Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphisms in innate immunity genes predispose to bacteremia and death in the medical intensive care unit*

Objective:Critically ill patients are at risk of sepsis, organ failure, and death. Studying the impact of genetic determinants may improve our understanding of the pathophysiology and allow identification of patients who would benefit from specific treatments. Our aim was to study the influence of single nucleotide polymorphisms in selected genes involved in innate immunity on the development of bacteremia or risk of death in patients admitted to a medical intensive care unit. Design, Setting, and Patients:DNA was available from 774 medical intensive care unit patients. We selected 31 single nucleotide polymorphisms in 14 genes involved in host innate immune defense. Serum levels of MASP2 and chemotactic capacity, phagocytosis, and killing capacity of monocytes at admission were quantified. Univariate Kaplan-Meier estimates with log-rank analysis and multivariate logistic regression were performed. Bootstrap resampling technique and ten-fold cross-validation were used to assess replication stability, prognostic importance of the variables, and repeatability of the final regression model. Main Results:Patients with at least one NOD2 variant were shown to have a reduced phagocytosis by monocytes (p = 0.03) and a higher risk of bacteremia than wild-type patients (p = 0.02). The NOD2/TLR4 combination was associated with bacteremia using survival analyses (time to bacteremia development, log-rank p < 0.0001), univariate regression (p = 0.0003), and multivariate regression analysis (odds ratio [OR] 4.26, 95% confidence interval [CI] 1.85–9.81; p = 0.0006). Similarly, the same combination was associated with hospital mortality using survival analysis (log-rank p = 0.03), univariate regression (p = 0.02), and multivariate regression analysis (OR 2.27, 95% CI 1.09–4.74; p = 0.03). Also variants in the MASP2 gene were significantly associated with hospital mortality (survival analysis log-rank-p = 0.003; univariate regression p = 0.02; multivariate regression analysis OR 2.35, 95% CI 1.38–3.99; p = 0.002). Conclusions:Functional polymorphisms in genes involved in innate immunity predispose to severe infections and death, and may become part of a risk model, allowing identification of patients at risk, who could benefit from early introduction of specific preventive or therapeutic interventions.
Combined influence of substrate relief and mechanical compression on topographical evolution of surface wrinkling

Controlled surface wrinkling could provide ordered and hierarchical structures in micro- and nano-meter scale. Here combined influence of out-of-plane compressive stress and in-plane substrate relief in Au/PDMS bilayer system was experimentally investigated to explore morphological evolution of surface wrinkling. Compared with single influence from out-of-plane compression or in-plane relief, the combined effect mainly reflected in two aspects: edge effect and rearrangement effect. Edge effect applied morphological change on the compressed fields near the edges, but patterns almost restored to the original shape after stress relaxation. Rearrangement effect made relaxed patterns on the rectangular convex regions to rearrange and led to the failure of shape memory effect. The results demonstrated that the combined effect could partly rearrange the original structures, which would be utilized to fabricate the complicated structures.
Failure analysis of MIM and MIS structures using spatial statistics

Within the wide variety of statistical techniques used to characterize the occurrence of failure events in metal-insulator-metal (MIM) and metal-insulator-semiconductor (MIS) structures, there is one that has received particular attention in recent years because of its relevance in oxide reliability analysis. Spatial statistics is a specialized branch of statistics aimed to summarize information about the spatial location of entities in 1, 2 and 3 dimensions. Since it has been shown that a device can still be operative after one or several breakdown events, it is of interest to investigate whether temporal and spatial correlations can occur among failure events. In this paper, the attention will be exclusively focused on the spatial aspect of the problem, with special emphasis on detecting departures from homogeneity. Two cases will be analyzed in which the failure events become visible on the top electrode as a 2D point pattern. These patterns can be assessed using a number of spatial statistical tools such as the intensity plot, the interevent distance histogram, the pair correlation function and residual analysis.
Linking Network Structure to Collaborative Governance

