bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment
Authors: Gálvez Sergio , Díaz David , Hernández Pilar , Esteban Francisco J. , Caballero Juan A. , Dorado Gabriel 
Published: January 2010

Abstract
Motivation: Bioinformatics algorithms and computing power are the main bottlenecks for analyzing huge amount of data generated by the current technologies, such as the ‘next-generation’ sequencing methodologies. At the same time, most powerful microprocessors are based on many-core chips, yet most applications cannot exploit such power, requiring parallelized algorithms. As an example of next-generation bioinformatics, we have developed from scratch a new parallelization of the Needleman–Wunsch (NW) sequence alignment algorithm for the 64-core Tile64 microprocessor. The unprecedented performance it offers for a standalone personal computer (PC) is discussed, optimally aligning sequences up to 20 times faster than the non-parallelized version, thus saving valuable time.
Availability: This algorithm is available as a free web service for the scientific community at http://www.sicuma.uma.es/multicore. The open source code is also available on such site.
Contact: galvez@uma.es
Supplementary information: Supplementary data are available here.
iDBPs: a web server for the identification of DNA binding proteins
Authors: Nimrod Guy , Schushan Maya , Szilágyi András , Leslie Christina , Ben-Tal Nir 
Published: January 2010

Abstract
Summary: The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies.
Availability: http://idbps.tau.ac.il/
Contact: NirB@tauex.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments
Authors: Droit Arnaud , Cheung Charles , Gottardo Raphael 
Published: January 2010

Abstract
Summary: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) has evolved as a popular technique to study DNA–protein binding or post-translational chromatin/histone modifications at the genomic level. However, the raw microarray intensities generate a massive amount of data, creating a need for efficient analysis algorithms and statistical methods to identify enriched regions.
Results: We present a fast, free and powerful, open source R package, rMAT, that allows the identification of regions enriched for transcription factor binding sites in ChIP-chip experiments on Affymetrix tiling arrays.
Availability: The R-package rMAT is available from the Bioconductor web site at http://bioconductor.org and runs on Linux, MAC OS and MS-Windows. rMAT is distributed under the terms of the Artistic Licence 2.0.
Contact: arnaud.droit@ircm.qc.ca; raphael.gottardo@ircm.qc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Right ventricular dysfunction is an independent predictor for mortality in ST‐elevation myocardial infarction patients presenting with cardiogenic shock on admission
Authors: Engström Annemarie E. , Vis Marije M. , Bouma Berto J. , van den Brink Renée B.A. , Baan Jan , Claessen Bimmer E.P.M. , Kikkert Wouter J. , Sjauw Krischan D. , Meuwissen Martijn , Koch Karel T. , de Winter Robbert J. , Tijssen Jan G.P. , Piek Jan J. , Henriques José P.S. 
Published: January 2010

AimsDespite improvement in prognosis for ST‐elevation myocardial infarction (STEMI) patients, mortality remains high in STEMI patients presenting with cardiogenic shock (CS). Right ventricular (RV) dysfunction is an established independent predictor for adverse prognosis in STEMI patients without CS. The purpose of our study was to determine the prognostic value of RV dysfunction on admission in STEMI patients presenting in CS.Methods and resultsTwo hundred and ninety‐two consecutive STEMI patients with CS on admission were treated by primary percutaneous coronary intervention (PCI) from January 1997 through March 2005. RV function was assessed by measurement of tricuspid annular plane systolic excursion (TAPSE) on early echocardiography in 184 of 292 patients. Right ventricular dysfunction was defined as a TAPSE of ≤14 mm. Right ventricular dysfunction was present on early echocardiography in 70 of 184 patients (38%). The Kaplan–Meier estimate for overall 4‐year survival was 57%. Kaplan–Meier estimates for 4‐year survival in patients with and without RV dysfunction were 33 and 73%, respectively (P< 0.001). Cox‐regression analysis revealed a hazard ratio of 2.1 (95% CI 1.3–3.4, P = 0.002) for RV dysfunction when adjusted for age, glucose on admission, and LVEF < 40%. In patients with and without RV dysfunction, the right coronary artery was the infarct‐related artery in 41 and 28% of patients, respectively (P = 0.06).ConclusionIn STEMI patients presenting with CS on admission and treated with primary PCI, RV dysfunction as assessed by echocardiography is an independent predictor for long‐term mortality.
Effects of Permissive Hypercapnia on Transient Global Cerebral Ischemia–Reperfusion Injury in Rats
Authors: Zhou Qiang , Cao Bo , Niu Li , Cui Xiaoguang , Yu Hongwei , Liu Jinfeng , Li Haibo , Li Wenzhi 
Published: January 2010

