Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of increasing age on the risk of surgical site infection.

BACKGROUND An increasing number of older persons undergo surgery, but the relationship between increasing age and risk of surgical site infection (SSI) has not been established. The objective of the present study was to determine the relationship between increasing age and risk of SSI. METHODS The present cohort study included patients who underwent surgery between February 1991 and July 2002. Patients >17 years of age were divided randomly into derivation and validation cohorts. The study was conducted at 11 hospitals. SSIs were prospectively identified by use of Centers for Disease Control and Prevention criteria. RESULTS The study included 144,485 consecutive surgical patients and 1684 SSIs (rate of SSI, 1.2%). There were 72,139 procedures and 873 SSIs in the derivation cohort. Adjusted analyses revealed a significant relationship between age and risk of SSI (P=.006). Risk of SSI increased by 1.1%/year between ages 17 and 65 years (P=.002). At age >/=65 years, risk of SSI decreased by 1.2% for each additional year (P=.008). There were 72,334 procedures and 811 SSIs in the validation cohort. The relationship between age and risk of SSI was similar in the validation cohort. CONCLUSIONS Increasing age independently predicted an increased risk of SSI until age 65 years. At ages >/=65 years, increasing age independently predicted a decreased risk of SSI.
Very sparse stable random projections for dimension reduction in lα (0 <α ≤ 2) norm

The method of <i>stable random projections</i> is a useful tool for efficiently computing the <i>l</i>α (0 < α ≤ 2) norms and distances in massive data in one pass. Consider a data matrix <b>A</b> ∈R<sup><i>nxD</i></sup>. If we multiply <b>A</b> with a projection matrix <b>R</b> ΕR <sup><i>Dxk</i></sup> (<i>k</i>« <i>D</i>),whose entries are i.i. d. samples of an α-stable distribution,then the projected matrix <b>B</b> = <b>A</b>x <b>R</b> Ε <b>R</b> <sup><i>nxk</i></sup>x containsenough information to approximately recover the <i>l</i> α properties in <b>A</b>. We propose <i>very sparse stable random projections</i>, by replacing the α stable distribution with a (much simpler) mixture of a symmetric α Pareto distribution (with probability Β, 0 β Β 1) and a point mass at the origin(with probability 1-Β). This leads to a significant 1 over Β fold speedup for small Β when computing <b>B</b> = <b>A</b>x<b>R</b> and a 1 over Β-fold cost reduction in storing <b>R}</b>. By analyzing the convergence, we show that in"reasonable" datasets Β often can be very small (e.g.,<i>D</i><sup>1/2</sup> without hurting the estimation accuracy. Some numerical evaluations are conducted, on synthetic data, Web crawldata, and gene expression microarray data.
Finite element method for simulation of tsunami run-up from quikibird satellite data

In this paper, work was carried out to simulate three-dimensional (3-D) tsunami run-up from high resolution remote sensing satellite data of QuickBird. In doing so, the tsunami wave spectra are extracted from QuickBird data using two dimensional di Fourier transform (2-DFFT). The tsunami propagation equation was then solved based on the standard Galerkin finite element approach to simulate 3-D tsunmai run-up. The results of this study have shown that the integration between different mathematical and numerical models is providing accurate 3-D reconstruction and simulation for tsunami run-up. Key words: QuickBird satellite data, tsunami run-up, 2-DFFT, 3-D reconstruction, finite element method, Galerkin finite element.
Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery

Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known active ligand. Two notable advantages of LBVS methods are that they do not require structural information of a target receptor and that they are faster than structure-based methods. LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D). Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed. In addition, four representative 3D methods were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability to find dissimilar active compounds, and computational speed.
Bayesian Decision Tree for the Classification of the Mode of Motion in Single-Molecule Trajectories

Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to improve our knowledge of the membrane architecture and to understand the nature of interactions between membrane proteins and their environments. Here, we present an analysis technique for single molecule tracking (SMT) trajectories that can determine the preferred model of motion that best matches observed trajectories. The method is based on Bayesian inference to calculate the posteriori probability of an observed trajectory according to a certain model. Information theory criteria, such as the Bayesian information criterion (BIC), the Akaike information criterion (AIC), and modified AIC (AICc), are used to select the preferred model. The considered group of models includes free Brownian motion, and confined motion in 2nd or 4th order potentials. We determine the best information criteria for classifying trajectories. We tested its limits through simulations matching large sets of experimental conditions and we built a decision tree. This decision tree first uses the BIC to distinguish between free Brownian motion and confined motion. In a second step, it classifies the confining potential further using the AIC. We apply the method to experimental Clostridium Perfingens -toxin (CPT) receptor trajectories to show that these receptors are confined by a spring-like potential. An adaptation of this technique was applied on a sliding window in the temporal dimension along the trajectory. We applied this adaptation to experimental CPT trajectories that lose confinement due to disaggregation of confining domains. This new technique adds another dimension to the discussion of SMT data. The mode of motion of a receptor might hold more biologically relevant information than the diffusion coefficient or domain size and may be a better tool to classify and compare different SMT experiments.
Application of Decision Tree Algorithm for Data Mining in Healthcare Operations: A Case Study

By means of data mining techniques, we can exploit furtive and precious information through medicine data bases. Because of huge amount of this information, study and analyses are too difficult. We want some methods to exploring through data and extract valuable information which can be used in the future similar cases. One of these cases is accouchement. The mechanism of accouchement is a natural and spontaneous process without the need to any intervention. In some conditions, maybe mother, baby or both of them are in hazard and need help and support. This help is provided by Caesarian Section which saves mother and baby. Nevertheless, we need to know when we should use surgery. This study explains utilization of medical data mining in determination of medical operation methods. We render this with accumulating 80 pregnant women information. The results show that decision tree algorithm designed for this case study generates correct prediction for more than 86.25% tests cases
Handling Unlike Coordinated Phrases in TAG by Mixing Syntactic Category and Grammatical Function

Coordination of phrases of different syntactic categories has posed a problem for generative systems based only on syntactic categories. Although some prefer to treat them as exceptional cases that should require some extra mechanism (as for elliptical constructions), or to allow for unrestricted cross-category coordination, they can be naturally derived in a grammatic functional generative approach. In this paper we explore the ideia on how mixing syntactic categories and grammatical functions in the label set of a Tree Adjoining Grammar allows us to develop grammars that elegantly handle both the cases of same- and cross-category coordination in an uniform way.
Abnormal Movement Preparation in Task-Specific Focal Hand Dystonia

Electrophysiological and behavioral studies in primary dystonia suggest abnormalities during movement preparation, but this crucial phase preceding movement onset has not yet been studied specifically with functional magnetic resonance imaging (fMRI). To identify abnormalities in brain activation during movement preparation, we used event-related fMRI to analyze behaviorally unimpaired sequential finger movements in 18 patients with task-specific focal hand dystonia (FHD) and 18 healthy subjects. Patients and controls executed self-initiated or externally cued prelearnt four-digit sequential movements using either right or left hands. In FHD patients, motor performance of the sequential finger task was not associated with task-related dystonic posturing and their activation levels during motor execution were highly comparable with controls. On the other hand reduced activation was observed during movement preparation in the FHD patients in left premotor cortex / precentral gyrus for all conditions, and for self-initiation additionally in supplementary motor area, left mid-insula and anterior putamen, independent of effector side. Findings argue for abnormalities of early stages of motor control in FHD, manifesting during movement preparation. Since deficits map to regions involved in the coding of motor programs, we propose that task-specific dystonia is characterized by abnormalities during recruitment of motor programs: these do not manifest at the behavioral level during simple automated movements, however, errors in motor programs of complex movements established by extensive practice (a core feature of FHD), trigger the inappropriate movement patterns observed in task-specific dystonia.
The tyranny of choice: a cross-cultural investigation of maximizing-satisficing effects on well-being

