Miracle-dz/UniFAR-FTUs huggingface dataset:
Do Omega-3 fatty acids prevent atrial fibrillation after open heart surgery? A meta-analysis of randomized controlled trials

OBJECTIVES: N-3 polyunsaturated fatty acids have been proposed as a novel treatment for preventing postoperative atrial fibrillation due to their potential anti-inflammatory and anti-arrhythmic effects. However, randomized studies have yielded conflicting results. The objective of this study is to review randomized trials of N-3 polyunsaturated fatty acid use for postoperative atrial fibrillation. METHODS: Using the CENTRAL, PUBMED, EMBASE, and LILACS databases, a literature search was conducted to identify all of the studies in human subjects that reported the effects of N-3 polyunsaturated fatty acids on the prevention of postoperative atrial fibrillation in cardiac surgery patients. The final search was performed on January 30, 2011. There was no language restriction, and the search strategy only involved terms for N-3 polyunsaturated fatty acids (or fish oil), atrial fibrillation, and cardiac surgery. To be included, the studies had to be randomized (open or blinded), and the enrolled patients had to be ≥18 years of age. RESULTS: Four randomized studies (three double-blind, one open-label) that enrolled 538 patients were identified. The patients were predominantly male, the mean age was 62.3 years, and most of the patients exhibited a normal left atrial size and ejection fraction. N-3 polyunsaturated fatty acid use was not associated with a reduction in postoperative atrial fibrillation. Similar results were observed when the open-label study was excluded. CONCLUSIONS: There is insufficient evidence to suggest that treatment with N-3 polyunsaturated fatty acids reduces postoperative atrial fibrillation. Therefore, their routine use in patients undergoing cardiac surgery is not recommended.
Trilobite Tagmosis and Body Patterning from Morphological and Developmental Perspectives1

Abstract The Trilobita were characterized by a cephalic region in which the biomineralized exoskeleton showed relatively high morphological differentiation among a taxonomically stable set of well defined segments, and an ontogenetically and taxonomically dynamic trunk region in which both exoskeletal segments and ventral appendages were similar in overall form. Ventral appendages were homonomous biramous limbs throughout both the cephalon and trunk, except for the most anterior appendage pair that was antenniform, preoral, and uniramous, and a posteriormost pair of antenniform cerci, known only in one species. In some clades trunk exoskeletal segments were divided into two batches. In some, but not all, of these clades the boundary between batches coincided with the boundary between the thorax and the adult pygidium. The repeated differentiation of the trunk into two batches of segments from the homonomous trunk condition indicates an evolutionary trend in aspects of body patterning regulation that was achieved independently in several trilobite clades. The phylogenetic placement of trilobites and congruence of broad patterns of tagmosis with those seen among extant arthropods suggest that the expression domains of trilobite cephalic Hox genes may have overlapped in a manner similar to that seen among extant arachnates. This, coupled with the fact that trilobites likely possessed ten Hox genes, presents one alternative to a recent model in which Hox gene distribution in trilobites was equated to eight putative divisions of the trilobite body plan.
MEROPS: the peptidase database

Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The classification framework is used for attaching information at each level. An important focus of the database has become distinguishing one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact. We have collected over 39 000 known cleavage sites in proteins, peptides and synthetic substrates. These allow us to display peptidase specificity and alignments of protein substrates to give an indication of how well a cleavage site is conserved, and thus its probable physiological relevance. While the number of new peptidase families and clans has only grown slowly the number of complete genomes has greatly increased. This has allowed us to add an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species.
Flicker ERG responses to stimuli parametrically modulated in color space.

