A comprehensive transcript index of the human genome generated using microarrays and computational approaches

BACKGROUND: Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22. RESULTS: The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale. CONCLUSIONS: These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized

Natural hazards and their impact on rural settlements in NE Romania – A cartographical approach

Natural hazards are the most significant threats in rural areas of Romania, while landslides, floods and bank river erosion are the geomorphological processes that impose the greatest risk in the Moldavian Plateau. We have identified 189 of disappeared, displaced and partially affected villages (in the area between Siret and Prut Rivers), using old cartographic materials as primary tool, and overlapping them with the present situation: ortophoto imagery and LiDAR derived high-resolution Digital Elevation Models (DEMs). The main natural hazards that affected the settlements were landslides (63%), floods (26%) and river bank erosion processes (11%) and in 19% of the cases the settlement completely disappeared. We also present seven study cases, three for landslides, three for floods and one for river bank erosion in order to detail how these natural hazards impacted the physical environment of the settlements. In the Moldavian Plateau the mentioned natural hazards played an important role in the dynamics of the settlement network, with variations induced mainly by the socio-political characteristics and not necessarily by the frequency variation of the natural hazard events. Such studies are needed in order to depict the vulnerability and risk scenarios, especially for the back-analysis, but also considering that future climate changes might impose changes in hazard, vulnerability and risk associated to settlements

Using RPAS derived images and LiDAR DEM's for the assessment of geomorphic changes in a cultural heritage site affected by recent landslides

The recent advances in the acquisition of aerial images using Remotely Piloted Aircraft Systems (RPAS) offer an efficient and low-cost solution for the assessment of geomorphologic changes in areas affected by landslides, gullies and rill erosion, river channel migration, through the creation of accurate Digital Elevation Models (DEM's). Despite many advantages of DEM's obtained through Structure from Motion (SfM) method (resources, availability, high resolution - spatial and temporal), they are suitable for reduced study areas, usually under 100-200 ha, where there is a significant intensity of geomorphic processes and where their effects threaten human assets or heritage. This study focus on the area of Poiana M\u103n\u103stirii Thraco-Getic fortress (2550-2050 yr BP), located in the central part of Moldavian Plateau, Romania. Covering a surface of 12 ha, the fortress is surrounded by a 2-3 m high wall, with a 10 m wide base, and a 1 m deep and 4-6 m wide trench. In its southern part, the landslides destroyed these remnants, and due to the deforestation of the slope in the last 30 years, these processes recorded almost yearly reactivations. The main landslide scarp is affected by a gully system that contributes to the archaeological site degradation. A DJI Phantom 4 Pro UAV was flown over the study area in October 2019 and acquired images with 80 % side and forward overlap at 20 MP resolution. Visual SFM open source software was used to obtain the point cloud and for georeferencing, a Ground Control Point network was measured with a Trimble GeoExplorer 6000 GPS. In order to detect and to map geomorphic changes, LiDAR point clouds (2012) were used as a reference dataset (with a spatial resolution of 0.25 m, and a vertical accuracy of 0.13 m). A detailed map showing the changes in topography between 2012 and 2019 has been carried out, supplementing a geomorphological mapping. The most dynamic portions of the landslide are accompanied by dense micro-topographic features like secondary scarps, longitudinal and transversal cracks, which have been mapped using the ortophotoimage. The most dynamic parts of the hillslope are an earthflow, shallow and slumps along with the eastern gully system, piping sinkholes, and the main scarp gullies. The evolution of the landslides and gullies indicate that the southern part of the fortress will be affected in the near future. Alongside the identification of the most active parts of the landslide, we conclude that the entire recently deforested area must return as quick as possible to the initial land use (forest)

Investigation of the Association between Bilateral Selective Anterograde Cerebral Perfusion and Postoperative Ischemic Stroke in Obese Patients with Emergency Surgery for Acute Type A Aortic Dissection

Background and objectives: The relationship between cerebral perfusion and new postoperative ischemic stroke in obese patients is not well defined. The aim of this study was to investigate the association between selective bilateral anterograde cerebral perfusion and new postoperative ischemic stroke in obese patients with emergency surgery for acute type A aortic dissection. Materials and methods: A total of 292 patients with emergency surgery for acute type A aortic dissection were included in this study. Patients with hemorrhagic stroke or ischemic stroke with severe neurological dysfunction at admission that were not candidates for surgery; patients who died in the first 48 h after intensive care admission and patients with incomplete medical records were excluded. Results: The mean age was 59.42 ± 10.68 years and the mean Euroscore was 9.12 ± 1.63. Obesity was present in 76.4%, the incidence of new postoperative ischemic stroke was 27.5%, and the postoperative mortality rate was 26.7%. The mean cardiopulmonary bypass time was 206.81 ± 75.48 min, the aortic cross-clamp time was 118.2 ± 46.42 min, and 90% of cases required cerebral perfusion. The mean cerebral perfusion time was 30.8 ± 24.41 min. Obese patients had a higher frequency of in-hospital death (p = 0.009), smoking (p = 0.036), hypertension (p = 0.023), left common carotid artery dissection (p p = 0.029), femoral artery cannulation (p = 0.026), aortic root replacement (p = 0.009), aortic valve replacement (p = 0.005) and early reintervention for bleeding (p = 0.004). Using logistic regression, selective bilateral anterograde cerebral perfusion over 40 min in obese patients was independently associated with new postoperative ischemic stroke (OR = 2.35; 95%CI = 1.36–4.86; p = 0.021). Conclusions: A patient-tailored strategy for cerebral perfusion should be considered in obese patients, considering the high atheromatous burden of the supra-aortic vessels in these patients and the potential risk of atheromatous embolization associated with this technique

