Miracle-dz/UniFAR-FTUs huggingface dataset:
An Electronic Tool for the Evaluation and Treatment of Sepsis in the ICU: A Randomized Controlled Trial*

Objectives:To determine whether addition of an electronic sepsis evaluation and management tool to electronic sepsis alerting improves compliance with treatment guidelines and clinical outcomes in septic ICU patients. Design:A pragmatic randomized trial. Setting:Medical and surgical ICUs of an academic, tertiary care medical center. Patients:Four hundred and seven patients admitted during a 4-month period to the medical or surgical ICU with a diagnosis of sepsis established at the time of admission or in response to an electronic sepsis alert. Interventions:Patients were randomized to usual care or the availability of an electronic tool capable of importing, synthesizing, and displaying sepsis-related data from the medical record, using logic rules to offer individualized evaluations of sepsis severity and response to therapy, informing users about evidence-based guidelines, and facilitating rapid order entry. Measurements and Main Results:There was no difference between the electronic tool (218 patients) and usual care (189 patients) with regard to the primary outcome of time to completion of all indicated Surviving Sepsis Campaign 6-hour Sepsis Resuscitation Bundle elements (hazard ratio, 1.98; 95% CI, 0.75–5.20; p = 0.159) or time to completion of each element individually. ICU mortality, ICU-free days, and ventilator-free days did not differ between intervention and control. Providers used the tool to enter orders in only 28% of available cases. Conclusions:A comprehensive electronic sepsis evaluation and management tool is feasible and safe but did not influence guideline compliance or clinical outcomes, perhaps due to low utilization.
Integrating task and data parallelism by means of coordination patterns

This paper shows, by means of some examples, the suitability and expressiveness of a pattern-based approach to integrate task and data parallelism. Coordination skeletons or patterns express task parallelism among a collection of data parallel HPF tasks. Patterns specify the interaction among domains involved in the application along with the processor and data layouts. On the one hand, the use of domains, i.e. regions together with some interaction information, improves pattern reusability. On the other hand, the knowledge at the coordination level of data distribution belonging to the different HPF tasks is the key for an efficient implementation of the communication among them. Besides that, our system implementation requires no change to the runtime system support of the HPF compiler used. We also present some experimental results that show the efficiency of the model.
A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP)

Meeting the goal of providing point of care (POC) tests for molecular detection of pathogens in low resource settings places stringent demands on all aspects of the technology. OmniAmp DNA polymerase (Pol) is a thermostable viral enzyme that enables true POC use in clinics or in the field by overcoming important barriers to isothermal amplification. In this paper, we describe the multiple advantages of OmniAmp Pol as an isothermal amplification enzyme and provide examples of its use in loop-mediated isothermal amplification (LAMP) for pathogen detection. The inherent reverse transcriptase activity of OmniAmp Pol allows single enzyme detection of RNA targets in RT-LAMP. Common methods of nucleic acid amplification are highly susceptible to sample contaminants, necessitating elaborate nucleic acid purification protocols that are incompatible with POC or field use. OmniAmp Pol was found to be less inhibited by whole blood components typical in certain crude sample preparations. Moreover, the thermostability of the enzyme compared to alternative DNA polymerases (Bst) and reverse transcriptases allows pretreatment of complete reaction mixes immediately prior to amplification, which facilitates amplification of highly structured genome regions. Compared to Bst, OmniAmp Pol has a faster time to result, particularly with more dilute templates. Molecular diagnostics in field settings can be challenging due to the lack of refrigeration. The stability of OmniAmp Pol is compatible with a dry format that enables long term storage at ambient temperatures. A final requirement for field operability is compatibility with either commonly available instruments or, in other cases, a simple, inexpensive, portable detection mode requiring minimal training or power. Detection of amplification products is shown using lateral flow strips and analysis on a real-time PCR instrument. Results of this study show that OmniAmp Pol is ideally suited for low resource molecular detection of pathogens.
Textured mesh generation of extracted regions from urban range-scanned LIDAR data

