Miracle-dz/UniFAR-FTUs huggingface dataset:
eal-time segmentation of burst suppression patterns in critical care

Objective: Develop a real-time algorithm to automatically discriminate suppressions from nonsuppressions (bursts) in electroencephalograms of critically ill adult patients. Methods: A real-time method for segmenting adult ICU EEG data into bursts and suppressions is presented based on thresholding local voltage variance. Results are validated against manual segmentations by two experienced human electroencephalographers. We compare inter-rater agreement between manual EEG segmentations by experts with inter-rater agreement between human vs automatic segmentations, and investigate the robustness of segmentation quality to variations in algorithm parameter settings. We further compare the results of using these segmentations as input for calculating the burst suppression probability (BSP), a continuous measure of depth-of-suppression. Results: Automated segmentation was comparable to manual segmentation, i.e. algorithm-vs-human agreement was comparable to human-vs-human agreement, as judged by comparing raw EEG segmentations or the derived BSP signals. Results were robust to modest variations in algorithm parameter settings. Conclusions: Our automated method satisfactorily segments burst suppression data across a wide range adult ICU EEG patterns. Performance is comparable to or exceeds that of manual segmentation by human electroencephalographers. Significance: Automated segmentation of burst suppression EEG patterns is an essential component of quantitative brain activity monitoring in critically ill and anesthetized adults. The segmentations produced by our algorithm provide a basis for accurate tracking of suppression depth. ∗ Corresponding author at: Wang 7 Neurology, Massachusetts General Hospital, 5 Fruit Street, Boston, MA 02114, United States. Tel. : +1 617 726 3311; ax: +1 617 724 6513. E-mail addresses: mwestover@partners.org, mb.westover@gmail.com M. Brandon Westover), mshafi@bidmc.harvard.edu (M.M. Shafi), hinung@neurostat.mit. edu (S. Ching), jessica.chemali@gmail.com (J.J. Chemali), atrickp@nmr.mgh. harvard.edu (P.L. Purdon), scash@partners.org (S.S. Cash), nb@neurostat.mit. edu (E.N. Brown). 1 These authors contributed equally to the work. 165-0270/$ – see front matter © 2013 Elsevier B.V. All rights reserved. ttp://dx.doi. org/10.1016/j.jneumeth. 2013.07. 003 © 2013 Elsevier B.V. All rights reserved.
Upon the Advent of Eternal September : a Case Study on Reddit Communities ’ Latent Networks

Although online communities often regard membership growth as an important goal of their development, research has shown that large influx of new users may interrupt a community’s wellness by introducing information overload and lowering content quality [1], [2], which is also know as “Eternal September”1 from the infamous case of Usenet’s fall[3]. Founded in 2005, Reddit, as one of the most popular online communities2, has accumulated a large user base over time. Among those popular subreddits, a handful of them have been made default for users throughout the past several years. Upon defaulted, those subreddits started to attract a substantial number of users every day and the trend has not shown a sign of decline. Did this surge of newcomers truly bring those subreddits increased popularity or it actually tore those communities down from inside? How did the older users react to newcomers? How did the newcomers reshape the community’s latent network structure as well as other community characteristics, if any at all? How does old and new users interact with each other after defaulting happens? We plan to look into these problems from a network perspective.
First Order and Second Order Characterizations of Metric Subregularity and Calmness of Constraint Set Mappings

A condition ensuring metric subregularity (respectively, calmness) of general multifunctions between Banach spaces is derived. This condition is expressed solely in terms of the given data at the reference point and does not involve any information concerning the solution set of the corresponding inclusion given by the multifunction. In finite dimensions this condition can be expressed in terms of a derivative which appears to be a combination of the coderivative and the contingent derivative. It is further shown that this sufficient condition is in some sense the weakest possible first order condition sufficient for subregularity. We extend this condition under the additional assumption that one part of the multifunction is known to be subregular in advance. We also derive second order conditions for metric subregularity, both sufficient and necessary, for multifunctions associated with constraint systems as they occur in optimization. We show that the main difference between the necessary and sufficient conditions is the replacement of an inequality by a strict inequality, just as in the case of “no gap” second order optimality conditions in optimization.
Automatic vessel segmentation using active contours in cine phase contrast flow measurements

