bluuebunny/crossref_metadata_2025_split huggingface dataset:
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis
Authors: Li Pei , Ji Guoli , Dong Min , Schmidt Emily , Lenox Douglas , Chen Liangliang , Liu Qi , Liu Lin , Zhang Jie , Liang Chun 
Published: July 2012

Abstract
Summary: To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects.
Availability: CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/
Contact: liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Association of QRS duration with left ventricular structure and function and risk of heart failure in middle‐aged and older adults: the Multi‐Ethnic Study of Atherosclerosis (MESA)
Authors: Ilkhanoff Leonard , Liu Kiang , Ning Hongyan , Nazarian Saman , Bluemke David A. , Soliman Elsayed Z. , Lloyd‐Jones Donald M. 
Published: July 2012

AimsProlonged QRS duration (QRSd) on the electrocardiogram (ECG) has been associated with cardiac structural and functional abnormalities by echocardiography and an increased risk of heart failure (HF). Data are sparse on these relationships in middle‐aged and elderly individuals free of baseline cardiovascular disease with respect to cardiac magnetic resonance imaging (MRI). We sought to determine whether QRSd is associated with incident HF and measures of cardiac structure and function by cardiac MRI.Methods and resultsWe analysed baseline ECGs in the Multi‐Ethnic Study of Atherosclerosis (MESA) to determine whether QRSd >100 ms was associated with incident HF. We adjusted for demographic and clinical risk factors, as well as MRI measures of left ventricular (LV) structure and function. Among 4591 eligible participants (51% women; 39% white; mean age 61 years), 75 developed incident HF over a mean follow‐up of 7.1 years. QRSd >100 ms was significantly associated with MRI measures of cardiac structure and function, as well as incident HF, even after adjustment for demographic covariates [hazard ratio (HR) 2.10, 95% confidence interval (CI) 1.29–3.42; P = 0.003] and clinical risk factors (HR 1.86, 95% CI 1.14–3.03; P = 0.01). With further adjustment for individual LV structural measures, findings were attenuated to non‐significance. Separate adjustment for LV functional measures yielded only mild attenuation.ConclusionIn middle‐aged and older adults without cardiovascular disease, a QRSd >100 ms was significantly associated with incident HF. After adjustment for LV structural measures, the association was attenuated to non‐significance, suggesting that prolonged QRSd is potentially a useful marker of LV structure that may predispose to HF risk.
Expression of the chloroplast thioredoxins f and m is linked to short-term changes in the sugar and thiol status in leaves of Pisum sativum
Authors: Barajas-López Juan de Dios , Tezycka Justyna , Travaglia Claudia N , Serrato Antonio Jesús , Chueca Ana , Thormählen Ina , Geigenberger Peter , Sahrawy Mariam 
Published: July 2012

AbstractThioredoxins (TRXs) f and m are key components in the light regulation of photosynthetic metabolism via thiol–dithiol modulation in chloroplasts of leaves; however, little is known about the factors modulating the expression of these proteins. To investigate the effect of sugars as photosynthetic products on the expression of PsTRX f and m1 genes, sucrose and glucose were externally supplied to pea plants during the day. There was an increase in the mRNA levels of PsTRX f and m1 genes in response mainly to glucose. When leaf discs were incubated for up to 4h in the dark, glucose also led to an increase in both mRNA and protein levels of TRXs f and m, while sucrose had no substantial effect. Expression of PsDOF7, a carbon metabolism-related transcription factor gene, was also induced by glucose. Protein–DNA interaction showed that PsDOF7 binds specifically to the DOF core located in PsTRX f and m1 gene promoters. Transient expression in agroinfiltrated pea leaves demonstrated that PsDOF7 activated transcription of both promoters. The incubation of leaf discs in dithiotreitol (DTT) to increase the redox status led to a marked increase in the mRNA and protein levels of both TRXs within 4h. The increase in TRX protein levels occurred after 1h DTT feeding, implying a rapid effect of the thiol status on TRX f and m1 protein turnover rates, while transcriptional regulation took 3h to proceed. These results show that the protein levels of both TRXs are under short-term control of the sugar and thiol status in plants.
Effect of Perioperative Oxygen Supplementation on 30-day Surgical Site Infection Rate in Abdominal, Gynecologic, and Breast Surgery
Authors: Thibon Pascal , Borgey France , Boutreux Sébastien , Hanouz Jean-Luc , Le Coutour Xavier , Parienti Jean-Jacques 
Published: July 2012

Background
Benefits and limitations of supplementation with 80% fraction of inspired oxygen for preventing surgical site infections have not yet been clearly defined. Some studies have reported benefits in colorectal surgery, whereas trials in abdominal and gynecologic surgery have reported either no effect or a deleterious effect.