LIDAR range scanners are a popular tool for data acquisition in the field of urban modeling, archaeological preservation, city planning, and more. However, range scanners output a series of discrete distance samples as disconnected points, providing a fundamentally incomplete representation of the underlying structure in a scene. Data from a single LIDAR scan of a region can be trivially triangulated, but when multiple scanners are involved, or when the acquisition platform is mobile, those inter-point relationships are lost. We propose a technique to triangulate such data by identifying logical surfaces within the data and triangulating those surfaces individually. The resulting triangulations are simplified dramatically by using information about the shape of the regions, and texture is applied from camera imagery on the scan vehicle. The result is a high fidelity representation of a scene which is more efficiently rendered on modern hardware than point sets, which occupies less space in memory, and which brings us closer to a solid representation of the true scanned scene.
Early detection of vasovagal syncope in tilt-up test with hemodynamic and autonomic study

The diagnosis of vasovagal syncope (VVS) is according to history, tilt table test and blood pressure change with postural stress. We collected 30 patients below 55 years-old, received tilt table test without pharmacological challenge from 2005 to 2010. Due to this disorder is the heterogeneity, multiple factor. The pathophysological pathway was not fully understood. We used logistic regression and neural network to evaluate variables during baseline and first 3 minutes tilt table test to early detect vasovagal syncope with tilt table test. We found using parameters of baseline heart rate, body mass index and mean blood pressure, cardiac index, left ventricular work index during 3 minutes of tilt up test for neural network model, the model revealed good train and test performance (accuracy:95.5%) with good sensitivity and specificity.
Causes of Variation in Malaria Infection Dynamics: Insights from Theory and Data

Parasite strategies for exploiting host resources are key determinants of disease severity (i.e., virulence) and infectiousness (i.e., transmission between hosts). By iterating the development of theory and empirical tests, we investigated whether variation in parasite traits across two genetically distinct clones of the rodent malaria parasite, Plasmodium chabaudi, explains differences in within-host infection dynamics and virulence. First, we experimentally tested key predictions of our earlier modeling work. As predicted, the more virulent genotype produced more progeny parasites per infected cell (burst size), but in contrast to predictions, invasion rates of red blood cells (RBCs) did not differ between the genotypes studied. Second, we further developed theory by confronting our earlier model with these new data, testing a new set of models that incorporate more biological realism, and developing novel theoretical tools for identifying differences between parasite genotypes. Overall, we found robust evidence that differences in burst sizes contribute to variation in dynamics and that differential interactions between parasites and host immune responses also play a role. In contrast to previous work, our model predicts that RBC age structure is not important for explaining dynamics. Integrating theory and empirical tests is a potentially powerful way of progressing understanding of disease biology.
Conservative-Bayesian Mechanism Design

Classical Bayesian mechanism design is “centralized”, that is, the designer is assumed to know the distribution D from which the players’ type profile has been drawn. We instead investigate a very “decentralized” Bayesian model, where the designer has no knowledge at all, and each player only has some probabilistic information about D. For this decentralized model and many contexts of interest, where the goal is to maximize revenue, we show that, for arbitrary type distributions D (in particular, correlated ones), it is possible to design mechanisms matching to a significant extent the performance of the optimal centralized mechanisms. Our results are “existential” for a broad class of contexts (including combinatorial auctions) and “constructive” for auctions of a single good. ∗This work has been partially funded by the Office of Naval Research under award number N00014091059. (Any opinions, findings, and conclusions or recommendations expressed in this email are those of the author (s) and do not necessarily reflect the views of the Office of Naval Research. )
A structure-based method for derivation of all-atom potentials for protein folding

A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a Cα distance rms from the native structure of less than 2 Å. Similar results were obtained for the hairpin and helices by using different potentials. We derived potentials for several different proteins and found a high correlation between the derived parameters, suggesting that a potential of this form eventually could be found that folds multiple, unrelated proteins at the atomic level of detail.
Building facade recognition from aerial images using Delaunay Triangulation induced feature perceptual grouping