The segmentation of images obtained by cine magnetic resonance (MR) phase contrast velocity mapping using manual or semi‐automated methods is a time consuming and observer‐dependent process that still hampers the use of flow quantification in a clinical setting. A fully automatic segmentation method based on active contour model algorithms for defining vessel boundaries has been developed. For segmentation, the phase image, in addition to the magnitude image, is used to address image distortions frequently seen in the magnitude image of disturbed flow fields. A modified definition for the active contour model is introduced to reduce the influence of missing or spurious edge information of the vessel wall. The method was evaluated on flow phantom data and on in vivo images acquired in the ascending aorta of humans. Phantom experiments resulted in an error of 0.8% in assessing the luminal area of a flow phantom equipped with an artificial heart valve. Blinded evaluation of the volume flow rates from automatic vs. manual segmentation of gradient echo (FFE) phase contrast images obtained in vivo resulted in a mean difference of −0.9 ± 3%. The mean difference from automatic vs. manual segmentation of images acquired with a hybrid phase contrast sequence (TFEPI) within a single breath‐hold was −0.9 ± 6%. J. Magn. Reson. Imaging 1999;10:41–51. © 1999 Wiley‐Liss, Inc.
Comparison of the metastasis‐inducing protein S100A4 (p9ka) with other prognostic markers in human breast cancer

Our aim was to compare the occurrence and prognostic significance over 14–20 years of immunocytochemically detected S100A4 and other tumour variables in primary tumours from 349 patients with operable breast cancer. For a cut‐off of 1% staining of the malignant cells, the antibody to S100A4 stains positively 56% of the carcinomas. There was a significant association of staining for S100A4 with tumours fixed to the chest wall, staining for c‐erbB‐2, c‐erbB‐3, pS2, cathepsin D and, inversely, at borderline levels with staining for estrogen receptor. Using Wilcoxon statistics in univariate analyses, staining for S100A4, nodal status, tumour class, histological grade and staining for c‐erbB‐2, p53 were associated negatively and staining for estrogen receptor, progesterone receptor were associated positively with patient survival times. The survival times of patients with S100A4‐negative carcinomas with or without one of the other tumour variables showed no significant differences, whilst those of patients with S100A4‐positive carcinomas showed significant differences in a negative or a positive way. Multivariate regression analysis for 137 patients showed that staining for S100A4 is most highly correlated with patient deaths, but involved lymph nodes, fixed tumours, high histological grade and staining for progesterone receptor were also significant independent prognostic variables. Our results suggest that in this set of patients, the tumour variable most tightly correlated with patient death is S100A4. Int. J. Cancer (Pred. Oncol.) 89:198–208, 2000. © 2000 Wiley‐Liss, Inc.
Application of VaR Methodology to Risk Management in the Stock Market in Iran

In this paper, the performance of RiskMetrics model for prediction of 1-day and 10-days value at risk were preceded in three confidence levels of 95%, 97.5% and 99%. The main data are TEDPIX Index that their fluctuations can be indicated market risk of Tehran Stock Exchange. Time series of this index has been applied from 21 March 2001 to 20 March 2010 with the total 2172 observations. As well, for validation of models, Kupiec test and Christoffersen test have been applied. The finding of this paper is that Risk Metrics model are good alternatives in modeling volatility and in estimating VaR. Also the results indicate that in Kupiec test for both periods, the accepting models number are equal, but in Christoffersen test, the results indicate that upon increasing the time period, the accepting models number are decreased.
Computational analysis of biological networks: Measuring evolutionary rewiring and predicting regulatory relationship