Methods
Controlled, randomized, assessor-blind multicenter trial, the ISO2 study, comparing the effects of hyperoxygenation (fraction of inspired oxygen, 80%) with those of 30% oxygen on the frequency of surgical site infections in routine abdominal, gynecologic, and breast surgery on 434 patients. Patients not seen in consultation after discharge were contacted.

Results
In total, 208 patients received 30% perioperative oxygen and 226 received 80%. There was no difference between the two groups for baseline, intraoperative, and postoperative characteristics, except for oxygen saturation at closure, higher in the 80% group (P=0.01). The frequency of 30-day surgical site infections was 7.2% (15/208) in the 30% group and 6.6% (15/226) in the 80% group (relative risk, 0.92; 95% CI [0.46-1.84], P=0.81). Frequency of adverse events (nausea and vomiting, sternal pain, cough, hypotension) was similar in the two groups. Desaturation and bradycardia were more frequent in the 30% group. In an updated meta-analysis including the result of this trial and those of eight published randomized trials, the overall relative risk was 0.97; 95% CI (0.68-1.40), I2 (inconsistency degree)=73%, (P=0.88).

Conclusions
The routine use of hyperoxygenation throughout abdominal, gynecologic, and breast surgery had no effect on the frequency of 30-day surgical site infections and was not accompanied by more frequent adverse effects.
Toward Stable Genetic Engineering of Human O-Glycosylation in Plants
Authors: Yang Zhang , Bennett Eric P. , Jørgensen Bodil , Drew Damian P. , Arigi Emma , Mandel Ulla , Ulvskov Peter , Levery Steven B. , Clausen Henrik , Petersen Bent L. 
Published: July 2012

Abstract
Glycosylation is the most abundant and complex posttranslational modification to be considered for recombinant production of therapeutic proteins. Mucin-type (N-acetylgalactosamine [GalNAc]-type) O-glycosylation is found in eumetazoan cells but absent in plants and yeast, making these cell types an obvious choice for de novo engineering of this O-glycosylation pathway. We previously showed that transient implementation of O-glycosylation capacity in plants requires introduction of the synthesis of the donor substrate UDP-GalNAc and one or more polypeptide GalNAc-transferases for incorporating GalNAc residues into proteins. Here, we have stably engineered O-glycosylation capacity in two plant cell systems, soil-grown Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum) Bright Yellow-2 suspension culture cells. Efficient GalNAc O-glycosylation of two stably coexpressed substrate O-glycoproteins was obtained, but a high degree of proline hydroxylation and hydroxyproline-linked arabinosides, on a mucin (MUC1)-derived substrate, was also observed. Addition of the prolyl 4-hydroxylase inhibitor 2,2-dipyridyl, however, effectively suppressed proline hydroxylation and arabinosylation of MUC1 in Bright Yellow-2 cells. In summary, stably engineered mammalian type O-glycosylation was established in transgenic plants, demonstrating that plants may serve as host cells for the production of recombinant O-glycoproteins. However, the present stable implementation further strengthens the notion that elimination of endogenous posttranslational modifications may be needed for the production of protein therapeutics.
Characterization of SOC1’s Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators
Authors: Immink Richard G.H. , Posé David , Ferrario Silvia , Ott Felix , Kaufmann Kerstin , Valentim Felipe Leal , de Folter Stefan , van der Wal Froukje , van Dijk Aalt D.J. , Schmid Markus , Angenent Gerco C. 
Published: July 2012

AbstractThe transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
Contribution of a harpin protein fromXanthomonas axonopodispv.citrito pathogen virulence
Authors: Sgro Germán G. , Ficarra Florencia A. , Dunger Germán , Scarpeci Telma E. , Valle Estela M. , Cortadi Adriana , Orellano Elena G. , Gottig Natalia , Ottado Jorgelina 
Published: July 2012

