Miracle-dz/UniFAR-FTUs huggingface dataset:
Patients’ recollections of stressful experiences while receiving prolonged mechanical ventilation in an intensive care unit*

Objective To describe stressful experiences of adult patients who received mechanical ventilation for ≥48 hrs in an intensive care unit. Design Prospective cohort study. Setting Four intensive care units within an East Coast tertiary-care university medical center. Patients Patients were 150 adult intensive care unit patients receiving mechanical ventilation for ≥48 hrs. Intervention None. Measurements and Main Results As part of a study of the long-term outcomes of adult patients requiring prolonged mechanical ventilation, we used a 32-item questionnaire to collect data on patients’ stressful experiences, both psychological (e.g., fearfulness, anxiety) and physical (e.g., pain, difficulty breathing), associated with the mechanical ventilation endotracheal tube and with being in an intensive care unit.Of 554 patients who met study criteria and survived prolonged mechanical ventilation, 150 consented and were oriented to person, place, and situation. Two thirds of these patients remembered the endotracheal tube and/or being in an intensive care unit. The median numbers of endotracheal tube and intensive care unit experiences remembered were 3 (of 7) and 9 (of 22), respectively. If a patient remembered an experience in the questionnaire, it was likely to be moderately to extremely bothersome.Some of the items that many patients found to be moderately to extremely bothersome were pain, fear, anxiety, lack of sleep, feeling tense, inability to speak/communicate, lack of control, nightmares, and loneliness. Stressful experiences associated with the endotracheal tube were strongly associated with subjects’ experiencing spells of terror, feeling nervous when left alone, and poor sleeping patterns. Conclusions Subjects were more likely to remember experiences that were moderately to extremely bothersome. This might be because the more bothersome experiences were easier to recall or because most of these experiences are common and significant stressors to many of these patients. In either case, these data indicate that these patients are subject to numerous stressful experiences, which many find quite bothersome. This suggests the potential for improved symptom management, which could contribute to a less stressful intensive care unit stay and improved patient outcomes.
Carcinogenic bacterial pathogen Helicobacter pylori triggers DNA double-strand breaks and a DNA damage response in its host cells

The bacterial pathogen Helicobacter pylori chronically infects the human gastric mucosa and is the leading risk factor for the development of gastric cancer. The molecular mechanisms of H. pylori-associated gastric carcinogenesis remain ill defined. In this study, we examined the possibility that H. pylori directly compromises the genomic integrity of its host cells. We provide evidence that the infection introduces DNA double-strand breaks (DSBs) in primary and transformed murine and human epithelial and mesenchymal cells. The induction of DSBs depends on the direct contact of live bacteria with mammalian cells. The infection-associated DNA damage is evident upon separation of nuclear DNA by pulse field gel electrophoresis and by high-magnification microscopy of metaphase chromosomes. Bacterial adhesion (e.g., via blood group antigen-binding adhesin) is required to induce DSBs; in contrast, the H. pylori virulence factors vacuolating cytotoxin A, γ-glutamyl transpeptidase, and the cytotoxin-associated gene (Cag) pathogenicity island are dispensable for DSB induction. The DNA discontinuities trigger a damage-signaling and repair response involving the sequential ataxia telangiectasia mutated (ATM)-dependent recruitment of repair factors—p53-binding protein (53BP1) and mediator of DNA damage checkpoint protein 1 (MDC1)—and histone H2A variant X (H2AX) phosphorylation. Although most breaks are repaired efficiently upon termination of the infection, we observe that prolonged active infection leads to saturation of cellular repair capabilities. In summary, we conclude that DNA damage followed by potentially imprecise repair is consistent with the carcinogenic properties of H. pylori and with its mutagenic properties in vitro and in vivo and may contribute to the genetic instability and frequent chromosomal aberrations that are a hallmark of gastric cancer.
How to estimate scavenger fish abundance using baited camera data