Background
Permissive hypercapnia is a widely practiced protective ventilatory strategy that has significant protective effects on several models of in vitro and in vivo neuronal injury. However, conclusive effects of permissive hypercapnia on cerebral ischemia are still unknown.

Methods
One hundred sixty male Wistar rats were divided into five groups: S group (control), ischemia-reperfusion (I/R) group, P1 group, P2 group, and P3 group. I/R was induced by bilateral occlusion of the common carotid arteries, combined with controlled hypotension for 15 min. In groups P1, P2, and P3, the rats inhaled carbon dioxide for 2 h during reperfusion to keep Paco2 within the ranges of 60-80 mmHg, 80-100 mmHg, and 100-120 mmHg, respectively. After 24 and 72 h, neurologic deficit scores, ultrastructural changes, apoptotic neurons, and brain wet-to-dry weight ratios were observed. Caspase-3 and aquaporin-4 protein expression and caspase-3 activity were analyzed.

Results
Compared with groups I/R and P3, groups P1 and P2 had better neurologic deficit scores and fewer ultrastructural histopathologic changes. I/R-induced cerebral apoptosis was also significantly reduced. The neuroprotective effect was significantly increased in the P2 group compared with the P1 group. There was a significant increase of brain water content and of aquaporin-4 levels in the P3 group.

Conclusions
Mild to moderate hypercapnia (Paco2 60-100 mmHg) is neuroprotective after transient global cerebral I/R injury. Such a protection might be associated with apoptosis-regulating proteins. In contrast, severe hypercapnia (Paco2 100-120 mmHg) increased brain injury, which may be caused by increased brain edema.
Impact of Subxiphoid Video Pericardioscopy with a Rigid Shaft on Cardiac Hemodynamics in a Porcine Model
Authors: Yokota Takenori , Ota Takeyoshi , Schwartzman David , Zenati Marco A. 
Published: January 2010

ObjectiveSingle-port subxiphoid videopericardioscopy with a rigid shaft is useful for left atrial exclusion, left ventricular (LV) pacing lead implantation, and epicardial mapping, but it may interfere with the cardiac rhythm and adversely alter hemodynamics. We examined the impact of this technique on hemodynamic indices in a porcine model.MethodsThe videopericardioscopy device was introduced into the pericardial space of five pigs (35–45 kg) via a subxiphoid approach and navigated to six anatomic targets [right atrial appendage, superior vena cava, ascending aorta, left atrial appendage (anterior and posterior approaches), transverse sinus, and atrioventricular (AV) groove]. After successful target acquisition, the device was withdrawn through the subxiphoid port. When the hemodynamics stabilized, the device was navigated to another target. The heart rate (HR), arterial blood pressure (BP), central venous pressure (CVP), pulmonary arterial pressure, and mixed venous oxygen saturation (SvO2) were measured at every pretarget (subxiphoid incision) and target point. After the navigation trials, the animals were killed and the mediastinum space was examined for procedure-related injuries.ResultsThe device afforded a good view, and the navigation trials were successfully performed on the beating heart. Four animals tolerated the procedures, whereas one died of device-induced ventricular fibrillation after the trials. Hemodynamics was severely compromised at all anatomic targets except the left atrial appendage (anterior approach).ConclusionsSubxiphoid videopericardioscopy significantly interferes with the cardiac rhythm, causing life-threatening arrhythmia and hemodynamic compromise, when the target is located deep and far from the pericardiotomy. A flexible or highly articulated device would enable intrapericardial navigation without hemodynamic compromise.
Minimally Invasive Direct Coronary Artery Bypass as a Primary Strategy for Reoperative Myocardial Revascularization
Authors: Balacumaraswami Lognathen , Patel Nirav C. , Gorki Hagen , Jennings Joan , Plestis Konstadinos A. , Subramanian Valavanur A. 
Published: January 2010

