Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Evolution and the Emergence of Fruiting Body Development in Myxococcus xanthus

Background Lateral gene transfer (LGT) is thought to promote speciation in bacteria, though well-defined examples have not been put forward. Methodology/Principle Findings We examined the evolutionary history of the genes essential for a trait that defines a phylogenetic order, namely fruiting body development of the Myxococcales. Seventy-eight genes that are essential for Myxococcus xanthus development were examined for LGT. About 73% of the genes exhibit a phylogeny similar to that of the 16S rDNA gene and a codon bias consistent with other M. xanthus genes suggesting vertical transmission. About 22% have an altered codon bias and/or phylogeny suggestive of LGT. The remaining 5% are unique. Genes encoding signal production and sensory transduction were more likely to be transmitted vertically with clear examples of duplication and divergence into multigene families. Genes encoding metabolic enzymes were frequently acquired by LGT. Myxobacteria exhibit aerobic respiration unlike most of the δ Proteobacteria. M. xanthus contains a unique electron transport pathway shaped by LGT of genes for succinate dehydrogenase and three cytochrome oxidase complexes. Conclusions/Significance Fruiting body development depends on genes acquired by LGT, particularly those involved in polysaccharide production. We suggest that aerobic growth fostered innovation necessary for development by allowing myxobacteria access to a different gene pool from anaerobic members of the δ Proteobacteria. Habitat destruction and loss of species diversity could restrict the evolution of new bacterial groups by limiting the size of the prospective gene pool.
Satellite Estimates of Precipitation-Induced Dissipation in the Atmosphere

When the Rain Comes When raindrops fall, frictional forces between the droplet and the surrounding air create a drag that limits the speed at which the raindrop can descend. This drag also dissipates some of the kinetic energy of the falling raindrops within the shear zones surrounding them and is a significant component of the atmospheric energy budget, according to Pauluis and Dias (p. 953; see the Perspective by Frierson). Using data from satellites, they find that precipitation-induced energy dissipation is of the same magnitude as that caused by atmospheric turbulence and therefore that of a strengthened hydrological cycle, which is widely expected to occur as a result of climate warming and could have an impact on the strength of atmospheric circulation. Falling precipitation rivals turbulence in dissipating atmospheric energy. A substantial amount of frictional dissipation in the atmosphere occurs in the microphysical shear zones surrounding falling precipitation. The dissipation rate is computed here from recently available satellite retrieval from the Tropical Rainfall Measurement Missions and is found to average 1.8 watts per square meter between 30°S and 30°N. The geographical distribution of the precipitation-induced dissipation is closely tied to that of precipitation but also reveals a stronger dissipation rate for continental convection than for maritime convection. Because the precipitation-induced dissipation is of the same magnitude as the turbulent dissipation of the kinetic energy in the atmosphere, changes in the hydrological cycle could potentially have a direct impact on the amount of kinetic energy generated and dissipated by the atmospheric circulation.
Hand-based tracking animatronics interaction

Natural user interfaces are becoming more affordable and are changing how people interact with daily activities. These interfaces take advantage of human ergonomics increasing comfort, accuracy and performance during several tasks. New trends in user interfaces allow developing innovative forms of interaction in different scenarios; such is the case of robot teleoperation where joysticks, voice command, inertial sensors, haptics, and even Kinect sensors are easing their usage in educational contexts where people is getting familiar with robotics. This project presents the development of hand tracking application whose motion controls different servos on an animatronic; the goal is to motivate better understanding of robot morphology, sensors, actuators and kinematics for beginners. The system was tested using the hand and fingers as the controller while basic concepts were presented. After using the application and the animatronic device, users found the idea compelling and expressed their motivation for more knowledge regarding robotics.
Myocardial Perfusion Grade After Late Infarct Artery Recanalization Is Associated With Global and Regional Left Ventricular Function at One Year: Analysis From the Total Occlusion Study of Canada-2

