. Medical records, anti‐tissue transglutaminase IgA serology and histology were reviewed. Of the 667 patients who underwent endoscopy, 127 had duodenal biopsies (152 biopsies). Of these, 87.5% were normal. Sixteen showed abnormal histology, and seven (43.8%) of these were on MPA at the time of biopsy. Significant features included coeliac‐like changes (shortened villi and increased intraepithelial lymphocyte counts), and novel findings included increased endocrine cell counts, apoptotic counts and lamina propria eosinophil counts in comparison with normal duodenal biopsies.ConclusionsPathologists should be aware of the features of MPA‐associated duodenal injury, including coeliac‐like changes and increased apoptotic counts. In those with abnormal histology, discontinuation or a reduction in the dose of MPA should be discussed.
Differentiation reprogramming in gastric intestinal metaplasia and dysplasia: role of SOX2 and CDX2
Authors: Camilo Vânia , Garrido Mónica , Valente Pedro , Ricardo Sara , Amaral Ana Luísa , Barros Rita , Chaves Paula , Carneiro Fátima , David Leonor , Almeida Raquel 
Published: September 2014

AimsIntestinal metaplasia (IM), which results from de‐novo expression of CDX2, and dysplasia are precursor lesions of gastric cancer that are associated with an increased risk for cancer development. There is much evidence suggesting a role for the transcription factor SOX2 in gastric differentiation. The aim of this study was to attempt to establish the relationship of SOX2 with CDX2 and with the differentiation reprogramming that characterizes gastric carcinogenesis, to assess their involvement in IM and dysplasia.Methods and resultsCharacterization of gastric (SOX2, MUC5AC, and MUC6) and intestinal (CDX2 and MUC2) markers in normal gastric mucosa, in 55 foci of IM and in 26 foci of dysplasia, was performed by immunohistochemistry. SOX2 was expressed in the normal gastric mucosa, in the presumptive stem cell compartment, and was maintained in 7% of the complete (MUC5AC‐negative) and 85% of the incomplete (MUC5AC‐positive) IM subtypes. Twelve per cent of the dysplastic lesions expressed SOX2, and the association with MUC5AC was lost. CDX2 was present in all IMs and dysplastic lesions.ConclusionsSOX2 is associated with gastric differentiation in incomplete IM and is lost in the progression to dysplasia, whereas CDX2 is acquired de novo in IM and maintained in dysplasia. This suggests that the balance between gastric and intestinal differentiation programmes impacts on the gastric carcinogenesis cascade progression.
Use and interpretation of routine outcome measures in forensic mental health
Authors: Shinkfield Gregg , Ogloff James 
Published: September 2014

AbstractThe present study aimed to both pilot a method of monitoring mental health nurses' use of routine outcome measures (ROM) and to examine the precision of ratings made with these tools within a forensic mental health environment. The audit protocol used in the present study was found to be effective in evaluating both the accuracy with which nurses were able to interpret ROM items and their degree of adherence with local procedures for completing such instruments. Moreover, the results suggest that despite these ROM having been developed for use in general mental health settings, they could be interpreted and rated with an adequate degree of reliability by nurses in a forensic mental health context. However, difficulties were observed in the applicability of several components of these tools within a forensic environment. Recommendations for future research and implications for practice are discussed.
Low‐Temperature Deposition of Hexagonal Boron Nitride via Sequential Injection of Triethylboron and N2/H2 Plasma
Authors: Haider Ali , Ozgit‐Akgun Cagla , Goldenberg Eda , Okyay Ali Kemal , Biyikli Necmi 
Published: September 2014

Hexagonal boron nitride (hBN) thin films were deposited on silicon and quartz substrates using sequential exposures of triethylboron and N2/H2 plasma in a hollow‐cathode plasma‐assisted atomic layer deposition reactor at low temperatures (≤450°C). A non‐saturating film deposition rate was observed for substrate temperatures above 250°C. BN films were characterized for their chemical composition, crystallinity, surface morphology, and optical properties. X‐ray photoelectron spectroscopy (XPS) depicted the peaks of boron, nitrogen, carbon, and oxygen at the film surface. B 1s and N 1s high‐resolution XPS spectra confirmed the presence of BN with peaks located at 190.8 and 398.3 eV, respectively. As deposited films were polycrystalline, single‐phase hBN irrespective of the deposition temperature. Absorption spectra exhibited an optical band edge at ~5.25 eV and an optical transmittance greater than 90% in the visible region of the spectrum. Refractive index of the hBN film deposited at 450°C was 1.60 at 550 nm, which increased to 1.64 after postdeposition annealing at 800°C for 30 min. These results represent the first demonstration of hBN deposition using low‐temperature hollow‐cathode plasma‐assisted sequential deposition technique.
Fabrication and Dielectric Properties of Ba0.63Sr0.37TiO3 Thin Films on SiC Substrates
Authors: Song Lirong , Chen Ying , Wang Genshui , Yang Lihui , Ge Jun , Dong Xianlin , Xiang Pinghua , Zhang Yuanyuan , Tang Xiaodong 
Published: September 2014

Ba0.63Sr0.37TiO3 (BST) films were first deposited on SiC substrates with LNO bottom electrodes by magnetron sputtering. The BST/LNO/SiC thin films exhibit high dielectric tunability and low dielectric loss while maintaining excellent temperature coefficient of dielectric constant in the temperature range between 250 and 350 K. We also investigated the effect of film thickness on the dielectric properties. BST(430 nm)/LNO/SiC film has higher tunability (68.09% @700 kV/cm), lower loss tangent (tanδ = 0.00987) and quite a bit higher figure of merit (FOM = 68.99) as compared with that of BST(300 nm)/LNO/SiC film. Our results demonstrate that combining ferroelectric BST films with SiC substrates is very promising for the development of tunable devices over a large temperature range.
Loss of SIRT4 decreases GLT‐1‐dependent glutamate uptake and increases sensitivity to kainic acid
Authors: Shih Jennifer , Liu Lei , Mason Andrew , Higashimori Haruki , Donmez Gizem 
Published: September 2014

AbstractGlutamate transport is a critical process in the brain that maintains low extracellular levels of glutamate to allow for efficient neurotransmission and prevent excitotoxicity. Loss of glutamate transport function is implicated in epilepsy, traumatic brain injury, and amyotrophic lateral sclerosis. It remains unclear whether or not glutamate transport can be modulated in these disease conditions to improve outcome. Here, we show that sirtuin (SIRT)4, a mitochondrial sirtuin, is up‐regulated in response to treatment with the potent excitotoxin kainic acid. Loss of SIRT4 leads to a more severe reaction to kainic acid and decreased glutamate transporter expression and function in the brain. Together, these results indicate a critical and novel stress response role for SIRT4 in promoting proper glutamate transport capacity and protecting against excitotoxicity.
image
Loss of sirtuin 4 (SIRT4) in mice leads to decreased glutamate transporter expression and function in the brain, which can ultimately cause increased excitotoxic effects. SIRT4 is up‐regulated in response to treatment with the potent excitotoxin kainic acid. These results indicate a critical and novel stress response role for SIRT4 in promoting proper glutamate transport capacity and protecting against excitotoxicity. GLT‐1, Glutamate Transporter 1, same as excitatory amino acid transporter 2; Glu, glutamate.