SummaryXanthomonas axonopodispv.citri(Xac), the bacterium that causes citrus canker, contains a gene in thehrp[for hypersensitive response (HR) and pathogenicity] cluster that encodes a harpin protein calledHpa1.Hpa1 producedHRin the nonhost plants tobacco, pepper andArabidopsis, whereas, in the host plant citrus, it elicited a weak defence response with no visible phenotype. Co‐infiltrations ofXac with or without the recombinantHpa1 protein in citrus leaves produced a larger number of cankers in the presence of the protein. To characterize the effect ofHpa1 during the disease, anXacΔhpa1 mutant was constructed, and infiltration of this mutant caused a smaller number of cankers. In addition, the lack ofHpa1 hindered bacterial aggregation both in solution andin planta. Analysis of citrus leaves infiltrated withHpa1 revealed alterations in mesophyll morphology caused by the presence of cavitations and crystal idioblasts, suggesting the binding of the harpin to plant membranes and the elicitation of signalling cascades. Overall, these results suggest that, even thoughHpa1 elicits the defence response in nonhost plants and, to a lesser extent, in host plants, its main roles in citrus canker are to alter leaf mesophyll structure and to aggregate bacterial cells, and thus increase virulence and pathogen fitness. We expressed theN‐terminal andC‐terminal regions and found that, although both regions elicitedHRin nonhost plants, only theN‐terminal region showed increased virulence and bacterial aggregation, supporting the role of this region of the protein as the main active domain.
‘He didn't mean to hit mom, I think’: positioning, agency and point in adolescents' narratives about domestic violence
Authors: Øverlien Carolina 
Published: July 2012

ABSTRACTThis paper analyses the narratives of adolescents who have experienced domestic violence. It focuses on what we can learn about being an adolescent who experiences domestic violence, using a narrative approach. Attentive to both form and content, the paper sheds light on why the narrative is being told, who the actors in the narratives are, who are positioned in the forefront/background and what the point of the narrative is. The analysis shows that through the storytelling, the father's position as the reluctant/dangerous/weak aggressor is negotiated, the mother is positioned both in the background as a victim and in the forefront as an actor resisting his violent behaviour. The children position themselves as actors with power to alter the progress, to protect and stop the violence. The point of the narratives is to describe the father as the aggressor, and to describe the important role of the children. This picture of the father, mother and child questions the traditional understanding of the father as the aggressor, the mother as the victim and the child as a powerless bystander being exposed to the violence, and underlines the complexities of the dynamics in families living with domestic violence.
Type I interferon induces CX3CL1 (fractalkine) and CCL5 (RANTES) production in human pulmonary vascular endothelial cells
Authors: Nakano M , Fujii T , Hashimoto M , Yukawa N , Yoshifuji H , Ohmura K , Nakaizumi A , Mimori T 
Published: July 2012

SummaryType I interferon (IFN) medications cause various adverse reactions, including vascular diseases. Although an association between chemokines and vascular diseases has also been reported, the relationship between type I IFN and chemokines in vascular endothelial cells (VEC) remains unclear. To provide clues to pathogenesis of the diseases, we analysed the effects of type I IFN on chemokine production in human VEC. Type I IFN induced higher CX3CL1 (fractalkine) mRNA expression and protein secretion in pulmonary arterial VEC than in umbilical vein VEC. Type I IFN also induced CCL5 [regulated upon activation normal T cell expressed and secreted (RANTES)] production in VEC, especially in lung micro-VEC. IFN-β induced much higher chemokine production than IFN-α, and Janus protein tyrosine kinase (JAK) inhibitor I prevented type I IFN-induced chemokine secretion. Type I IFN-induced chemokines may be involved in the pathophysiology of pulmonary vascular diseases, and the JAK inhibitor may serve as a therapeutic option for these diseases.
Impact of spring upwelling variability off southern‐central Chile on common sardine (Strangomera bentincki) recruitment
Authors: GOMEZ FABIAN , MONTECINOS ALDO , HORMAZABAL SAMUEL , CUBILLOS LUIS A. , CORREA‐RAMIREZ MARCO , CHAVEZ FRANCISCO P. 
Published: July 2012

AbstractOff southern‐central Chile, the impact of spring upwelling variability on common sardine (Strangomera bentincki) recruitment was examined by analyzing satellite and coastal station winds, satellite chlorophyll, and common sardine recruitment from a stock assessment model. In austral spring, the intensity of wind‐driven upwelling is related to sea surface temperature (SST) from the Niño 3.4 region, being weak during warm periods (El Niño) and strong during cold periods (La Niña). Interannual changes in both spring upwelling intensity and SST from the Niño 3.4 region are related to changes in remotely sensed chlorophyll over the continental shelf. In turn, year‐to‐year changes in coastal chlorophyll are tightly coupled to common sardine recruitment. We propose that, in the period 1991–2004, interannual changes in the intensity of spring upwelling affected the abundance and availability of planktonic food for common sardine, and consequently determined pre‐recruit survival and recruitment strength. However, the importance of density‐dependent factors on the reproductive dynamic cannot be neglected, as a negative association exists between spawning biomass and recruitment‐per‐spawning biomass. Coastal chlorophyll, upwelling intensity, and SST anomalies from the Niño 3.4 region could potentially help to predict common sardine recruitment scenarios under strong spring upwelling and El Niño Southern Oscillation (ENSO)‐related anomalies.
Reciprocal trophic niche shifts in native and invasive fish: salmonids and galaxiids in Patagonian lakes
Authors: CORREA CRISTIÁN , BRAVO ANDREA P. , HENDRY ANDREW P. 
Published: July 2012