Author(s): Ulibarri, N; Scott, TA | Abstract: © The Author 2016. Published by Oxford University Press on behalf of the Journal of Public Administration Research and Theory, Inc. All rights reserved. How do social networks differ between highly collaborative and less collaborative forms of governance? Drawing on a prior study that characterized the level of collaboration for three federal hydropower relicensing processes, we develop exponential random graph models of meeting attendance and participation networks. We find that the highly collaborative relicensing process had lower overall density and a propensity for relatively fewer and stronger interactions. Reciprocity is highest in the high-collaboration process, indicating that it is characterized by mutual interactions. In the low-collaboration process, patterns of connections between any three members of the network displayed a more unidirectional structure, suggesting asymmetrical interactions between active versus passive members of the network. By linking network structure to collaborative dynamics, this study helps elaborate potential mechanisms of successful collaboration.
Using search engine technology for protein function prediction

Prediction of protein function is one of the most challenging problems in the post-genomic era. In this paper, we propose a novel algorithm Improved ProteinRank (IPR) for protein function prediction, which is based on the search engine technology and the preferential attachment criteria. In addition, an improved algorithm IPRW is developed from IPR to be used in the weighted protein? protein interaction (PPI) network. The proposed algorithms IPR and IPRW are applied to the PPI network of S.cerevisiae. The experimental results show that both IPR and IPRW outweigh the previous methods for the prediction of protein functions.
Protective effects of PPARγ agonist in acute nephrotic syndrome.

BACKGROUND Peroxisome proliferator-activated receptor gamma (PPARγ) agonists have beneficial effects on renal structure and function in models of diabetes and chronic kidney diseases. However, the increased incidence of weight gain and edema potentially limits their usefulness. We studied an acute minimal-change disease-like nephrotic syndrome model to assess effects of PPARγ agonist on acute podocyte injury and effects on fluid homeostasis. METHODS Acute podocyte injury and nephrotic syndrome were induced by puromycin aminonucleoside (PAN) injection in rats. RESULTS PPARγ agonist, given at the time or after, but not before PAN, reduced proteinuria, restored synaptopodin, decreased desmin and trended to improve foot process effacement. There was no significant difference in glomerular filtration, effective circulating volume, blood pressure or fractional sodium excretion. PAN-injured podocytes had decreased PPARγ, less nephrin and α-actinin-4, more apoptosis and reduced phosphorylated Akt. In PAN-injured cultured podocytes, PPARγ agonist also reversed abnormalities only when given simultaneously or after injury. CONCLUSIONS These results show that PPARγ agonist has protective effects on podocytes in acute nephrotic syndrome without deleterious effects on fluid homeostasis. PPARγ agonist-induced decrease in proteinuria in acute nephrotic syndrome is dependent at least partially on regulation of peroxisome proliferator-response element-sensitive gene expression such as α-actinin-4 and nephrin and the restoration of podocyte structure.
Vancomycin-associated acute kidney injury in pediatric cardiac intensive care patients.