Computational analysis of biological networks: Measuring evolutionary rewiring and predicting regulatory relationship Chong Shou 2011 Biological networks represent various types of molecular organizations in a cell. In the previous decade, large amount of network data have accumulated that facilitates our knowledge of the composition, topological structure, and functional significance of biological systems. Recently, great scientific achievement has been made to unravel interand intraspecies variations at both molecular and system levels. Understanding how biological networks evolve could eventually help explain the general mechanism of cellular system. To this end, this thesis investigates the evolution of biological networks in terms of network rewiring. It compares rewiring rate differences among the common types of biological networks utilizing experimental data across species. Then it applies the rewiring rate formulism to show that regulatory networks generally evolve faster than non-regulatory collaborative networks, which is consistent among all species compared. It goes on to address network data quality issue and to computationally model the process of network rewiring with a simulation algorithm. Currently, building high quality biological networks is still the main goal in the system biology community. The final part of this thesis introduces a novel approach to predict transcription factor (TF) target genes in yeast, with significantly better prediction power than previously reported methods. It identifies histone sensitive and insensitive TFs to be distinct and biologically meaningful clusters. Computational analysis of biological networks: Measuring evolutionary rewiring and predicting regulatory relationship A Dissertation Presented to the Faculty of the Graduate School of Yale University in Candidacy for the Degree of Doctor of Philosophy
Synergism of Accessory Factors in Functional Expression of Mammalian Odorant Receptors*

The discovery of odorant receptors led to endeavors in matching them with their cognate ligands. Although it has been challenging to functionally express odorant receptors in heterologous cells, previous studies have linked efficient odorant receptor expression with N-terminal modifications and accessory proteins, including the receptor-transporting proteins (RTPs) and Ric8b. Here we have shown that a shorter form of RTP1, RTP1S, supports robust cell-surface and functional expression of representative odorant receptors. Using a combination of accessory proteins, including RTP1S, Ric8b, and Gαolf, a diverse set of untagged odorant receptors were successfully expressed heterologously due to the synergistic effects among the various accessory proteins. Furthermore, the addition of an N-terminal rhodopsin tag to the odorant receptors, along with the same set of accessory proteins, exhibits an additional level of synergism, inducing enhanced odorant receptor responses to odorants and thus defining a more efficient heterologous expression system. We then showed that the presence or absence of different N-terminal tags has little effect on the ligand specificity of odorant receptors, although the amount of receptor expressed can play a role in the ligand response profile. The accuracy of the odorant receptor heterologous expression system involving tagged odorant receptors and various accessory proteins promises success in high throughput de-orphaning of mammalian odorant receptors.
Oral candidiasis as a clinical marker related to viral load, CD4 lymphocyte count and CD4 lymphocyte percentage in HIV-infected patients.

BACKGROUND High viral load is currently considered to be one of the main indicators of the progression of HIV-induced immunodepression, but few studies have analysed its relationship to the presence of oral candidiasis (OC). The aim of this cross-sectional study is to analyse the relationship between viral load, total CD4 lymphocyte count, and percentage of CD4 lymphocytes to the occurrence of OC. METHODS The present cross-sectional study included 156 HIV-infected patients seen at a clinic for sexually transmitted diseases and HIV. We assessed the presence or absence of OC, and microbiological samples were obtained from the palatine mucosa and dorsal tongue for a smear stained with KOH (potassium hydroxide) and culture on Sabouraud's dextrose agar in all patients. Viral load was determined by quantification of viral RNA in peripheral blood with a minimum detectable level of 500 RNA copies/ml. CD4+ counts/CD4+ percentage were categorized as <200/<14%, 200-499/14-28%, and >500/>29%, and HIV viral loads were categorized as <500, 500-10,000, >10,000 copies/ml. RESULTS Thirty-eight percent (37.8%) of the patients had OC. Patients with CD4+ lymphocyte counts below 200 x 10(6)/l and CD4+ percentages below 14% showed a significantly higher frequency of OC (57.9% and 48.0%, respectively). Patients with a viral load over 10,000 copies/ml also had OC more frequently (44.8%). In the multiple logistic regression analysis, OC showed a statistically significant association with high viral load [>10,000 vs <500, odds ratio (OR)=11.4], low percentage of CD4+ lymphocytes (<14% vs >28%, OR=5), and injection drug use (IDU vs heterosexual transmission, OR=10.2). In HIV-infected patients, high viral load was associated with more frequent OC, regardless of CD4+ lymphocyte level. CONCLUSIONS These findings suggest that oral candidiasis could be a useful clinical marker of patients with high viral load. In view of these results, emphasis should be placed on the importance of systematic examination of the oral cavity in all medical follow-up examinations of HIV-infected patients.
[Anthropometry of elderly people living in geriatric institutions, Brazil].