Baited cameras are often used for abundance estimation wherever alternative techniques are precluded, e.g. in abyssal systems and areas such as reefs. This method has thus far used models of the arrival process that are deterministic and, therefore, permit no estimate of precision. Furthermore, errors due to multiple counting of fish and missing those not seen by the camera have restricted the technique to using only the time of first arrival, leaving a lot of data redundant. Here, we reformulate the arrival process using a stochastic model, which allows the precision of abundance estimates to be quantified. Assuming a non-gregarious, cross-current-scavenging fish, we show that prediction of abundance from first arrival time is extremely uncertain. Using example data, we show that simple regression-based prediction from the initial (rising) slope of numbers at the bait gives good precision, accepting certain assumptions. The most precise abundance estimates were obtained by including the declining phase of the time series, using a simple model of departures, and taking account of scavengers beyond the camera’s view, using a hidden Markov model.
Government Employment Expenditure and the Effects of Fiscal Policy Shocks

Since World War II, about 75 percent of consumption expenditure by the U.S. government has consisted of wages and salaries for government employees. I distinguish between the goods and the employment expenditure components of government consumption in assessing the effects of fiscal shocks on the macroeconomy. Identifying exogenous fiscal shocks with the onset of military buildups, I show that they lead to a substantial increase in both the number of hours worked and output for the government. I also show that allowing for the distinction between the two main components of government consumption improves the quantitative performance of the neoclassical growth model. In particular, a neoclassical model economy with government employment does a good job of accounting for the dynamic response of private consumption to a fiscal policy shock. Government employment expenditure acts as a transfer payment for households, thereby dampening substantially the wealth effect on consumption and labor supply associated with fiscal shocks. keywords: Government employment; Fiscal policy jel classification codes: E20; E24; E32; E62; H30 I thank Mark Gertler, Fabrizio Perri and Nouriel Roubini for advice, Silvia Ardagna for her thoughtful discussion, Charlie Gilbert for help with data, Judith Goff and Anita Todd for editorial assistance, Gregory Snyders and Thien Nguyen for excellent research assistance, and seminar participants at Bank of England, Erasmus Universiteit, Federal Reserve Bank of Boston, Federal Reserve Bank of San Francisco, Federal Reserve Board, New York University, Sveriges Riksbank, University of British Columbia, University of Maryland, SED 2003 Annual Meeting, and at 2005 North American Winter Meeting of the Econometric Society for useful comments. I also benefited from helpful conversations with Shaghil Ahmed, Stefania Albanesi, George Alessandria, Pierpaolo Benigno, David Bowman, Xiaohong Chen, Martin Eichenbaum, Stefano Eusepi, Jon Faust, John Fernald, Michael Feroli, Jonas Fisher, Charles Fleischman, Jeffrey Fuhrer, Jordi Gaĺı, Dale Henderson, Òscar Jordà, Boyan Jovanovic, Andy Levin, Sydney Ludvigson, Fabio Natalucci, Giorgio Primiceri, Vincenzo Quadrini, Pau Rabanal, John Rogers, Daniele Terlizzese, Bharat Trehan, Gianluca Violante, Karl Wheelan, and John Williams. I started this project during my internship in the Division of International Finance at the Federal Reserve Board. I owe my gratitude to its members for their stimulating hospitality. All remaining errors are my own. The views in this paper are solely my responsibility and should not be interpreted as reflecting the views of the Federal Reserve Bank of San Francisco, or the Federal Reserve System.
Perceived Benefits in Trauma Research: Examining Methodological and Individual Difference Factors in Responses to Research Participation

This study examined methodological and individual difference factors in relation to perceived benefits and cost-benefit ratios among adult participants in trauma-related research. In two samples (N's = 72 and 118), ethnically-diverse community participants completed trauma-related questionnaires plus an in-depth interview. In separate community (N = 213) and undergraduate (N = 130) samples, participants completed trauma-related questionnaires, but no interviews. Participants rated their perceptions of the research process using the Response to Research Participation Questionnaire (RRPQ). Cost-benefit ratios were favorable in all samples. The research procedures (questionnaires only versus questionnaires plus interviews) explained unique variance in RRPQ scale scores and cost-benefit ratios, as did trauma-related distress. Implications of these findings for developing trauma research protocols are discussed.
Gene Therapy for the Management of Pain: Part II: Molecular Targets