Background—Whether myocardial perfusion grade (MPG) following late recanalization of infarct-related arteries (IRAs) predicts left ventricular (LV) function recovery beyond the acute phase of myocardial infarction (MI) is unknown. Methods and Results—The Total Occlusion Study of Canada-2 enrolled stable patients with a persistently occluded IRA beyond 24 hours and up to 28 days post-MI. We studied the relationship between the initial MPG and changes in LV function and volume as well as the change in MPG from immediate post-percutaneous coronary intervention (PCI) to 1 year in 139 PCI patients with thrombolysis in myocardial infarction grade 3 epicardial flow post-PCI and with paired values grouped into impaired or good MPG groups (MPG 0/1 or MPG 2/3). MPG 0/1 patients were more likely to have received thrombolytic therapy and to have a left anterior descending IRA. They had lower blood pressure and LV ejection fraction (LVEF) and a higher heart rate and systolic sphericity index at baseline. Changes in the MPG 0/1 and MPG 2/3 groups from baseline to 1 year were LVEF, 3.3±9.0% and 4.8±8.9% (P=0.42); LV end-systolic volume index (LVESVI), −1.1±9.2 and −4.7±12.3 mL/m2 (P=0.25); LV end-diastolic volume index (LVEDVI), 0.08±19.1 and −2.4±22.2 mL/m2 (P=0.67); and SDs/chord for infarct zone wall motion index (WMI), 0.38±0.70 and 0.84±1.11 (P=0.01). By covariate-adjusted analysis, post-PCI MPG 0/1 predicted lower WMI (P<0.001), lower LVEF (P<0.001), and higher LVESVI (P<0.01) but not LVEDVI at 1 year. Of the MPG 0/1 patients, 60% were MPG 2 or 3 at 1 year. Conclusions—Preserved MPG is present in a high proportion of patients following late PCI of occluded IRAs post-MI. Poor MPG post-PCI frequently improves MPG over 1 year. MPG graded after IRA recanalization undertaken days to weeks post MI is associated with LV recovery, indicating that MPG determined in the subacute post-MI period remains a marker of viability. Clinical Trial Registration—URL: http://www.clinicaltrials. gov. Unique identifier: NCT00025766.
Large Clothing Size in Children Is Associated with High Body Mass Index and Clustering of Medical Comorbidities

Background. Since most people are aware of their clothing size (CS), this prospective study explored the potential utility of CS as a proxy for body size and as a predictor of incident obesity-related health conditions in children. Methods. This was a prospective, cross-sectional study of 725 children aged 6–18 yr. We collected clinical, anthropometric, and sartorial data on all study subjects. Parents reported their children's usual CS. This was compared with US clothing chart for children. Based on this we determined whether a child's CS was appropriate or large for age. Results. The prevalence of overweight/obese was 31.4%. Among the study subjects, 36% usually wore large CS. Children who wore large CS were more likely to be overweight/obese compared to those in the normal CS group (OR = 5.6; 95% CI = 4.0–8.0, P < 0.001). Similarly, large CS was associated with higher rates of incident asthma (P = 0.003), obstructive sleep apnea (P = 0.01), habitual snoring (P = 0.02), and elevated preoperative blood pressure (P = 0.03). Conclusion. CS in children is associated with higher indices of adiposity and increased rates of obesity-related comorbidities.
Cognitive Therapy for Anxiety

Cognitive therapy for depression is well-established. However, it is only recently that Beck and his colleagues have turned their attention to the development of a cognitive therapy for anxiety. The present article provides a brief overview of cognitive therapy for anxiety and also presents outcome data on six anxious patients who were treated with cognitive therapy. Considerable reductions in anxiety and depression occurred during the course of treatment. In addition, much of the observed improvement occurred after as little as eight sessions. These results suggest that cognitive therapy is a promising approach to the treatment of anxiety disorders. However, final evaluation of its effectiveness must await the publication of large scale, controlled trials.
Scalable Multigigabit Pattern Matching for Packet Inspection