Objective Conventional reoperative coronary artery bypass grafting is associated with risk of sternal re-entry, injury to patent grafts, and embolization from diseased grafts. Sternal sparing minimally invasive direct coronary artery bypass (MIDCAB) avoids such risks in cases where it is technically feasible. We sought to examine in-hospital outcomes of reoperative MIDCAB surgery. Methods We recorded prospective standardized data from the New York Cardiac Surgical Reporting System database of 369 reoperative MIDCAB cases from 1996 to 2006 and compared with 822 primary MIDCAB patients in the same time period. We compared the preoperative risk profile and postoperative in-hospital outcomes and length of stay for both groups. Results There was a significantly higher risk profile typical of the reoperative patient population (P < 0.001 for stroke, peripheral/cerebrovascular disease, extensive aortic calcification, renal failure, and left ventricular ejection fraction <40%) compared with the primary MIDCAB group. Despite this fact, there was no difference in the in-hospital outcomes and length of hospital stay between the two groups. Conclusions Reoperative MIDCAB provides targeted coronary revascularization and avoids hazards of sternal re-entry, graft injury and manipulation, and deleterious effects of cardiopulmonary bypass. This hastens recovery and provides excellent early outcomes equivalent to primary MIDCAB procedures.
Cerebral Emboli Generation during Off-Pump Coronary Artery Bypass Grafting with a Clampless Device versus Partial Clamping of the Ascending Aorta
Authors: Eldaif Shady M. , Thourani Vinod H. , Puskas John D. 
Published: January 2010

Objective It is not known whether use of a clampless facilitating device during proximal graft anastamosis decreases intraoperative cerebral emboli in patients with mild atherosclerotic ascending aorta (AAA) having off-pump coronary artery bypass. Methods After intraoperative epiaortic ultrasound showed no more than mild (grade I–II) atherosclerotic ascending aorta, 20 patients were randomized to receive either partial clamping (PC, n = 10) or the HEARTSTRING clampless device (HS, n = 9) for proximal graft construction on the ascending aorta. Continuous transcranial Doppler monitoring, with capability to discern gaseous from solid particulates, was used intraoperatively to monitor high-intensity transient signals (HITS) in the middle cerebral arteries. Postoperative diffusion-weighted brain magnetic resonance imaging documented old and new ischemic brain lesions. Results There were no significant differences between the groups in the number of proximals (P = 0.14), distals (P = 0.4), or intraoperative cell saver transfusions (P = 0.69). The total number of HITS was not significantly different between the PC and HS groups (P = 0.2). However, the number of solid HITS was significantly lower in the HS than in the PC group (2.7 ± 2.6 versus 14.0 ± 8.1; P < 0.001). The number of gaseous emboli in the HS group was fourfold greater when a mister-blower rather than a suction device was used to clear blood away from the HS site. Postoperatively, there were no deaths, myocardial infarctions, or clinical strokes observed in either group. Diffusion-weighted cerebral magnetic resonance imaging revealed no statistical difference between groups for new infarct lesions. Conclusions Use of the HS device during off-pump coronary artery bypass was associated with significantly fewer intraoperative solid emboli in the middle cerebral artery than PC of the ascending aorta.
Hemin Exerts Multiple Protective Mechanisms and Attenuates Dextran Sulfate Sodium–induced Colitis
Authors: Zhong Wenwei , Xia Zhenwei , Hinrichs David , Rosenbaum James T , Wegmann Keith W , Meyrowitz Jeffery , Zhang Zili 
Published: January 2010