OBJECTIVE Acute kidney injury (AKI) is a significant source of morbidity among critically ill pediatric patients, including those that have undergone cardiac surgery. Vancomycin may contribute to AKI in pediatric patients admitted to a cardiac intensive care unit. DESIGN AND SETTING Patients admitted to the cardiac intensive care unit at Texas Children's Hospital and received vancomycin over a 4-year period were included in a case-control study. Patients were excluded if they underwent renal replacement therapy during vancomycin therapy. Patient demographic and disease state variables, vancomycin therapy variables, and use of other nephrotoxic medications were collected. The overall incidence of AKI was calculated based on doubling of serum creatinine during or within 72 hours of vancomycin therapy (vancomycin-associated AKI [vAKI]). Patients who developed vAKI were matched with three patients who did not develop vAKI, and conditional logistic regression was used to determine independent risk factors for vAKI. RESULTS A total of 418 patients met study criteria (males 57.8%) and infants (31 days to 2 years) were the most populous age group (48.6%). Vancomycin-associated AKI occurred in 30 patients (7.2%), which resulted in a total of 120 patients (30 cases; 90 controls). No significant differences were noted in vancomycin dosing between groups. Vancomycin-associated AKI patients were less likely to have undergone cardiac surgery (P < .05), more likely to have undergone extracorporeal membrane oxygenation (P < .05), and had greater exposure to nephrotoxic medications (P < .05). A conditional logistic regression model identified extracorporeal membrane oxygenation as associated with vAKI (odds ratio 14.4, 95% confidence interval 1.02-203, P = .048) and patients with prior cardiovascular surgery (odds ratio 0.10, 95% confidence interval 0.02-0.51, P < .01) or an elevated baseline serum creatinine (odds ratio 0.009, 95% confidence interval 0.0002-0.29, P < .01) as less likely to develop vAKI. CONCLUSIONS Vancomycin-associated AKI occurs infrequently in the pediatric cardiac intensive care population and is strongly associated with patient critical illness.
FNGLVQ FPGA design for sleep stages classification based on electrocardiogram signal

Commonly sleep stages detection can be done using electroencephalogram (EEG) that is recorded in hospitals using Polysomnography (PSG) systems. PSG not only records brain signal but also electrocardiogram (ECG). In this paper an automatic sleep stages detection using FNGLVQ algorithm based solely on ECG signal is reported. We have compared two neural network algorithms' accuracies and implemented algorithms with the best accuracies into Field Programmable Gate Array. The two algorithms were Generalized Learning Vector Quantization (GLVQ) and Fuzzy Neuro Generalized Learning Vector Quantization (FNGLVQ). The result shows that FNGLVQ is capable in achieving 68% accuracy for MIT-BIH data, and 70% accuracy for Mitra data. The experiment conducted on FPGA also shows similar result.
Perception and Processing of Faces in the Human Brain Is Tuned to Typical Feature Locations

Faces are salient social stimuli whose features attract a stereotypical pattern of fixations. The implications of this gaze behavior for perception and brain activity are largely unknown. Here, we characterize and quantify a retinotopic bias implied by typical gaze behavior toward faces, which leads to eyes and mouth appearing most often in the upper and lower visual field, respectively. We found that the adult human visual system is tuned to these contingencies. In two recognition experiments, recognition performance for isolated face parts was better when they were presented at typical, rather than reversed, visual field locations. The recognition cost of reversed locations was equal to ∼60% of that for whole face inversion in the same sample. Similarly, an fMRI experiment showed that patterns of activity evoked by eye and mouth stimuli in the right inferior occipital gyrus could be separated with significantly higher accuracy when these features were presented at typical, rather than reversed, visual field locations. Our findings demonstrate that human face perception is determined not only by the local position of features within a face context, but by whether features appear at the typical retinotopic location given normal gaze behavior. Such location sensitivity may reflect fine-tuning of category-specific visual processing to retinal input statistics. Our findings further suggest that retinotopic heterogeneity might play a role for face inversion effects and for the understanding of conditions affecting gaze behavior toward faces, such as autism spectrum disorders and congenital prosopagnosia. SIGNIFICANCE STATEMENT Faces attract our attention and trigger stereotypical patterns of visual fixations, concentrating on inner features, like eyes and mouth. Here we show that the visual system represents face features better when they are shown at retinal positions where they typically fall during natural vision. When facial features were shown at typical (rather than reversed) visual field locations, they were discriminated better by humans and could be decoded with higher accuracy from brain activity patterns in the right occipital face area. This suggests that brain representations of face features do not cover the visual field uniformly. It may help us understand the well-known face-inversion effect and conditions affecting gaze behavior toward faces, such as prosopagnosia and autism spectrum disorders.
Comparative effectiveness of sphincter-sparing surgery versus abdominoperineal resection in rectal cancer: patient-reported outcomes in National Surgical Adjuvant Breast and Bowel Project randomized trial R-04.