In this paper, we consider hardware-based scanning and analyzing packets payload in order to detect hazardous contents. We present two pattern matching techniques to compare incoming packets against intrusion detection search patterns. The first approach, decoded partial CAM (DpCAM), predecodes incoming characters, aligns the decoded data, and performs logical and on them to produce the match signal for each pattern. The second approach, perfect hashing memory (PHmem), uses perfect hashing to determine a unique memory location that contains the search pattern and a comparison between incoming data and memory output to determine the match. Both techniques are well suited for reconfigurable logic and match about 2200 intrusion detection patterns using a single Virtex2 field-programmable gate-array device. We show that DpCAM achieves a throughput between 2 and 8 Gb/s requiring 0.58-2.57 logic cells per search character. On the other hand, PHmem designs can support 2-5.7 Gb/s using a few tens of block RAMs (630-1404 kb) and only 0.28-0.65 logic cells per character. We evaluate both approaches in terms of performance and area cost and analyze their efficiency, scalability, and tradeoffs. Finally, we show that our designs achieve at least 30% higher efficiency compared to previous work, measured in throughput per area required per search character.
Persons and artificial intelligence

This dissertation seeks to answer the question: "Can a computer be a person? " In the first part, the muddle of claims and counterclaims surrounding Artificial Intelligence (A.I.) are examined. This work takes the position that there is a radical difference between persons and machines, and that this difference holds no matter what form machines may take, now or in the future. At the same time, the inability of the dominant views, grounded in materialism, to come to grips with the question, will be criticized. The inadequacy of arguments proposed by those on both sides of the question is explained through an examination of the materialistic presuppositions both groups begin with. On the one hand, the advocates of A.I. claim that their computer models provide both necessary and sufficient conditions for mind, but there is much they cannot account for. On the other hand, those who argue against A.I. are able to point out those aspects of mental life that the machine models don't cover, but they do not explain why. A.I. advocates deny well-known features of persons because there is no way of accounting for such phenomena within a materialistic context. A.I. antagonists argue from these known features of persons, but because they, for the most part, also accept materialism, they are unable to provide a convincing explanation of these phenomena. The second part of the work attempts to show that the understanding of symbols or signs is not just another way of using marks. It rests with the having of them as symbols or signs. This cannot occur on a material level. Where there are only coordinate bodies there can only be alongsidedness, in which case something may make a difference to something else, but could never be possessed; be something for that thing. In a world which is exhaustively public there are only physical occurrences and reactions to these; responding to a symbol requires a sustaining by that which is privately grounded.
Intestinal Fatty Acid Binding Protein: A Sensitive Marker in Abdominal Surgery and Abdominal Infection.

BACKGROUND Intestinal fatty acid binding protein (iFABP) is elevated in plasma by intestinal injury. We investigated the influence of surgical trauma and severe sepsis caused by abdominal and pulmonary infection on plasma iFABP concentrations. METHODS Seventy-nine patients were included in this prospective observational study: 31 patients before elective major abdominal surgery (EMS), 33 patients with severe sepsis on admission to the intensive care unit (ICU), and 15 healthy volunteers who served as controls. Blood samples were taken before and after surgery for a period up to 5 d. RESULTS Prior to surgery, EMS patients had increased iFABP concentrations in those patients with intestinal cancer compared with patients without intestinal cancer (217 pg/mL, interquartile range [IQR] I-III 100-369 pg/mL versus 79 pg/mL, IQR I-III: 0-182 pg/mL; p<0.01) and with controls (114 pg/mL, IQR I-III: 103-124 pg/mL; p<0.01). Surgical trauma increased iFABP levels in patients without intestinal cancer (240 pg/mL, IQR I-III 111-305 pg/mL; p<0.01). Within 24 h after surgery, iFABP levels decreased to normal values. Patients with severe sepsis of abdominal origin had elevated concentrations compared with controls (324 pg/mL [IQR I-III 0-649 pg/mL]; p=0.05); in patients with pneumonia, iFABP levels were not significantly increased. Discrimination between intestinal- and pulmonary-induced sepsis was low (area under the curve [AUC] 0.693; 95% confidence interval 0.512-0.874). CONCLUSIONS Surgical trauma and severe sepsis lead to elevated iFABP concentrations. However, intestinal malignant disease and in some patients severe sepsis caused by pneumonia also resulted in elevated iFABP concentrations. The results support the idea that epithelial injury of many causes leads to elevated concentrations of iFABP. The value of iFABP for differentiating pulmonary from intestinal sepsis is limited.
Positioning hydrogen atoms by optimizing hydrogen‐bond networks in protein structures