PURPOSE To develop methods for recording human electroretinogram (ERG) responses to stimuli that modulate different classes of cones in various ratios, to draw inferences about the combination of cone signal in early retinal processing. METHODS Subjects viewed large-field temporal modulations presented on a computer-controlled color monitor. A flicker photometric paradigm was used to equate the ERG response elicited by interleaved reference and test modulations. Test modulations were chosen to stimulate the L- and M-cones in various ratios. Results were obtained from color-normal subjects, dichromats, and an anomalous trichromat. RESULTS Reliable signals were obtained from all subjects to both L- and M-cone-isolating modulations and to intermediate modulations. Signals from color-defective subjects were predominantly determined by the modulation seen by only one cone type, whereas signals from color-normal subjects were sensitive to both L- and M-cone modulations. For most color-normal subjects, the recorded signal was a linear function of the contrasts seen by the L- and M-cones. There was individual variability in how strongly each cone type contributed to the overall signal. CONCLUSIONS It is straightforward to record signals to color modulations presented on a CRT by using the flicker photometric ERG. For most observers, signals from L- and M-cones combine linearly. The relative contribution of the two cone classes varies across observers, probably because of individual differences in the relative numbers of L- and M-cones.
Accumulation of Phenolic Compounds and Expression Profiles of Phenolic Acid Biosynthesis-Related Genes in Developing Grains of White, Purple, and Red Wheat

Polyphenols in whole grain wheat have potential health benefits, but little is known about the expression patterns of phenolic acid biosynthesis genes and the accumulation of phenolic acid compounds in different-colored wheat grains. We found that purple wheat varieties had the highest total phenolic content (TPC) and antioxidant activity. Among phenolic acid compounds, bound ferulic acid, vanillic, and caffeic acid levels were significantly higher in purple wheat than in white and red wheat, while total soluble phenolic acid, soluble ferulic acid, and vanillic acid levels were significantly higher in purple and red wheat than in white wheat. Ferulic acid and syringic acid levels peaked at 14 days after anthesis (DAA), whereas p-coumaric acid and caffeic acid levels peaked at 7 DAA, and vanillic acid levels gradually increased during grain filling and peaked near ripeness (35 DAA). Nine phenolic acid biosynthesis pathway genes (TaPAL1, TaPAL2, TaC3H1, TaC3H2, TaC4H, Ta4CL1, Ta4CL2, TaCOMT1, and TaCOMT2) exhibited three distinct expression patterns during grain filling, which may be related to the different phenolic acids levels. White wheat had higher phenolic acid contents and relatively high gene expression at the early stage, while purple wheat had the highest phenolic acid contents and gene expression levels at later stages. These results suggest that the expression of phenolic acid biosynthesis genes may be closely related to phenolic acids accumulation.
Speech-Language Pathology 8-2008 Associations Between Performance on the Rey-Osterrieth Complex Figure and Regional Brain Volumes in Children with and without Velocardiofacial Syndrome

Ninety-two children with velocardiofacial syndrome (VCFS), a genetic disorder caused by a microdeletion of chromosome 22q11.2 and an age, race and gender-ratio comparable sample of 59 control participants were included in the project. Participants received a MRI as well as a comprehensive neuropsychological battery; the primary outcome measure in the current report is the Rey-Osterrieth Complex Figure (ROCF). Children with VCFS performed less well on the ROCF and have lower whole brain volume compared to controls. After controlling for whole brain volume differences, children with VCFS have bilaterally less parietal lobe gray and white matter yet more frontal lobe white matter. Brain behavior relationships include: (a) for both groups, parietal volumes (both gray and white matter) predicted ROCF Copy Organization performance and frontal volumes (both gray and white matter) predicted ROCF Copy Accuracy performance; (b) for controls, frontal white matter also predicted ROCF Copy Organization performance; (c) ROCF Recall Organization performance was best predicted by frontal gray matter volume only in our controls; ROCF Recall Accuracy performance was best predicted by frontal gray matter volume in both groups; and (d) in children with VCFS, performance on the ROCF-Copy Structural Elements Accuracy scale was predicted by right hemisphere white matter volume. Our hypotheses were also retested using IQmatched and whole brain volume-matched subsamples. Identical results were obtained in these analyses. Assumptions about the organization of and the localization of the brain structures that subserve specific cognitive functions in the typically developing brain may not apply in the abnormally developing brain.
Guanine-Nucleotide Exchange Factor H1 Mediates Lipopolysaccharide-Induced Interleukin 6 and Tumor Necrosis Factor &agr; Expression in Endothelial Cells Via Activation of Nuclear Factor &kgr;B