This paper presents a novel feature grouping based framework for building facade recognition from aerial images. A combination of Maximally Stable Extremal Regions (MSERs and steered Determinant-of-Hessian (steered-DoH) are proposed to detect different shapes of blobs from images. Then we employ local parallelogram grouped by these repetitive and evenly distributed blobs to form an point-based regularity measurement. Building facade regions are indicated by these local parallelograms. In our work, we use Delaunay Triangulation (DT) to guide the search of local parallelograms. Our approach can handle images with large range of resolution. Vertical and horizontal assumptions of facades are not required. The experimental results conducted on images with different resolutions and different types of facades demonstrate superior performance on facade recognition both in terms of speed and accuracy (F1 - score over 80%) over state-of-the-art methods.
Intestinal microflora of Estonian and Swedish infants

The intestinal microflora of 1‐y‐old healthy Estonian (n= 27) and Swedish infants (n= 29) was studied by quantitative culture of faecal samples. The major differences were high counts of lactobacilli and eubacteria in the former and increased numbers of Clostridia in the latter babies. Bifidobacteria and anaerobic cocci prevailed equally in both groups, while eubacteria and enterococci were the major microorganisms in many Estonian infants and bacteroides and Clostridia in many Swedish infants. The microflora of the Estonian infants was in many aspects similar to the flora prevailing in infants of western Europe in the 1960s. The results suggest a shift in the intestinal microflora among infants in western industrialized countries.
A multipronged strategy of an anti-terminator protein to overcome Rho-dependent transcription termination

One of the important role of Rho-dependent transcription termination in bacteria is to prevent gene expressions from the bacteriophage DNA. The transcription anti-termination systems of the lambdoid phages have been designed to overcome this Rho action. The anti-terminator protein N has three interacting regions, which interact with the mRNA, with the NusA and with the RNA polymerase. Here, we show that N uses all these interaction modules to overcome the Rho action. N and Rho co-occupy their overlapping binding sites on the nascent RNA (the nutR/tR1 site), and this configuration slows down the rate of ATP hydrolysis and the rate of RNA release by Rho from the elongation complex. N-RNA polymerase interaction is not too important for this Rho inactivation process near/at the nutR site. This interaction becomes essential when the elongation complex moves away from the nutR site. From the unusual NusA-dependence property of a Rho mutant E134K, a suppressor of N, we deduced that the N-NusA complex in the anti-termination machinery reduces the efficiency of Rho by removing NusA from the termination pathway. We propose that NusA-remodelling is also one of the mechanisms used by N to overcome the termination signals.
THE LIPID COMPOSITION OF HUMAN PLASMA CHYLOMICRONS.

The lipid composition of human chylomicrons has been studied using blood collected from normal male volunteers after ingestion of 200 g of butter fat. The concentration of chylomicrons in the blood samples varied widely among 12 subjects but in each case the following lipids were present : triglycerides, diglycerides (probably the 1,2-isomers), monoglycerides, free and esterified cholesterol, traces of free fatty acids, phosphatidyl ethanolamine, phosphatidyl choline, sphingomyelin (two components), and lysolecithin. The fatty acid composition of chylomicron triglycerides was usually similar to that of butter, but myristic and shorter-chain acids showed concentrations lower than those in butter. Pooled phospholipids were fractionated by preparative thinlayer chromatography. Phosphorus determinations indicated the following proportions of components (mole per cent of total phospholipids) : phosphatidyl ethanolamine region, 6y0 ; phosphatidyl choline, 79% ; sphingomyelins, 12% ; lysolecithin, 4%. The fatty acid compositions of the chylomicron phospholipids have been determined. The total sphingomyelin region contained C22, Cza, Cz4, and C24 monoenoic acids as major components.
Determining Suitability of Locations for Installation of Solar Power Station Based on Probabilistic Inference