A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy. For this goal, an empirical hydrogen bond force field was derived from small molecule crystal structures. Bifurcated hydrogen bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, sidechain conformations of His, Gln, and Asn residues are allowed to change their last χ angle by 180° to compensate for crystallographic misassignments. Crystal structure symmetry is taken into account where appropriate. The results can have significant implications for molecular dynamics simulations, protein engineering, and docking studies. The largest impact, however, is in protein structure verification: over 85% of protein structures tested can be improved by using our procedure. Proteins 26:363–376 © 1996 Wiley‐Liss, Inc.
Rexplore: Unveiling the dynamics of scholarly data

Rexplore is a novel system that integrates semantic technologies, data mining techniques, and visual analytics to provide an innovative environment for making sense of scholarly data. Its functionalities include: i) a variety of views to make sense of important trends in research; ii) a novel semantic approach for characterising research topics; iii) a very fine-grained expert search with detailed multi-dimensional parameters; iv) an innovative graph view to relate a variety of academic entities; iv) the ability to detect and explore the main communities within a research topic; v) the ability to analyse research performance at different levels of abstraction, including individual researchers, organizations, countries, and research communities.
C-Type Natriuretic Peptide Induces Anti-contractile Effect Dependent on Nitric Oxide, Oxidative Stress, and NPR-B Activation in Sepsis

Aims: To evaluate the role of nitric oxide, reactive oxygen species (ROS), and natriuretic peptide receptor-B activation in C-type natriuretic peptide-anti-contractile effect on Phenylephrine-induced contraction in aorta isolated from septic rats. Methods and Results: Cecal ligation and puncture (CLP) surgery was used to induce sepsis in male rats. Vascular reactivity was conducted in rat aorta and resistance mesenteric artery (RMA). Measurement of survival rate, mean arterial pressure (MAP), plasma nitric oxide, specific protein expression, and localization were evaluated. Septic rats had a survival rate about 37% at 4 h after the surgery, and these rats presented hypotension compared to control-operated (Sham) rats. Phenylephrine-induced contraction was decreased in sepsis. C-type natriuretic peptide (CNP) induced anti-contractile effect in aortas. Plasma nitric oxide was increased in sepsis. Nitric oxide-synthase but not natriuretic peptide receptor-B expression was increased in septic rat aortas. C-type natriuretic peptide-anti-contractile effect was dependent on nitric oxide-synthase, ROS, and natriuretic peptide receptor-B activation. Natriuretic peptide receptor-C, protein kinase-Cα mRNA, and basal nicotinamide adenine dinucleotide phosphate (NADPH)-dependent ROS production were lower in septic rats. Phenylephrine and CNP enhanced ROS production. However, stimulated ROS production was low in sepsis. Conclusion: CNP induced anti-contractile effect on Phenylephrine contraction in aortas from Sham and septic rats that was dependent on nitric oxide-synthase, ROS, and natriuretic peptide receptor-B activation.
Efficient Solution for a Class of Markov Chain Models of Tandem Queueing Networks

We present a new numerical method for the computation of the steady-state solution of Markov chains. Theoretical analyses show that the proposed method, with a contraction factor α, converges to the one-dimensional null space of singular linear systems of the form Ax = 0. Numerical experiments are used to illustrate the effectiveness of the proposed method, with applications to a class of interesting models in the domain of tandem queueing networks. Keywords—Markov chains, tandem queueing networks, convergence, effectiveness.
Classical simulation of commuting quantum computations implies collapse of the polynomial hierarchy

We consider quantum computations comprising only commuting gates, known as IQP computations, and provide compelling evidence that the task of sampling their output probability distributions is unlikely to be achievable by any efficient classical means. More specifically, we introduce the class post-IQP of languages decided with bounded error by uniform families of IQP circuits with post-selection, and prove first that post-IQP equals the classical class PP. Using this result we show that if the output distributions of uniform IQP circuit families could be classically efficiently sampled, either exactly in total variation distance or even approximately up to 41 per cent multiplicative error in the probabilities, then the infinite tower of classical complexity classes known as the polynomial hierarchy would collapse to its third level. We mention some further results on the classical simulation properties of IQP circuit families, in particular showing that if the output distribution results from measurements on only lines then it may, in fact, be classically efficiently sampled.
Hyperoxaluria in adults