ABSTRACT The development of sepsis is multifactorial. Tissue damage and organ dysfunction may be caused not only by the microorganisms but also by the inflammatory mediators released in response to the infection. Interleukin 6 (IL-6) and tumor necrosis factor &agr; (TNF-&agr;) levels in serum are well known to be upregulated in humans with sepsis and can be used to predict outcome. Using human umbilical vein endothelial cells, we analyzed the role of guanine-nucleotide exchange factor H1 (GEF-H1) on lipopolysaccharide (LPS)–dependent IL-6/TNF-&agr; expression in endothelial cells. Lipopolysaccharide upregulated IL-6 secretion in a dose- and time-dependent manner. Specific inactivation of RhoA/Cdc42/Rac1 by Clostridium difficile toxin B-10463 (TcdB-10463) reduced LPS-induced nuclear factor &kgr;B (NF-&kgr;B) p65 phosphorylation, IL-6/TNF-&agr; messenger RNA (mRNA), and IL-6/TNF-&agr; protein productions. Guanine-nucleotide exchange factor H1 protein expression remained on a high level among 1 to 9 h in response to LPS challenge of endothelial cells. Inhibition of GEF-H1 by specific small interfering RNA or inactivation of Rho-associated kinase with Y-27632 not only significantly reduced LPS-induced p38 and extracellular signal–regulated kinase 1/2 (ERK1/2) activities but also blocked LPS-induced NF-&kgr;B translocation and activation, thereby inhibiting IL-6/TNF-&agr; mRNA and protein productions. Furthermore, SB203580 (p38 inhibitor) but not PD98059 (ERK1/2 inhibitor) blocked LPS-induced NF-&kgr;B activation; however, both inhibitors significantly suppressed IL-6/TNF-&agr; mRNA and protein expression. In summary, our data suggest that LPS rapidly upregulates GEF-H1 expression. Activated Rho-associated kinase by GEF-H1 subsequently activates p38 and ERK1/2, thereby increasing IL-6/TNF-&agr; expression in endothelial cells. P38 and ERK1/2 regulate LPS-induced IL-6/TNF-&agr; expression through an NF-&kgr;B–dependent manner and an NF-&kgr;B–independent manner, respectively.
Repositioning Titanium: An In Vitro Evaluation of Laser-Generated Microporous, Microrough Titanium Templates As a Potential Bridging Interface for Enhanced Osseointegration and Durability of Implants

Although titanium alloys remain the preferred biomaterials for the manufacture of biomedical implants today, such devices can fail within 15 years of implantation due to inadequate osseointegration. Furthermore, wear debris toxicity due to alloy metal ion release has been found to cause side-effects including neurotoxicity and chronic inflammation. Titanium, with its known biocompatibility, corrosion resistance, and high elastic modulus, could if harnessed in the form of a superficial scaffold or bridging device, resolve such issues. A novel three-dimensional culture approach was used to investigate the potential osteoinductive and osseointegrative capabilities of a laser-generated microporous, microrough medical grade IV titanium template on human skeletal stem cells (SSCs). Human SSCs seeded on a rough 90-µm pore surface of ethylene oxide-sterilized templates were observed to be strongly adherent, and to display early osteogenic differentiation, despite their inverted culture in basal conditions over 21 days. Limited cellular migration across the template surface highlighted the importance of high surface wettability in maximizing cell adhesion, spreading and cell-biomaterial interaction, while restricted cell ingrowth within the conical-shaped pores underlined the crucial role of pore geometry and size in determining the extent of osseointegration of an implant device. The overall findings indicate that titanium only devices, with appropriate optimizations to porosity and surface wettability, could yet play a major role in improving the long-term efficacy, durability, and safety of future implant technology.
Genetic polymorphism in leaf-cutting ants is phenotypically plastic