OBJECTIVE To provide anthropometric and body composition information on elderly people living in geriatric institutions. METHODS Three-hundred and five elderly people, of both sexes, living in six geriatric institutions in Fortaleza were assessed. The following anthropometric variables were studied: weight, height, body mass index, mid-arm circumference, triceps skinfold thickness, arm muscle circumference, and corrected arm-muscle area. The body mass index was calculated as weight divided by the square of the height (m2). The arm muscle circumference and corrected arm-muscle area were calculated using specific equations. The results are presented as means, standard deviations and percentiles (5th, 10th, 25th, 50th, 75th, 90th and 95th). The analyses included Student t-test to detect differences in mean values of the variables between both sexes. Age impact was investigated by ANOVA. RESULTS In all variables, mean values in men were higher than those in women, except for triceps skinfold thickness . The mean difference of the variables body mass index and mid-arm circumference for both sexes were not statistically significant (p>0.05). Age has significantly contributed to reducing the variables' values. This means that specific reference standards are needed for elderly people. CONCLUSIONS Despite being institutionalized, there was seen a trend of decreasing anthropometric values in the study population similar to that found in other studies of elderly people but with different values. Thereby, such values could be useful in the nutritional assessment of institutionalized elderly people.
Development of peripheral vision tests for driver assessment

In the interests of identifying older drivers at higher risk of crashing, with a view to restricting their driving, fitness to drive tests require development and validation. One particular test that makes claim for inclusion in any battery of fitness to drive tests is the Useful Field of View test (UFOV)1. UFOV subtests appear to depend heavily on speed of visual processing, and on indexing crowding in peripheral vision. However, UFOV is a proprietary instrument and other custom software is available for measuring speed of visual processing and crowding in peripheral vision. Sixty participants aged over 60 completed UFOV. They also completed inspection time (IT), a measure of speed of visual processing, and crowding across the visual field (CAVF), a measure indexing effects of strength of crowding in peripheral vision. Thus, the current study compared performance on UFOV, inspection time (IT) and crowding across the visual field (CAVF). The main outcomes here were that the IT and CAVF measures had high test-retest reliability over a period of about one week and did not exhibit statistically significant practice effects. By way of contrast, although UFOV measures were also highly reliable, two of three UFOV measures, Divided Attention and Selective Attention, showed practice effects; the third measure, Processing Speed, showed severe range restriction in the current sample of healthy older adults. Correlations between CAVF, IT and UFOV Selective Attention were very high. These outcomes suggests that IT and CAVF together may well prove appropriate and useful as part of an assessment of fitness to drive. This suggestion needs to be validated by research investigating whether these tests predict crash risk in the same way that UFOV does. http://casr.adelaide. edu.au/casrpubfile/54/CASR019.pdf
Hypometabolism as the ultimate defence in stress response: how the comparative approach helps understanding of medically relevant questions

First conceptualized from breath‐hold diving mammals, later recognized as the ultimate cell autonomous survival strategy in anoxia‐tolerant vertebrates and burrowing or hibernating rodents, hypometabolism is typically recruited by resilient organisms to withstand and recover from otherwise life‐threatening hazards. Through the coordinated down‐regulation of biosynthetic, proliferative and electrogenic expenditures at times when little ATP can be generated, a metabolism turned ‘down to the pilot light’ allows the re‐balancing of energy demand with supply at a greatly suppressed level in response to noxious exogenous stimuli or seasonal endogenous cues. A unifying hallmark of stress‐tolerant organisms, the adaptation effectively prevents lethal depletion of ATP, thus delineating a marked contrast with susceptible species. Along with disengaged macromolecular syntheses, attenuated transmembrane ion shuttling and PO2‐conforming respiration rates, the metabolic slowdown in tolerant species usually culminates in a non‐cycling, quiescent phenotype. However, such a reprogramming also occurs in leading human pathophysiologies. Ranging from microbial infections through ischaemia‐driven infarcts to solid malignancies, cells involved in these disorders may again invoke hypometabolism to endure conditions non‐permissive for growth. At the same time, their reduced activities underlie the frequent development of a general resistance to therapeutic interventions. On the other hand, a controlled induction of hypometabolic and/or hypothermic states by pharmacological means has recently stimulated intense research aimed at improved organ preservation and patient survival in situations requiring acutely administered critical care. The current review article therefore presents an up‐to‐date survey of concepts and applications of a coordinated and reversibly down‐regulated metabolic rate as the ultimate defence in stress responses.
Antioxidant α‐tocopherol/γ‐cyclodextrin–inclusion complex encapsulated poly(lactic acid) electrospun nanofibrous web for food packaging