TREATMENT of chronic pain, particularly of neuropathic etiology, is extremely difficult and resistant to many available pharmacologic therapies. Current analgesic agents may be limited with regard to analgesic efficacy or side effects. Newer and experimental pharmacologic agents may also have significant limitations. By targeting a specific receptor or other specific protein targets, a gene therapy approach to the treatment of pain may provide greater analgesic efficacy without the limitations associated with current pharmacotherapy. Advances in the field of gene therapy, along with significant increases in our understanding of the neurobiology of nociception and knowledge of the fundamental genetic structure of many nociceptive targets, have made gene therapy for the management of pain a conceivable reality. In part I of this review, we introduced the basic concepts of gene therapy with an emphasis on the available tools (e.g., viral vectors and antisense oligonucleotides) and strategies for upregulating antinociceptive or downregulating pronociceptive targets. In part II, we summarize current knowledge regarding the nociceptive role, molecular biology, and antisense and knockout data of several novel nociceptive targets for gene therapy. We base our selection of the targets included in this review on the three aforementioned criteria. The targets selected are the best characterized and, in our opinion, most likely amenable to the gene therapeutic approach. A simple but feasible strategy and potential gene therapy targets for the management of pain are summarized in figure 1. However, the list is admittedly incomplete, and the readers are referred to other recent reviews cited in part I of this review for a broader perspective on potential targets for the management of pain.
Modulation of Lipid Metabolism and Spiramycin Biosynthesis in Streptomyces ambofaciens Unstable Mutants

ABSTRACT Streptomyces ambofaciens is prone to genetic instability involving genomic rearrangements at the extremities of the chromosomal DNA. An amplified DNA sequence (ADS205), including an open reading frame (orfPS), is responsible for the reversible loss of spiramycin production in the mutant strain NSA205 (ADS205+ Spi−). The product oforfPS is homologous to polyketide synthase systems (PKSs) involved in the biosynthesis of erythromycin and rapamycin and is overexpressed in strain NSA205 compared with the parental strain RP181110. As PKSs and fatty acid synthase systems have the same precursors, we tested the possibility that overexpression oforfPS also affects lipid metabolism in strain NSA205. This report focuses on comparative analysis of lipids in strain RP181110, the mutant strain NSA205, and a derivative, NSA228 (ADS205− Spi+). NSA205 showed a dramatically depressed lipid content consisting predominantly of phospholipids and triacylglycerols. This lipid content was globally restored in strain NSA228, which had lost ADS205. Furthermore, strains RP181110 and NSA205 presented similar phospholipid and triacylglycerol compositions. No abnormal fatty acids were detected in NSA205.
Usability Evaluation of NLP-PIER: A Clinical Document Search Engine for Researchers

NLP-PIER (Natural Language Processing – Patient Information Extraction for Research) is a self-service platform with a search engine for clinical researchers to perform natural language processing (NLP) queries using clinical notes. We conducted user-centered testing of NLP-PIER’s usability to inform future design decisions. Quantitative and qualitative data were analyzed. Our findings will be used to improve the usability of NLP-PIER.
Prospective study of prostate tumor angiogenesis and cancer-specific mortality in the health professionals follow-up study.