Advanced societies owe their success to an efficient division of labour that, in some social insects, is based on specialized worker phenotypes. The system of caste determination in such species is therefore critical. Here, we examine in a leaf-cutting ant (Acromyrmex echinatior) how a recently discovered genetic influence on caste determination interacts with the social environment. By removing most of one phenotype (large workers; LW) from test colonies, we increased the stimulus for larvae to develop into this caste, while for control colonies we removed a representative sample of all workers so that the stimulus was unchanged. We established the relative tendencies of genotypes to develop into LW by genotyping workers before and after the manipulation. In the control colonies, genotypes were similarly represented in the large worker caste before and after worker removal. In the test colonies, however, this relationship was significantly weaker, demonstrating that the change in environmental stimuli had altered the caste propensity of at least some genotypes. The results indicate that the genetic influence on worker caste determination acts via genotypes differing in their response thresholds to environmental cues and can be conceptualized as a set of overlapping reaction norms. A plastic genetic influence on division of labour has thus evolved convergently in two distantly related polyandrous taxa, the leaf-cutting ants and the honeybees, suggesting that it may be a common, potentially adaptive, property of complex, genetically diverse societies.
Decolorization of the Dye, Reactive Blue 19, Using Ozonation, Ultrasound, and Ultrasound‐Enhanced Ozonation

Reactive dyes constitute a significant portion of colorants used in industries ranging from the textile industry to the paper industry. In most cases, the effluent streams from textile plants are highly colored, and treatment methods for dye decolorization such as chemical oxidation need to be explored. The oxidation processes investigated in this study are those of ozonation, ultrasound, and ultrasound‐enhanced ozonation. The oxidation of an anthraquinone dye was studied under conditions of varying ultrasonic power, dye concentration, ozone concentration, pH, and temperature. Laboratory experiments were performed using a semibatch reactor by ozonating dye samples with and without ultrasound. Under conditions of constant ultrasonic radiation and continuous gas application, decolorization rates have been enhanced by ultrasound. The apparent first‐order rate constants increased between 35 and 204% for the ultrasonic power inputs between 40 W/L and 120 W/L compared with ozonation alone.The effects of ultrasonic power input on the gas‐liquid mass‐transfer coefficient were also investigated and the results indicate that an increase in ultrasonic power input increases the mass‐transfer coefficient. The mass‐transfer coefficient increased between 89 and 93% for ozone inlet concentrations between 5.4 and 9.4 mg/L at an ultrasonic power of 120 W/L compared with ozonation alone. The reactions of the dye with ultrasound‐enhanced ozone occurred through the hydroxyl radical pathway.
Outpatient palliative care for chronic obstructive pulmonary disease: a case series.

BACKGROUND Patients with chronic obstructive pulmonary disease (COPD) have well-documented symptoms that affect quality of life. Professional societies recommend palliative care for such patients, but the optimal way of delivering this care is unknown. OBJECTIVE To describe an outpatient palliative medicine program for patients with COPD. DESIGN Retrospective case series. SETTING/SUBJECTS Thirty-six patients with COPD followed in a United States academic outpatient palliative medicine clinic. MEASUREMENTS Descriptive analysis of sociodemographic data, disease severity and comorbidities, treatments, hospitalizations, mortality, topic discussion, and symptom assessment. RESULTS Thirty-six patients (representing 5% of the total number of patients with COPD seen in a specialty pulmonary clinic) were seen over 11 months and followed for 2 years. Seventy-seven percent of patients were Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 3-4 and 72% were on oxygen at home. No patients had documented advanced directives at the initial visit but documentation increased to 61% for those who had follow-up appointments. The most commonly documented topics included symptoms (100%), social issues (94%), psychological issues (78%), and advance care planning (75%). Of symptoms assessed, pain was the least prevalent (51.6%), and breathlessness and fatigue were the most prevalent (100%). Symptoms were often undertreated prior to the palliative care appointment. During the 3-year study period, there were 120 hospital admissions (median, 2) and 12 deaths (33%). CONCLUSIONS The patients with COPD seen in the outpatient palliative medicine clinic had many comorbid conditions, severe illness, and significant symptom burden. Many physical and psychological symptoms were untreated prior to the palliative medicine appointment. Whether addressing these symptoms through a palliative medicine intervention affects outcomes in COPD is unknown but represents an important topic for future research.
Complexity of the Search Space in a Model of Artificial Evolution of Gene Regulatory Networks Controlling 3D Multicellular Morphogenesis