OBJECTIVE National Surgical Adjuvant Breast and Bowel Project (NSABP) R-04 was a randomized controlled trial of neoadjuvant chemoradiotherapy in patients with resectable stage II-III rectal cancer. We hypothesized that patients who underwent abdominoperineal resection (APR) would have a poorer quality of life than those who underwent sphincter-sparing surgery (SSS). METHODS To obtain patient-reported outcomes (PROs) we administered two symptom scales at baseline and 1 year postoperatively: the Functional Assessment of Cancer Therapy-Colorectal (FACT-C) and the European Organization for the Research and Treatment of Cancer module for patients with Colorectal Cancer Quality of Life Questionnaire (EORTC QLQ-CR38). Scoring was stratified by nonrandomly assigned definitive surgery (APR vs SSS). Analyses controlled for baseline scores and stratification factors: age, sex, stage, intended surgery, and randomly assigned chemoradiotherapy. RESULTS Of 1,608 randomly assigned patients, 987 had data for planned analyses; 62% underwent SSS; 38% underwent APR. FACT-C total and subscale scores were not statistically different by surgery at 1 year. For the EORTC QLQ-CR38 functional scales, APR patients reported worse body image (70.3 vs 77.0, P = 0.0005) at 1 year than did SSS patients. Males undergoing APR reported worse sexual enjoyment (43.7 vs 54.7, P = 0.02) at 1 year than did those undergoing SSS. For the EORTC QLQ-CR38 symptom scale scores, APR patients reported worse micturition symptoms than the SSS group at 1 year (26.9 vs 21.5, P = 0.03). SSS patients reported worse gastrointestinal tract symptoms than did the APR patients (18.9 vs 15.2, P < 0.0001), as well as weight loss (10.1 vs 6.0, P = 0.002). CONCLUSIONS Symptoms and functional problems were detected at 1 year by EORTC QLQ-CR38, reflecting different symptom profiles in patients who underwent APR than those who underwent SSS. Information from these PROs may be useful in counseling patients anticipating surgery for rectal cancer.
Impact of Aid for Trade to Agricultural Development and Trade

Aid for Trade (AfT) has emerged as a significant mechanism for development of developing countries by helping them to participate in the global value chain. Grants on agricultural part in AfT has been gradually increased since 2002 and invested in various ways from agrarian reform, agricultural education and training to plant and post-harvest protection and pest control. In spite of the increase, there were only few researches on significance between AfT and agricultural development. This research aims to evaluate whether AfT has significant relation with agricultural development and trade. It also examines whether there is heterogeneity in the response to AfT across recipient countries with different national characteristics. We conducted a subgroup analysis using a panel tobit model. Also, UN COMTRADE(PC-TAS) for the export data, the World Bank data for agricultural GDP, OECD QWIDS for AfT data from 2002 to 2013 were used. Our results show that AfT in agriculture has increased both agricultural GDP and exports of the recipient countries. This study also found the most effective form of AfT in agriculture which differs from country to country depending on the characteristics of each country.
EVIDENCE ON THE SLUTSKY CONDITIONS FOR DEMAND EQUATIONS

T HE MODERN theory of consumer demand has been in the core of economic theory from its very beginning around the 1870's. Somewhat earlier (1857) Engel [6] published his study for the Kingdom of Saxony, which marks the start of systematic measurement of consumer behaviour. Both theory and measurement have developed enormously since their beginnings. Remarkably enough, the links between these two branches of study of consumer demand have remained rather weak. Nobody will deny the importance of those classics on theory and measurement of consumer demand as the monumental monographs by Schultz [15], Wold [22] and Stone [17], but even there the relation between the exposition of the theory and the derivation of the empirical results is frequently superficial. In this connection we can quote Cramer [4]:
Epitope Specificity and Relative Clonal Abundance Do Not Affect CD8 Differentiation Patterns during Lymphocytic Choriomeningitis Virus Infection