This paper presents a novel system is to develop to determine the suitability of a location for installation of solar power stations. Necessary data including speed and direction of wind, solar radiation and rainfall are received from a meteorology station, and data acquired are then converted to the labels. Finally, the labels are evaluated in a Naive Bayes algorithm to determine the suitability of the location for the installation and axial structure of a Solar Power Plant. This helps to determine complicated calculations by means of the support system developed.
IL‐10 and TGF‐β cooperate in the regulatory T cell response to mucosal allergens in normal immunity and specific immunotherapy

The regulation of normal and allergic immune responses to airborne allergens in the mucosa is still poorly understood, and the mechanism of specific immunotherapy (SIT) in normalizing the allergic response to such allergens is currently not clear. Accordingly, we have investigated the immunoregulatory mechanism of both normal and allergic responses to the major house‐dust mite (HDM) and birch pollen allergens — Dermatophagoides pteroynyssinus (Der p)1 and Bet v 1, respectively — as well as the immunologic basis of SIT to HDM in rhinitis and asthma patients. In normal immunity to HDM and birch pollen, an allergen‐specific peripheral T cell suppression to Der p 1 and Bet v 1 was observed. The deviated immune response was characterized by suppressed proliferative T celland Th1 (IFN‐γ) and Th2 (IL‐5, IL‐13) cytokine responses, and increased IL‐10 and TGF‐β secretion by allergen‐specific T cells. Neutralization of cytokine activity showed that T cell suppression was induced by IL‐10 and TGF‐β during SIT and in normal immunity to the mucosal allergens. In addition, SIT induced an antigen‐specific suppressive activity in CD4+ CD25+ T cells of allergic individuals. Together, these results demonstrate a deviation towards a regulatory/suppressor T cell response during SIT and in normal immunity as a key event for the healthy immune response to mucosal antigens.
Generation and enumeration of carbon skeletons

Two different programs were written to enumerate all possible carbon skeletons, i.e., saturated hydrocarbons. These enumerations were carried out fully to 11 carbon atoms and for limited numbers of rings to 16 carbon atoms. The results of the two programs were consistent with each other as well as with such previous enumerations as were available. A program to show graphically the stored skeletons was also prepared. The skeletons of commercially available starting materials are a minute subset of the total. Various ways of classifying the data into subsets are illustrated as are superstructure searches from seed skeletons
Consequences of maternal postpartum depression: A systematic review of maternal and infant outcomes

Introduction: The postpartum period represents the time of risk for the emergence of maternal postpartum depression. There are no systematic reviews of the overall maternal outcomes of maternal postpartum depression. The aim of this study was to evaluate both the infant and the maternal consequences of untreated maternal postpartum depression. Methods: We searched for studies published between 1 January 2005 and 17 August 2016, using the following databases: MEDLINE via Ovid, PsycINFO, and the Cochrane Pregnancy and Childbirth Group trials registry. Results: A total of 122 studies (out of 3712 references retrieved from bibliographic databases) were included in this systematic review. The results of the studies were synthetized into three categories: (a) the maternal consequences of postpartum depression, including physical health, psychological health, relationship, and risky behaviors; (b) the infant consequences of postpartum depression, including anthropometry, physical health, sleep, and motor, cognitive, language, emotional, social, and behavioral development; and (c) mother–child interactions, including bonding, breastfeeding, and the maternal role. Discussion: The results suggest that postpartum depression creates an environment that is not conducive to the personal development of mothers or the optimal development of a child. It therefore seems important to detect and treat depression during the postnatal period as early as possible to avoid harmful consequences.
Effect of creatine supplementation and a lacto-ovo-vegetarian diet on muscle creatine concentration.