The present research investigated the relationship between individual differences in maximizing versus satisficing (i.e., seeking to make the single best choice, rather than a choice that is merely good enough) and well-being, in interaction with the society in which an individual lives. Data from three distinct cultural groups (adults), drawn respectively from the U.S. (N=307), Western Europe (N=263), and China (N=218), were analyzed. The results showed that, in societies where choice is abundant (i.e., U.S. and Western Europe), maximizers reported less well-being than satisficers, and this difference was mediated by experienced regret. However, in the non-western society (China), maximizing was unrelated to well-being. Although in China maximizing was associated with more experiences of regret, regret had no substantial relationship to well-being. These patterns also emerged for the individual facets of the maximizing scale, although with a notable difference between the U.S. and Europe for the High Standards facet. It is argued that, in societies where abundant individual choice is highly valued and considered the ultimate route to personal happiness, maximizers’ dissatisfaction and regret over imperfect choices is a detrimental factor in well-being, whereas it is a much less crucial determinant of well-being in societies that place less emphasis on choice as the way to happiness.
Indications, patient selection and timing of referral for lung transplantation

Lung transplantation (LTx) is now generally accepted as a useful modality of care for patients with severe life-threatening respiratory diseases that are refractory to other medical or surgical therapies. With the huge development of LTx over the last 15 yrs, the disparity between the number of potential recipients and the number of donor organs available has become a major constraint, with many patients dying on the waiting lists. Therefore, it is of primary importance to control and optimise the use of this limited organ resource by weighting the risks and benefits of transplantation in individual patients, and to identify those patients who have a better chance of having a favourable outcome with transplantation. This article discusses the selection process of potential candidates and the currently accepted absolute and relative contraindications, and proposes general and disease-specific recommendations for optimising the timing of referral. Early referral for consideration of lung transplantation is highly desirable as it enhances the patient's chance of surviving to transplant and allows the transplant team to actively manage identified comorbidities during the waiting period.
Prodefensins are matrix proteins of specific granules in human neutrophils

Defensins are potent antimicrobial and proinflammatory peptides. The human neutrophil defensins human neutrophil peptide (HNP)‐1–3 are synthesized as 94 amino acide (aa) preproHNPs, which are converted to 75 aa proHNPs by cotranslational removal of a 19 aa endoplasmic reticulum signal peptide. At the promyelocytic stage of myelopoiesis, proHNPs are further proteolytically modified and accumulate in azurophil granules as 29–30 aa HNPs. In contrast, proHNPs produced by more mature myeloid cells are not subjected to proteolytic cleavage and undergo a high degree of constitutive exocytosis. The proHNPs are devoid of antimicrobial potential, and the significance of their secretion is unknown. To investigate whether mature neutrophils contain proHNPs, we developed antibodies against proHNP‐1 by DNA immunization of rabbits. In addition, antibodies against the 45 aa proHNP pro‐piece were raised by conventional immunization procedures. These antibodies allowed detection of proHNPs in homogenates of peripheral blood neutrophils. The proHNPs were isolated by affinity chromatography, and their identity was confirmed by mass spectrometry and N‐terminal aa sequence analysis. Finally, the neutrophil proHNPs were identified as novel matrix proteins of specific granules by subcellular fractionation experiments, release studies, and immunoelectron microscopy. Thus, human neutrophils not only store large amounts of mature defensins in azurophil granules but also contain a more easily mobilized reservoir of unprocessed prodefensins in specific granules.
Retrograde catheterization of haemodialysis fistulae and grafts: angiographic depiction of the entire vascular access tree and stenosis treatment.