PURPOSE Tumor growth requires the development of independent vascular networks that are often primitive in morphology and function. We examined whether microvessel morphology contributes to the considerable biologic heterogeneity of prostate cancer. METHODS We evaluated microvessel morphology as a predictor of prostate cancer mortality among 572 men in the Health Professionals Follow-Up Study diagnosed with cancer during 1986 to 2000. We immunostained prostatectomy tumor block sections for endothelial marker CD34 and assessed microvessel density, vessel size (area and diameter), and irregularity of vessel lumen using image analysis. Proportional hazards models were used to assess microvessel density and morphology in relation to lethal prostate cancer. RESULTS Poorly differentiated tumors exhibited greater microvessel density, greater irregularity of the vessel lumen, and smaller vessels. During 20 years of follow-up, 44 men developed bone metastases or died of cancer. Men with tumors exhibiting the smallest vessel diameter, based on quartiles, were 6.0 times more likely (95% CI, 1.8 to 20.0) to develop lethal prostate cancer. Men with the most irregularly shaped vessels were 17.1 times more likely (95% CI, 2.3 to 128) to develop lethal disease. Adjusting for Gleason grade and prostate-specific antigen levels did not qualitatively change the results. Microvessel density was not linked to cancer-specific mortality after adjusting for clinical factors. CONCLUSION Aggressive tumors form vessels that are primitive in morphology and function, with consequences for metastases. Vascular size and irregularity reflect the angiogenic potential of prostate cancer and may serve as biomarkers to predict prostate cancer mortality several years after diagnosis.
Perceptually-Informed Accelerated Rendering of High Quality Walkthrough Sequences

In this paper, we consider accelerated rendering of walkthrough animation sequences using combination of ray tracing and Image-Based Rendering (IBR) techniques. Our goal is to derive as many pixels as possible using inexpensive IBR techniques without affecting the animation quality. A perception-based spatio-temporal Animation Quality Metric (AQM) is used to automatically guide such a hybrid rendering. The Pixel Flow (PF) obtained as a by-product of the IBR computation is an integral part of the AQM. The final animation quality is enhanced by an efficient spatio-temporal antialiasing, which utilize the PF to perform a motion-compensated filtering.
Multi-Frequency Constrained SAR Focusing for Patient Specific Hyperthermia Treatment

In hyperthermia treatments, the possibility of generating a specific absorption rate distribution peaked into the tumor and bounded elsewhere represents the main clinical need. As multi-frequency applicators can be exploited to reduce the occurrence of undesired hot-spots, an optimal multi-frequency approach is proposed and discussed. Being formulated in terms of a convex programming problem, the globally optimal solution can be determined (only for very special cases). The procedure, presented for the case of scalar fields, can be extended both to the case of vector fields and to the more interesting problem of shaping (rather than just focusing) the specific absorption rate distribution.
EKG Criteria for Fibrinolysis: What’s Up with the J Point?

The exact location of the J point, as well as its use for determining STE is open to some debate. Even the exact place to measure ST segment elevation for fibrinolytics is a point of contention, as is the degree of ST segment elevation that warrants consideration of fibrinolytic therapy. Interpreting ST segment elevation must be made in the context of the clinical setting. Like any test, the pre-test probability of the disease (myocardial infarction in this case) is essential in interpreting the results of the test (degree, type and amount of ST segment elevation).
Quantitative measurement of telomerase reverse transcriptase (hTERT) mRNA in urothelial cell carcinomas

Telomerase reverse transcriptase (hTERT) messenger RNA has been detected in 95% of bladder tumors using RT‐PCR. In this study, we quantified the expression of hTERT in 35 bladder urothelial cell carcinomas and in 6 normal bladder epithelia using a real‐time quantitative PCR assay. hTERT expression was detected in all 35 urothelial cell carcinomas of varying grade and stage, but not in normal tissue samples. An increase in both pathological grade and clinical stage as prognostic parameters correlated with increased hTERT expression. Using different cutoff values for grades and stages, normalized hTERT expression values could discriminate among low, medium, and high grade tumors and between superficial and muscle‐invasive tumors. We conclude that standardized real‐time measurement of hTERT expression can be used for early tumor detection and may be used for determination of prognosis in urothelial cell carcinomas of the bladder. Int. J. Cancer 87:217–220, 2000. © 2000 Wiley‐Liss, Inc.
TRIBUTE: a phase III trial of erlotinib hydrochloride (OSI-774) combined with carboplatin and paclitaxel chemotherapy in advanced non-small-cell lung cancer.