The purpose of this investigation was to examine the effects of preceding oral creatine monohydrate with a lacto-ovo-vegetarian diet on muscle creatine concentration. Thirty-two healthy men, who regularly consumed an omnivorous diet, were randomly assigned to consume a weight maintaining, lacto-ovo-vegetarian (LOV; n = 16) or omnivorous (Omni; n = 16) diet for 26 days. In addition to their assigned diet, on day 22 of the study, subjects were assigned in a double-blind manner to receive either creatine monohydrate (CM; 0.3 g kg d 1 + 20 g Polycose) or an equivalent dose of placebo (PL) for 5 days. There were no significant differences between the LOV and Omni groups at baseline with respect to age, height, and weight. The results demonstrated that consuming a LOV diet for 21 days was an effective procedure to decrease muscle creatine concentration (p <.01) in individuals who normally consume meat and fish in their diet. However, muscle total creatine (TCr) following creatine supplementation did not differ statistically between LOV and Omni diet groups (148.6 4.5 vs. 141.7 4.5 mmol kg-1 d.m.).
Role of Cannabinoid Receptor Type 1 in Insulin Resistance and Its Biological Implications

Endogenous cannabinoids (ECs) are lipid-signaling molecules that specifically bind to cannabinoid receptor types 1 and 2 (CB1R and CB2R) and are highly expressed in central and many peripheral tissues under pathological conditions. Activation of hepatic CB1R is associated with obesity, insulin resistance, and impaired metabolic function, owing to increased energy intake and storage, impaired glucose and lipid metabolism, and enhanced oxidative stress and inflammatory responses. Additionally, blocking peripheral CB1R improves insulin sensitivity and glucose metabolism and also reduces hepatic steatosis and body weight in obese mice. Thus, targeting EC receptors, especially CB1R, may provide a potential therapeutic strategy against obesity and insulin resistance. There are many CB1R antagonists, including inverse agonists and natural compounds that target CB1R and can reduce body weight, adiposity, and hepatic steatosis, and those that improve insulin sensitivity and reverse leptin resistance. Recently, the use of CB1R antagonists was suspended due to adverse central effects, and this caused a major setback in the development of CB1R antagonists. Recent studies, however, have focused on development of antagonists lacking adverse effects. In this review, we detail the important role of CB1R in hepatic insulin resistance and the possible underlying mechanisms, and the therapeutic potential of CB1R targeting is also discussed.
Loss of the Coffin-Lowry syndrome-associated gene RSK2 alters ERK activity, synaptic function and axonal transport in Drosophila motoneurons

ABSTRACT Plastic changes in synaptic properties are considered as fundamental for adaptive behaviors. Extracellular-signal-regulated kinase (ERK)-mediated signaling has been implicated in regulation of synaptic plasticity. Ribosomal S6 kinase 2 (RSK2) acts as a regulator and downstream effector of ERK. In the brain, RSK2 is predominantly expressed in regions required for learning and memory. Loss-of-function mutations in human RSK2 cause Coffin-Lowry syndrome, which is characterized by severe mental retardation and low IQ scores in affected males. Knockout of RSK2 in mice or the RSK ortholog in Drosophila results in a variety of learning and memory defects. However, overall brain structure in these animals is not affected, leaving open the question of the pathophysiological consequences. Using the fly neuromuscular system as a model for excitatory glutamatergic synapses, we show that removal of RSK function causes distinct defects in motoneurons and at the neuromuscular junction. Based on histochemical and electrophysiological analyses, we conclude that RSK is required for normal synaptic morphology and function. Furthermore, loss of RSK function interferes with ERK signaling at different levels. Elevated ERK activity was evident in the somata of motoneurons, whereas decreased ERK activity was observed in axons and the presynapse. In addition, we uncovered a novel function of RSK in anterograde axonal transport. Our results emphasize the importance of fine-tuning ERK activity in neuronal processes underlying higher brain functions. In this context, RSK acts as a modulator of ERK signaling. Summary: Mutations in the human kinase RSK2 are associated with severe mental retardation (Coffin-Lowry syndrome). Here, the function of Drosophila RSK in synaptic plasticity is described, which might help in understanding the complex pathophysiology.