BACKGROUND The European Best Practice Guidelines on Vascular Access propose magnetic resonance angiography (MRA) of dysfunctional dialysis fistulae and grafts if visualization of the complete arterial inflow and outflow vessels is needed. In a prospective multi-centre study we determined the technical success rate of complete vascular access tree depiction by digital subtraction angiography (DSA) as an alternative to MRA. Instead of a more invasive brachial artery of femoral artery approach, we performed a retrograde catheterization of the venous outflow or graft, and stenoses were treated in connection with DSA. METHODS A catheter was advanced into the central arterial inflow after retrograde puncture of the venous outflow or graft for depiction of the complete inflow, access region and complete outflow. Access DSA through femoral artery puncture was done if the retrograde approach failed to depict the complete vascular access tree. Stenoses with a luminal diameter reduction >or=50% were treated, if possible, in connection with DSA. RESULTS A total of 116 dysfunctional haemodialysis fistulae and 50 grafts were included. Retrograde DSA depicted the complete vascular tree in 162 patients (97.6%). The arteriovenous anastomosis of four fistulae could not be negotiated by a catheter. DSA demonstrated 247 significant stenoses: 30, 128 and 89 were located in the arterial inflow (12.1%), AV anastomosis and graft region (51.8%) and venous outflow (36.0%), respectively. Ten patients (6.0%) had no stenosis. Eight (4.8%), 55 (33.1%) and 33 (19.9%) patients demonstrated stenoses in only inflow, access region or outflow, respectively. Stenoses in two or three vascular territories were present in 53 (31.9%) and 7 (4.2%) patients, respectively. A technically successful endovascular intervention was obtained in 135 of the 139 patients (97.1%) who underwent angioplasty and/or stent placement. Additional sheath insertion by antegrade outflow puncture was needed in 46 patients (33.1%) for the treatment of coexisting venous outflow stenoses, located downstream from the retrograde positioned sheath. Two minor complications were observed at DSA/angioplasty. CONCLUSION As an alternative to MRA, full retrograde DSA is safe and effective for stenosis detection and stenosis treatment. However, access evaluation by a non-invasive imaging modality such as colour duplex ultrasound will be sufficient in most cases as proximal inflow stenoses are encountered in a minority of patients. Full retrograde DSA, including complete arterial inflow depiction, may then be reserved for cases with an unsuccessful outcome following endovascular intervention of stenoses depicted at ultrasound.
E-AODV for Wireless Mesh Networks and Its Performance Evaluation

Wireless Mesh Networks (WMNs) consist of static router backbone which provide connectivity and coverage to mobile clients. They can also be viewed as a special case of wireless multi-hop Mobile Ad-hoc Networks (MANETs). The IETF group as well as the IEEE 802.11s working group have recommended applicability of several existing MANETs routing protocols for WMNs. However, in WMNs, client to client communications are through parent gateway via static routers, while in MANETs every arbitrary node pairs can act as source or destination. Therefore, it is of practical importance to re-evaluate MANETs routing protocols and make suitable modifications so that the protocols perform efficiently in WMNs environment. In this paper, we propose E-AODV, which is a variant of traditional Ad-hoc On-demand Distant Vector (AODV) routing, a protocol developed for MANETs. To evaluate E-AODV's performance and suitability in WMNs, a comparison of the protocol with traditional AODV and M-OLSR (a modified OLSR for WMNs), is carried out.
Dimensionality Reduction and Latent Variable Models for Online Collective Intelligence Systems