INTEREST in the urinary excretion of oxalic acid has arisen mainly because of the frequent occurrence of calcium oxalate in urinary calculi. Most patients with urinary calculi excrete normal quantities of oxalic acid in their urine, but in some cases excretion is moderately elevated and in a few cases grossly elevated (Hodgkinson, 1958; Dempsey, Forbes, Melick, and Henneman, 1960; Nordin and Hodgkinson, 1967). Oxalate excretion may be increased by a number of dietary and other factors, for example, a high intake of oxalic acid-containing foods (Archer, Dormer, Scowen, and Watts, 1958), a low-calcium diet (Hodgkinson, 1958), the ingestion of ethylene glycol (Gessner, Parke, and Williams, 1961), or a deficiency of pyridoxine (Gershoff, Faragalla, Nelson, and Andrus, 1959; Faber, Feitler, Bleiler, Ohlson, and Hodges, 1963). Hyperoxaluria has also been reported in patients with hepatic cirrhosis, renal tubular acidosis, and sarcoidosis (Dempsey and others, 1960). A marked hyperoxaluria in patients with urinary calculus is associated most commonly with a genetically determined metabolic disorder, the clinical features of which were f i s t described in detail by Davis, Klingberg, and Stowell (1950). The presence of hyperoxaluria in this condition was confirmed chemically by Newns and Black (1953) and the disorder was subsequently named ‘primary hyperoxaluria’ by Archer, Dormer, Scowen, and Watts
Strain sensing fabric characterization

Electrically conductive elastomer (CE) composites show piezoresistive properties when a deformation is applied. In several applications, CE can be integrated into fabric or into other flexible substrates and can be employed as a strain sensor. Moreover, integrated CE sensors may be used in biomechanical analysis to realize wearable kinesthetic interfaces able to detect the posture and movement of a subject. Unfortunately, the long transient time (up to several minutes) and some peculiar non-linear phenomena in CE require a complex treatment of signals which is described in the present work.
Peroxisome biogenesis

Peroxisomes are eukaryotic organelles that are the subcellular location of important metabolic reactions. In humans, defects in the organelle's function are often lethal. Yet, relative to other organelles, little is known about how cells maintain and propagate peroxisomes or how they direct specific sets of newly synthesized proteins to these organelles (peroxisome biogenesis/assembly). In recent years, substantial progress has been made in elucidating aspects of peroxisome biogenesis and in identifying PEX genes whose products, peroxins, are essential for one or more of these processes. The most progress has been made in understanding the mechanism by which peroxisome matrix proteins are imported into the organelles. Signal sequences responsible for targeting proteins to the organelle have been defined. Potential signal receptor proteins, a receptor docking protein and other components of the import machinery have been identified, along with insights into how they operate. These studies indicate that multiple peroxisomal protein‐import mechanisms exist and that these mechanisms are novel, not simply variations of those described for other organelles.
The Impact of the Prechoice Process on Product Returns

This article introduces a framework to help researchers understand the mechanisms underlying product returns. The framework draws on research in consumer choice, consumer memory, and attitude stability to predict how the process that consumers go through at a predecisional stage affects their postpurchase behavior. The likelihood of product returns is considered contingent on the amount and nature of cognitive responses generated during the choice process. In Study 1, the authors focus on the impact of the nature of cognitive responses and show that the generation of responses of a different nature while choosing directly affects the likelihood of choice reversal. The comparative versus non-comparative nature of thoughts generated influences their diagnosticity and, accordingly, their impact on product returns when consumers are exposed to disconfirming information. In Study 2, the authors draw on the inoculation theory to manipulate the number of prechoice thoughts. They find that when faced with disconfirming information favoring a new brand, inoculated consumers who are presented with choice alternatives sequentially are less likely to return a brand than consumers who are exposed solely to positive information about the chosen brand at a prepurchase stage.