Surgical Strategy for Sternal Closure in Patients with Surgical Myocardial Revascularization Using Mammary Arteries

Background: Coronary artery bypass grafting has evolved from all venous grafts to bilateral mammary artery (BIMA) grafting. This was possible due to the long-term patency of the left and right internal mammary demonstrated in angiography studies compared to venous grafts. However, despite higher survival rates when using bilateral mammary arteries, multiple studies report a higher rate of surgical site infections, most notably deep sternal wound infections, a so-called “never event”. Methods: We designed a prospective study between 1 January 2022 and 31 December 2022 and included all patients proposed for total arterial myocardial revascularization in order to investigate the rate of surgical site infections (SSI). Chest closure in all patients was performed using a three-step protocol. The first step refers to sternal closure. If the patient’s BMI is below 35 kg/m2, sternal closure is achieved using the “butterfly” technique with standard steel wires. If the patient’s BMI exceeds 35 kg/m2, we use nitinol clips or hybrid wire cable ties according to the surgeon’s preference for sternal closure. The main advantages of these systems are a larger implant-to-bone contact with a reduced risk of bone fracture. The second step refers to presternal fat closure with two resorbable monofilament sutures in a way that the edges of the skin perfectly align at the end. The third step is skin closure combined with negative pressure wound therapy. Results: This system was applied to 217 patients. A total of 197 patients had bilateral mammary artery grafts. We report only 13 (5.9%) superficial SSI and only one (0.46%) deep SSI. The preoperative risk of major wound infection was 3.9 +/− 2.7. Bilateral mammary artery grafting was not associated with surgical site infection in a univariate analysis. Conclusions: We believe this strategy of sternal wound closure can reduce the incidence of deep surgical site infection when two mammary arteries are used in coronary artery bypass surgery

Association between Bilateral Selective Antegrade Cerebral Perfusion and Postoperative Ischemic Stroke in Patients with Emergency Surgery for Acute Type A Aortic Dissection—Single Centre Experience

Acute type A aortic dissection (ATAAD) is a surgical emergency with a mortality of 1–2% per hour. Since its discovery over 200 years ago, surgical techniques for repairing a dissected aorta have evolved, and with the introduction of hypothermic circulatory arrest and cerebral perfusion, complex techniques for replacing the entire aortic arch were possible. However, postoperative neurological complications contribute significantly to mortality in this group of patients. The aim of this study was to determine the association between different bilateral selective antegrade cerebral perfusion (ACP) times and the incidence of postoperative ischemic stroke in patients with emergency surgery for ATAAD. Patients with documented hemorrhagic or ischemic stroke, clinical signs of stroke or neurological dysfunction prior to surgery, that died on the operating table or within 48 h after surgery, from whom the postoperative neurological status could not be assessed, and with incomplete medical records were excluded from this study. The diagnosis of postoperative stroke was made using head computed tomography imaging (CT) when clinical suspicion was raised by a neurologist in the immediate postoperative period. For selective bilateral antegrade cerebral perfusion, we used two balloon-tipped cannulas inserted under direct vision into the innominate artery and the left common carotid artery. Each cannula is connected to a separate pump with an independent pressure line. Near-infrared spectroscopy was used in all cases for cerebral oxygenation monitoring. The circulatory arrest was initiated after reaching a target core temperature of 25–28 °C. In total, 129 patients were included in this study. The incidence of postoperative ischemic stroke documented on a head CT was 24.8% (31 patients), and postoperative death was 20.9% (27 patients). The most common surgical technique performed was supravalvular ascending aorta and Hemiarch replacement with a Dacron graft in 69.8% (90 patients). The mean cardiopulmonary bypass time was 210 +/− 56.874 min, the mean aortic cross-clamp time was 114.775 +/− 34.602 min, and the mean cerebral perfusion time was 37.837 +/− 18.243 min. Using logistic regression, selective ACP of more than 40 min was independently associated with postoperative ischemic stroke (OR = 3.589; 95%CI = 1.418–9.085; p = 0.007). Considering the high incidence of postoperative stroke in our study population, we concluded that bilateral selective ACP should be used with caution, especially in patients with severely calcified ascending aorta and/or aortic arch and supra-aortic vessels. All efforts should be made to minimize the duration of circulatory arrest when using bilateral selective ACP with a target of less than 30 min, in hypothermia, at a body temperature of 25–28 °C

Utilizing PTA data as an expression index

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive transcript index of the human genome generated using microarrays and computational approaches"</p><p>Genome Biology 2004;5(10):R73-R73.</p><p>Published online 23 Sep 2004</p><p>PMCID:PMC545593.</p><p>Copyright © 2004 Schadt et al.; licensee BioMed Central Ltd.</p> Absolute transcript abundance over the 60 conditions described in [19] for two expression-supported transcripts. RLP09885002 represents a known gene (, ATPase, Na/Ktransporting, alpha 1 polypeptide) whereas RLP10406004 was supported solely by gene model predictions before microarray validation