ABSTRACTObjective:Inflammatory bowel disease (IBD) is characterized by recurrent and severe gastrointestinal inflammation. Activation of inflammatory cells, such as TH17 lymphocytes, and/or deficiency of regulatory T cells (Treg) are responsible for the pathogenesis of IBD. As an acute phase reactant, heme oxygenase‐1 (HO‐1) has been shown to play an anti‐inflammatory and immunomodulatory role in many disease processes. In this study, we used a dextran sulfate sodium (DSS)–induced murine colitis model to investigate the effect of upregulating HO‐1 by hemin on the development of colonic inflammation.Materials and Methods:The mice were enterically challenged with 4% DSS. In addition, some mice were intraperitoneally administered with hemin or Sn‐protoporphyrin (SnPP) on days 0, 1, and 6 after DSS treatment. The severity of colitis was evaluated by daily monitoring of weight change and diarrhea. At the end of the experiment, the colon, spleen, and mesenteric lymph nodes were harvested for histology and various immunological assays.Results:Compared to control groups, DSS challenge markedly induced HO‐1 expression in the colon epithelium. Upregulation of HO‐1 by hemin was further correlated with attenuation of DSS‐induced colitis. In contrast, inhibition of endogenous HO‐1 by SnPP aggravated the colitis. To further assess the anti‐inflammatory mechanisms, we examined whether hemin enhanced the proliferation of Treg cells and suppressed the production of interleukin (IL)‐17. Flow cytometry analysis revealed that hemin markedly expanded the CD4 + CD25 + Foxp3+ Treg population. Moreover, hemin attenuated IL‐17 and TH17‐related cytokines. This inhibition coincided with the attenuation of DSS‐induced colitis. Finally, terminal deoxynucleotidyl transferase deoxyuridine triphosphate nick end‐labeling assay showed that hemin treatment markedly reduced programmed cell death of colonic epithelium, indicating that hemin exerts a modulatory effect on the induction of Treg, IL‐17, and apoptosis.Conclusions:These results demonstrate that upregulation of HO‐1 by hemin ameliorated experimental colitis. Moreover, our study suggests a broader protective mechanism of hemin.
The Heat-Inducible Transcription Factor HsfA2 Enhances Anoxia Tolerance in Arabidopsis
Authors: Banti Valeria , Mafessoni Fabrizio , Loreti Elena , Alpi Amedeo , Perata Pierdomenico 
Published: January 2010

Abstract
Anoxia induces several heat shock proteins, and a mild heat pretreatment can acclimatize Arabidopsis (Arabidopsis thaliana) seedlings to subsequent anoxic treatment. In this study, we analyzed the response of Arabidopsis seedlings to anoxia, heat, and combined heat + anoxia stress. A significant overlap between the anoxic and the heat responses was observed by whole-genome microarray analysis. Among the transcription factors induced by both heat and anoxia, the heat shock factor A2 (HsfA2), known to be involved in Arabidopsis acclimation to heat and to other abiotic stresses, was strongly induced by anoxia. Heat-dependent acclimation to anoxia is lost in an HsfA2 knockout mutant (hsfa2) as well as in a double mutant for the constitutively expressed HsfA1a/HsfA1b (hsfA1a/1b), indicating that these three heat shock factors cooperate to confer anoxia tolerance. Arabidopsis seedlings that overexpress HsfA2 showed an increased expression of several known targets of this transcription factor and were markedly more tolerant to anoxia as well as to submergence. Anoxia failed to induce HsfA2 target proteins in wild-type seedlings, while overexpression of HsfA2 resulted in the production of HsfA2 targets under anoxia, correlating well with the low anoxia tolerance experiments. These results indicate that there is a considerable overlap between the molecular mechanisms of heat and anoxia tolerance and that HsfA2 is a player in these mechanisms.
Glycolysis and the Tricarboxylic Acid Cycle Are Linked by Alanine Aminotransferase during Hypoxia Induced by Waterlogging of Lotus japonicus
Authors: Rocha Marcio , Licausi Francesco , Araújo Wagner L. , Nunes-Nesi Adriano , Sodek Ladaslav , Fernie Alisdair R. , van Dongen Joost T. 
Published: January 2010