α-Tocopherol (α-TC) and α-TC/cyclodextrin (CD)–inclusion complex (IC) incorporated electrospun poly(lactic acid) (PLA) nanofibers (NF) were developed via electrospinning (PLA/α-TC–NF and PLA/α-TC/γ-CD–IC–NF). The release of α-TC into 95% ethanol (fatty food simulant) was much greater from PLA/α-TC/γ-CD–IC–NF than from PLA/α-TC–NF because of the solubility increase in α-TC; this was confirmed by a phase-solubility diagram. 2,2-Diphenyl-1-picrylhydrazyl radical-scavenging assay shows that PLA/α-TC–NF and PLA/α-TC/γ-CD–IC–NF had 97% antioxidant activities; this value was expected to be high enough to inhibit lipid oxidation. PLA/α-TC–NF and PLA/α-TC/γ-CD–IC–NF were tested directly on beef with the thiobarbituric acid reactive substance (TBARS) method, and the nanofibers displayed a lower TBARS content than the unpackaged meat sample. Thus, active packaging significantly enhanced the oxidative stability of the meat samples at 4 °C. In conclusion, PLA/α-TC/γ-CD–IC–NF was shown to be promising as an active food-packaging material for prolonging the shelf life of foods. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 133, 44858.
Rat primary embryo fibroblast cells suppress transformation by the E6 and E7 genes of human papillomavirus type 16 in somatic hybrid cells

The E6 and E7 genes of human papillomavirus type 16 (HPV-16) transform established lines of rat cells but not rat cells in primary culture irrespective of the expression of the two genes. The reason for this difference between the susceptibilities of cell lines and primary cells was examined by using hybrid cells obtained by somatic cell fusion of rat cell lines transformed by the E6 and E7 genes of HPV-16 and freshly isolated rat embryo fibroblast cells. In these hybrid cells, transformed phenotypes, including colony formation in soft agar, saturation density, and tumorigenicity in nude mice, were suppressed, whereas hybrid cells between E6/E7-transformed cell lines and normal rat cell lines retained these transformed phenotypes. RNA analysis showed that the E6 and E7 genes were transcribed in both types of hybrid cells. These results suggest that primary rat cells possess intracellular functions that cause posttranscriptional suppression of induction of the transformed phenotypes by the E6 and E7 genes of HPV-16.
Hierarchical decomposition of laparoscopic surgery: a human factors approach to investigating the operating room environment

Hierarchical decomposition of complex behaviour and systems is a valuable research methodology from human factors and information-processing psychology that can be applied to laparoscopic surgery. This article describes results of research on surgeons performing several different laparoscopic procedures, conducted in Vancouver, Canada 1995–98. Through top-down analyses of surgical procedures and bottom-up analyses of tool motions, results included detailed decomposition of the procedures through surgical steps, sub-steps, tasks, sub-tasks and tool motions. Analyses at all levels provided valuable information. In addition to specific surgeon- and technology-related observations, such as the effect of dividing the short gastrics on performance of Nissen fundoplication, gaze patterns of surgeons and factors related to patient safety were analysed. The hierarchical decomposition approach can be extended to other aspects of the complex system that consists of the surgeon and operating room team, the technologies and the operating room environment. Other frameworks for assessment are also considered.