Summary1. Rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta) are widespread and invasive salmonids with important lethal effects as predators, although indirect effects are also possible. We used stable isotope analyses (δ15N, δ13C) to explore how the density of invasive trout in 25 Patagonian lakes alters the trophic niche (TN) of a widespread native fish, Galaxias platei (Galaxiidae). We also explored how the density of the galaxiid influences the TN of invasive trout.2. We quantified two aspects of the TN: (i) the proportion of littoral carbon (PL) and (ii) trophic height (TH) (i.e. the ‘height’ at which the fish feeds in the food web). We related these measures of TN in a given species to the density of other species (as estimated by catch‐per‐unit‐effort).3. As G. platei body size increased, their PL increased (increasing littoral feeding) in several lakes. However, none of the fish species investigated showed changes in PL with increasing density of the other fish species. TH increased with body size in all three species. In addition, the TH of large G. platei declined with increasing trout density and, reciprocally, the TH of large S. trutta decreased with decreasing G. platei density.4. The reciprocal effects of native and the invasive fish on TH were as large as a shift of one trophic level. This pattern is consistent with an exhaustion of galaxiid prey for both piscivorous G. platei and S. trutta in lakes with high trout density.5. These finding support the suggested management strategy of culling trout from overpopulated lakes, which should simultaneously protect native fish and enhance a lucrative sport fishery for large trout.
Livestock greenhouse gas emissions and mitigation potential in Europe
Authors: Bellarby Jessica , Tirado Reyes , Leip Adrian , Weiss Franz , Lesschen Jan Peter , Smith Pete 
Published: July 2012

AbstractThe livestock sector contributes considerably to global greenhouse gas emissions (GHG). Here, for the year 2007 we examined GHG emissions in the EU27 livestock sector and estimated GHG emissions from production and consumption of livestock products; including imports, exports and wastage. We also reviewed available mitigation options and estimated their potential. The focus of this review is on the beef and dairy sector since these contribute 60% of all livestock production emissions. Particular attention is paid to the role of land use and land use change (LULUC) and carbon sequestration in grasslands. GHG emissions of all livestock products amount to between 630 and 863 Mt CO2e, or 12–17% of total EU27 GHG emissions in 2007. The highest emissions aside from production, originate from LULUC, followed by emissions from wasted food. The total GHG mitigation potential from the livestock sector in Europe is between 101 and 377 Mt CO2e equivalent to between 12 and 61% of total EU27 livestock sector emissions in 2007. A reduction in food waste and consumption of livestock products linked with reduced production, are the most effective mitigation options, and if encouraged, would also deliver environmental and human health benefits. Production of beef and dairy on grassland, as opposed to intensive grain fed production, can be associated with a reduction in GHG emissions depending on actual LULUC emissions. This could be promoted on rough grazing land where appropriate.
Lymph node infarction: role of underlying malignancy, tumour proliferation fraction and vascular compromise – a study of 35 cases and a comprehensive review of the literature
Authors: Jiang Xiaoyin ‘Sara’ , West Dava S , Lagoo Anand S 
Published: July 2012

Aims:  To determine the roles of the presence of malignancy, tumour proliferation fraction, vascular compromise and therapeutic and diagnostic manipulations in lymph node infarction (LNI).Methods and results:  Thirty‐five cases of LNI were identified over a 20‐year period. Of the 35 patients, 31 (89%) had an underlying malignancy: 27 of the 31 (87%) were haematologic malignancies, the rest being metastatic carcinoma (two), melanoma, and seminoma. Of the four patients without evidence of malignancy, two were diagnosed with viral infection, one had LNI adjacent to a thrombosed pancreas graft, and one was lost to follow‐up. Ki67 immunostaining in viable tumour demonstrated a range (5–60%) of proliferation fractions. A history of fine needle aspiration alone was present in seven of the 35 patients (20%), a history of chemotherapy alone in 11 (31%), and a history of both in two (5.7%). Factor VIII immunostaining highlighted thrombosed and recanalized vessels next to the infarction.Conclusions:  Infarction of lymph nodes is associated with previous, concurrent or subsequent diagnosis of malignancy in the vast majority of cases. Chemotherapy or previous fine needle aspiration can precipitate infarction in some cases, but infarction may occur without such intervention, possibly because of an underlying subacute or chronic vascular compromise produced by vascular thrombosis.