PURPOSE Erlotinib is a potent reversible HER1/epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor with single-agent activity in patients with non-small-cell lung cancer (NSCLC). Erlotinib was combined with chemotherapy to determine if it could improve the outcome of patients with NSCLC. PATIENTS AND METHODS TRIBUTE randomly assigned patients with good performance status and previously untreated advanced (stage IIIB/IV) NSCLC to erlotinib 150 mg/d or placebo combined with up to six cycles of carboplatin and paclitaxel, followed by maintenance monotherapy with erlotinib. Random assignment was stratified by stage, weight loss in the previous 6 months, measurable disease, and treatment center. The primary end point was overall survival (OS). Secondary end points included time to progression (TTP), objective response (OR), and duration of response. RESULTS There were 1,059 assessable patients (526 erlotinib; 533 placebo). Median survival for patients treated with erlotinib was 10.6 v 10.5 months for placebo (hazard ratio, 0.99; 95% CI, 0.86 to 1.16; P = .95). There was no difference in OR or median TTP. Patients who reported never smoking (72 erlotinib; 44 placebo) experienced improved OS in the erlotinib arm (22.5 v 10.1 months for placebo), though no other prespecified factors showed an advantage in OS with erlotinib. Erlotinib and placebo arms were equivalent in adverse events (except rash and diarrhea). CONCLUSION Erlotinib with concurrent carboplatin and paclitaxel did not confer a survival advantage over carboplatin and paclitaxel alone in patients with previously untreated advanced NSCLC. Never smokers treated with erlotinib and chemotherapy seemed to experience an improvement in survival and will undergo further investigation in future randomized trials.
Estimating the Sea State Bias of Jason-2 Altimeter From Crossover Differences by Using a Three-Dimensional Nonparametric Model

With a standard deviation as large as 2 cm, the sea state bias (SSB) has become the dominant source of error in satellite altimetry. The operational SSB correction models are two-dimensional (2-D) empirical (parametric or nonparametric) models based on the altimeter-measured wind speed (U) and significant wave height (SWH). However, these 2-D SSB models cannot entirely parameterize the range bias variability. The SSB uncertainty may be lowered through improved SSB models including additional measurable or predictable correlatives. This paper presents a method to estimate the SSB from crossover differences by using a three-dimensional (3-D) nonparametric model. The model is based on U, SWH from Jason-2 altimeter ocean observations, and the mean wave period from the European Centre for Medium-Range Weather Forecasts reanalysis project ERA-Interim (The SSB model developed with the method presented in this paper is called “3-D SSB model” and the SSB estimated with the 3-D SSB model is called “3-D SSB estimate”). Simulations indicate that the wave period can greatly affect the SSB. Evaluated by the separate annual datasets from 2009 to 2011, the 3-D SSB estimates can increase the explained variance by 1.32 cm2, or 1.15-cm RMS relative to the traditional 2-D SSB estimates based on U and SWH. Spatial evaluation of improvement shows that the 3-D SSB estimates are better than the traditional 2-D SSB estimates at all latitudes. The enhancement from 2-D to 3-D SSB estimates is of great significance to improve the precision of the altimeter product. [COMP]: Please set math TYPE gin the sentence below (40) as per the authors PDF.
Improving a Particle Swarm Optimization model to solve assignment problems in an industrial environment

The use of the Particle Swarm Optimization (PSO) model in workload problems resolution is discussed in this article. This kind of problems are usually resolved by a linear programming model, however, as the amount of assignments and machines grow, the workload problem becomes a complex issue, bigger than what a linear programming model can handle. PSO changes the values of the particle’s speed and inertia weight to move the swarm along the solution search space. This research proposes the substitution of the classical uniform distribution to initialize the velocity of the particle with the beta distribution. Comparing both models, the results demonstrate statistical equivalences between the convergence values found by both models, however, it is shown how the amount of iterations required to reach the optimal value is lower when using the beta distribution. This paper shows how the proposed model decreases the number of iterations needed to reach a heuristic solution with a coefficient of variation of 84% and a central tendency of 21. Future research lines can include implementing this approach in a more complex model; studying the initialization of the velocity with other probability distributions, and using crossover operators to generate offspring.