ABSTRACT To evaluate the impact of immunodominance on CD8 T-cell properties, we compared the functional properties of dominant and subdominant populations in the response to lymphocytic choriomeningitis virus (LCMV). To improve functional discrimination, in addition to the usual tests of phenotype and function, we used a sensitive technique that allows the screening of all CD8 effector genes simultaneously in single cells. Surprisingly, these methods failed to reveal a major impact of clonal dominance in CD8 properties throughout the response. Aiming to increase clonal dominance, we examined high-frequency transferred P14 T-cell receptor transgenic (TCR Tg) cells. Under these conditions LCMV is cleared faster, and accordingly we found an accelerated response. However, when Tg and endogenous cells were studied in the same mice, where they should be subjected to the same antigen load, they showed overlapping properties, and the presence of P14 cells did not modify endogenous responses to other LCMV epitopes or a perturbed immunodominance hierarchy in the memory phase. Using allotype-labeled Tg cells, we found that during acute infection up to 80% downregulated their TCR and were undetectable by tetramer binding, and that tetramer-negative and tetramer-positive cells had very different features. Since Tg cells are not available to evaluate immune responses in humans and, in many cases, are not available from the mouse, the tetramer-based evaluation of early immune responses in most situations of high viremia may be incomplete and biased.
Development of a cone angle weighted three-dimensional image reconstruction algorithm to reduce cone-beam artefacts.

OBJECTIVES Image reconstruction from cone-beam projections collected along a single circular source trajectory is commonly done using the Feldkamp algorithm, which performs well only with a small cone angle. In this report, we propose an algorithm to reduce cone-beam artefacts by increasing the cone angle by several fold to achieve satisfactory image quality at the same radiation dose. METHODS To examine the factors involved in the occurrence of cone-beam artefacts, a microspheres-phantom was arranged longitudinally at different positions and a computer simulation was performed. Due to differences in projection angle, data projected onto the detector surface were projected along trajectories shown as different periodic functions depending on the distance and position from the mid-plane position. Therefore, projection along several detector channels based on different projection data resulting from different periodic functions is considered responsible for the increase in cone-beam artefacts associated with an increase in the distance of reconstruction planes from the mid-plane position. Our recommended algorithm to reduce such artefacts features a change in weighting with respect to projection data obtained at different projection angles, three-dimensional back-projection of corrected projection data. RESULTS Numerical phantom simulation and real human head origin study (a prototype cone-beam CT) showed that the effect of the reduction in cone-beam artefacts of an object located at the edges was markedly enhanced at reconstruction planes at positions further from the mid-plane position. CONCLUSION We propose a projection angle weight-based algorithm to increase the cone angle by several fold to achieve satisfactory image quality at the same radiation dose. These findings confirmed that this algorithm reduces cone-beam artefacts and generates high-quality reconstruction images.
An ElGamal-based efficient and privacy-preserving data aggregation scheme for smart grid

Smart Grid technologies are ever-increasingly being adopted by nations and governments, primarily for a huge technological advancement in the areas of power management and information and communications. The smart meters deployed in a household can monitor electricity usage in real-time, and aggregate the data for further analysis and control; however, the existing solutions mainly depend on Paillier's additive homomorphic encryptions, which are of high computational complexity. This inefficiency makes them impracticable in smart grid, which embraces thousands of users and requires frequent data aggregation. In this paper, we propose a privacy-preserving aggregation framework, followed by a concrete construction using Elgamal encryption, which is secure under chosen plaintext attack (CPA) but not chosen ciphertext attack (CCA). Then, we further extend the concrete construction into a CCA-secure counterpart. In addition to efficient data aggregation, the proposed scheme can protect the user's meter data from sophisticated attacks, which are sponsored by the community gateway and the users. The formal security proof and performance evaluations illustrate the efficiency and the practicability of our scheme as well as its strong security.