We explore dimensionality reduction and latent variable inference problems in an online Collective Intelligence system, Opinion Space. We propose a new dimensionality reduction algorithm derived from a spectral clustering model called Distributed Spectral Dimensionality Reduction (DSDR) and implemented it on the SPARK distributed platform. We applied our algorithm to visualize a 2D graphical map of associated terms from a corpus of Opinion Space textual data. For this dataset, our experiments on Amazon EC2 suggest that the algorithm scales nearly linearly with the number of nodes in the computing cluster. Furthermore, the results also suggest that DSDR is better at preserving high-dimensional cluster structure than PCA, MDS, LLE, and ISOMAP. In addition, we propose an uncertainty minimizing sampling algorithm to mitigate the effects of preferential attachment in Opinion Space idea evaluations. After the integrating the algorithm in Opinion Space, we found statistically significant reductions in biases in the number of evaluations. We further study online participation patterns in a crowdsourced system to spread awareness of California State Proposition 30 before the Fall 2012 election. We confirmed that the arrival process of participants can be modeled as a Poisson thinning process and the growth of the system is dependent on the branching factor and the power law nature of participant activity. In addition, we formulate a geometric algorithm based on a linear regression model to efficiently detect rogue evaluation activity in Opinion Space, and our data suggests that it is effective at detecting rouge raters. Finally, we report detailed results and analysis from two Opinion Space projects which use the algorithms and models proposed in this report; one soliciting best Social Media practices in K-12 learning and one engaging the UC Berkeley student body on a historic photo archive.
Smoke, Choline Acetyltransferase, Muscarinic Receptors, and Fibroblast Proliferation in Chronic Obstructive Pulmonary Disease

Acetylcholine (ACh), synthesized by choline acetyltransferase (ChAT), and muscarinic M1, M2, and M3 receptors (MRs) are involved in fibroblast proliferation. We evaluated ChAT, MRs, and extracellular signal-regulated kinase (ERK) 1/2 and nuclear factor (NF) κB activation in lung fibroblasts from patients with chronic obstructive pulmonary disease (COPD), control smokers, and controls. Human fetal lung fibroblasts (HFL-1) stimulated with interleukin (IL)-1β, tumor necrosis factor (TNF)-α, and cigarette smoke extracts (CSEs) were evaluated for ChAT and MR expression. We tested the effects of ACh on fibroblast proliferation and its ability to bind fibroblasts from patients with COPD, control smokers, controls, and HFL-1 stimulated with IL-1β, TNF-α, and CSE. ChAT, M1, and M3 expression and ERK1/2 and NFκB activation were increased, whereas M2 was reduced, in COPD and smoker subjects compared with controls. IL-1β increased the ChAT and M3, TNF-α down-regulated M2, and CSE increased ChAT and M3 expression while down-regulating the expression of M2 in HFL-1 cells. ACh stimulation increased fibroblast proliferation in patients with COPD, control smokers, and controls, with higher effect in control smokers and patients with COPD and increased HFL-1 proliferation only in CSE-treated cells. The binding of ACh was higher in patients with COPD and in control smokers than in controls and in CSE-treated than in IL-1β- and TNF-α-stimulated HFL-1 cells. Tiotropium (Spiriva; [1α,2β,4β,5α,7β-7-hydroxydi-2-thienylacetyl)oxy]-9,9-dimethyl-3-oxa-9-azoniatrcyclo[3.3. 1.024], C19H22 NO4S2Br·H2O), gallamine triethiodide (C19H22N4O2S·2HCl·H2O), telenzepine [4,9-d-dihydro-3-methyl-4-[(4-methyl-1piperazinyl) acetyl]-10H-thieno [3,4-b][1,5]benzodiazepine-10-one dihydrobromide, C30H60I3N3O3], 4-diphenylacetoxy-N-methylpiperidine, PD098059 [2-(2-amino-3methoxyphenyl)-4H-1benzopyran-4-one, C16H13NO3], and BAY 11-7082 [(E)-3-(4-methylphenylsulfonyl)-2-propenetrile, C10H9NO2C], down-regulated the ACh-induced fibroblast proliferation, promoting the MRs and ERK1/2 and NFκB pathways involvement in this phenomenon. These results suggest that cigarette smoke might alter the expression of ChAT and MRs, promoting airway remodeling in COPD and that anticholinergic drugs, including tiotropium, might prevent these events.
Improving the sample complexity using global data

We study the sample complexity of proper and improper learning problems with respect to different q-loss functions. We improve the known estimates for classes which have relatively small covering numbers in empirical L/sub 2/ spaces (e.g. log-covering numbers which are polynomial with exponent p<2). We present several examples of relevant classes which have a "small" fat-shattering dimension, and hence fit our setup, the most important of which are kernel machines.