Abstract
The role of nitrogen metabolism in the survival of prolonged periods of waterlogging was investigated in highly flood-tolerant, nodulated Lotus japonicus plants. Alanine production revealed to be a critical hypoxic pathway. Alanine is the only amino acid whose biosynthesis is not inhibited by nitrogen deficiency resulting from RNA interference silencing of nodular leghemoglobin. The metabolic changes that were induced following waterlogging can be best explained by the activation of alanine metabolism in combination with the modular operation of a split tricarboxylic acid pathway. The sum result of this metabolic scenario is the accumulation of alanine and succinate and the production of extra ATP under hypoxia. The importance of alanine metabolism is discussed with respect to its ability to regulate the level of pyruvate, and this and all other changes are discussed in the context of current models concerning the regulation of plant metabolism.
Actin-Binding Proteins Implicated in the Formation of the Punctate Actin Foci Stimulated by the Self-Incompatibility Response inPapaver
Authors: Poulter Natalie S. , Staiger Christopher J. , Rappoport Joshua Z. , Franklin-Tong Vernonica E. 
Published: January 2010

AbstractThe actin cytoskeleton is a key target for signaling networks and plays a central role in translating signals into cellular responses in eukaryotic cells. Self-incompatibility (SI) is an important mechanism responsible for preventing self-fertilization. The SI system of Papaver rhoeas pollen involves a Ca2+-dependent signaling network, including massive actin depolymerization as one of the earliest cellular responses, followed by the formation of large actin foci. However, no analysis of these structures, which appear to be aggregates of filamentous (F-)actin based on phalloidin staining, has been carried out to date. Here, we characterize and quantify the formation of F-actin foci in incompatible Papaver pollen tubes over time. The F-actin foci increase in size over time, and we provide evidence that their formation requires actin polymerization. Once formed, these SI-induced structures are unusually stable, being resistant to treatments with latrunculin B. Furthermore, their formation is associated with changes in the intracellular localization of two actin-binding proteins, cyclase-associated protein and actin-depolymerizing factor. Two other regulators of actin dynamics, profilin and fimbrin, do not associate with the F-actin foci. This study provides, to our knowledge, the first insights into the actin-binding proteins and mechanisms involved in the formation of these intriguing structures, which appear to be actively formed during the SI response.
Reconstruction of Metabolic Pathways, Protein Expression, and Homeostasis Machineries across Maize Bundle Sheath and Mesophyll Chloroplasts: Large-Scale Quantitative Proteomics Using the First Maize Genome Assembly
Authors: Friso Giulia , Majeran Wojciech , Huang Mingshu , Sun Qi , van Wijk Klaas J. 
Published: January 2010

Abstract
Chloroplasts in differentiated bundle sheath (BS) and mesophyll (M) cells of maize (Zea mays) leaves are specialized to accommodate C4 photosynthesis. This study provides a reconstruction of how metabolic pathways, protein expression, and homeostasis functions are quantitatively distributed across BS and M chloroplasts. This yielded new insights into cellular specialization. The experimental analysis was based on high-accuracy mass spectrometry, protein quantification by spectral counting, and the first maize genome assembly. A bioinformatics workflow was developed to deal with gene models, protein families, and gene duplications related to the polyploidy of maize; this avoided overidentification of proteins and resulted in more accurate protein quantification. A total of 1,105 proteins were assigned as potential chloroplast proteins, annotated for function, and quantified. Nearly complete coverage of primary carbon, starch, and tetrapyrole metabolism, as well as excellent coverage for fatty acid synthesis, isoprenoid, sulfur, nitrogen, and amino acid metabolism, was obtained. This showed, for example, quantitative and qualitative cell type-specific specialization in starch biosynthesis, arginine synthesis, nitrogen assimilation, and initial steps in sulfur assimilation. An extensive overview of BS and M chloroplast protein expression and homeostasis machineries (more than 200 proteins) demonstrated qualitative and quantitative differences between M and BS chloroplasts and BS-enhanced levels of the specialized chaperones ClpB3 and HSP90 that suggest active remodeling of the BS proteome. The reconstructed pathways are presented as detailed flow diagrams including annotation, relative protein abundance, and cell-specific expression pattern. Protein annotation and identification data, and projection of matched peptides on the protein models, are available online through the Plant Proteome Database.