The question of what properties of biological systems allow for efficient evolutionary search in complex fitness landscapes (evolvability) is one of the central interests both for the research in the field of evolutionary biology and artificial life. Here, we attempt to address this issue by using a model of 3D multicellular development in which cell fate is determined by differential gene expression in each cell. In our model, cells can vary in size and can move freely in 3D space, affected by forces of adhesion and repulsion. The development relies on an indirect mapping between the genotype and the morphology (the phenotype). Cell differentiation is allowed by positional information provided by diffusible factors. The state of the gene regulatory network (GRN) coded by the genome determines the cell fate (such as division, death, growth). The genetic elements in our systems define points in N-dimensional space. The connectivity in the GRN is determined by the proximity of these points; one can imagine the evolutionary process as their movement in space. Changing the number of dimensions of this space allows to ask directly the questions about the effect of the complexity of the search space on the efficiency of the evolutionary search. Higher dimensionality results in a larger search space, but in our model this search space can still be explored thanks to the action of genetic operators that allow for duplications of genetic elements, a mutational mechanism that allows for regulatory innovations in the network.
Evolution of parasite virulence when host responses cause disease

The trade-off hypothesis of virulence evolution rests on the assumption that infection-induced mortality is a consequence of host exploitation by parasites. This hypothesis lies at the heart of many empirical and theoretical studies of virulence evolution, despite growing evidence that infection-induced mortality is very often a by-product of host immune responses. We extend the theoretical framework of the trade-off hypothesis to incorporate such immunopathology and explore how this detrimental aspect of host defence mechanisms affects the evolution of pathogen exploitation and hence infection-induced mortality. We argue that there are qualitatively different ways in which immunopathology can arise and suggest ways in which empirical studies can tease apart these effects. We show that immunopathology can cause infection-induced mortality to increase or decrease as a result of pathogen evolution, depending on how it covaries with pathogen exploitation strategies and with parasite killing by hosts. Immunopathology is thus an important determinant of whether public and animal health programmes will drive evolution in a clinically beneficial or detrimental direction. Immunopathology complicates our understanding of disease evolution, but can nevertheless be readily accounted for within the framework of the trade-off hypothesis.
Characteristics of Problem-Based Learning *

Problem-based learning (PBL) is widely regarded as a successful and innovative method for engineering education. Since the development of the PBL model at McMaster University in Canada in the late 1960s, many different varieties have emerged. This paper highlights the Dutch approach of directing the learning process through problem analysis and the Danish model of project-organised learning. Various definitions of the concept PBL identify characteristics at the levels of theoretical learning principles, educational models and educational practices. The McMaster±Maastricht PBL model and the Aalborg model of project work share characteristic features such as the theoretical principle of the problem analysis at the basis of the learning process, integration of knowledge and practice, collaboration and group work. Notable differences were found with respect to the type of assignments, assessment methods and organisation of the group work. In comparison to traditional engineering curricula, the PBL models appear to inspire a higher degree of involvement in study activities and, consequently, a higher level of complex comprehension. A possible drawback is the risk of gaps in specific knowledge areas. Therefore, it is crucial that the students in a PBL curriculum become lifelong learners who have learned to take responsibility for their own learning process.