Miracle-dz/UniFAR-FTUs huggingface dataset:
A Strategy for Rapid Quantification of Uncertainty in Reservoir Performance Prediction

This paper will describe a strategy for rapid quantification of uncertainty in reservoir performance prediction. The strategy is based on a combination of streamline and conventional finite difference simulators. Our uncertainty framework uses the Neighbourhood Approximation algorithm to generate an ensemble of history match models, and has been described previously. A speedup in generating the misfit surface is essential since effective quantification of uncertainty can require thousands of reservoir model runs. Our speedup strategy for quantifying uncertainty in performance prediction involves using an approximate streamline simulator to rapidly explore the parameter space to identify good history matching regions, and to generate an approximate misfit surface. We then switch to a conventional, finite difference simulator, and selectively explore the identified parameter space regions. This paper will show results from a parallel version of the Neighbourhood Approximation algorithm on a Linux cluster, demonstrating the advantages of perfect parallelism. We show how it is possible to sample from the posterior probability distribution both to assess accuracy of the approximate misfit surface, and also to generate automatic history match models.
Effects of flow and energy metabolism on injury and Rb+ uptake in pig hearts: An 87Rb and 31P NMR study

In this work the roles of coronary flow (CF) and metabolism in Rb+ (K+ congener) uptake were studied. In isolated pig hearts the left anterior descending artery (LAD) was cannulated to maintain adequate perfusion of the LAD bed. Rb+ loading was initiated and the LAD flow was either completely stopped (no flow (NF)) or reduced to 12% (low flow (LF)), or buffer was deoxygenated without change in flow (hypoxic flow (HYP)) for 2 h. CF through the LAD was then restored to normal, or perfusion was switched to oxygenated buffer. Serial 87Rb MR images or localized 31P spectra were acquired to compare the Rb+ uptake and energetics in the left ventricular (LV) anterior (ischemic/hypoxic) and posterior (normal) walls. End‐ischemic/hypoxic 87Rb signal intensities in the anterior wall were higher and the fluxes were greater in the HYP and LF groups than in the NF group. Phosphocreatine and ATP decreased less significantly and recovered better in the HYP and LF groups. Upon reperfusion/reoxygenation, the HYP and LF groups showed higher 87Rb signal intensities and smaller or no infarctions in the anterior wall compared to those in the NF group. Ischemia reduces Rb+ uptake due to both flow limitations and metabolic inhibition of cellular transport. 87Rb MRI has a potential for distinguishing necrotic and reversibly damaged tissue. Magn Reson Med 46:963–973, 2001. © 2001 Wiley‐Liss, Inc.
In Vitro Efficient Expansion of Tumor Cells Deriving from Different Types of Human Tumor Samples

Obtaining human tumor cell lines from fresh tumors is essential to advance our understanding of antitumor immune surveillance mechanisms and to develop new ex vivo strategies to generate an efficient anti-tumor response. The present study delineates a simple and rapid method for efficiently establishing primary cultures starting from tumor samples of different types, while maintaining the immuno-histochemical characteristics of the original tumor. We compared two different strategies to disaggregate tumor specimens. After short or long term in vitro expansion, cells analyzed for the presence of malignant cells demonstrated their neoplastic origin. Considering that tumor cells may be isolated in a closed system with high efficiency, we propose this methodology for the ex vivo expansion of tumor cells to be used to evaluate suitable new drugs or to generate tumor-specific cytotoxic T lymphocytes or vaccines.
Path confidence based lookahead prefetching

Designing prefetchers to maximize system performance often requires a delicate balance between coverage and accuracy. Achieving both high coverage and accuracy is particularly challenging in workloads with complex address patterns, which may require large amounts of history to accurately predict future addresses. This paper describes the Signature Path Prefetcher (SPP), which offers effective solutions for three classic challenges in prefetcher design. First, SPP uses a compressed history based scheme that accurately predicts complex address patterns. Second, unlike other history based algorithms, which miss out on many prefetching opportunities when address patterns make a transition between physical pages, SPP tracks complex patterns across physical page boundaries and continues prefetching as soon as they move to new pages. Finally, SPP uses the confidence it has in its predictions to adaptively throttle itself on a per-prefetch stream basis. In our analysis, we find that SPP improves performance by 27.2% over a no-prefetching baseline, and outperforms the state-of-the-art Best Offset prefetcher by 6.4%. SPP does this with minimal overhead, operating strictly in the physical address space, and without requiring any additional processor core state, such as the PC.
Condom failures in women presenting for abortion.

AIMS To document the main reasons for condom failure in women presenting for first trimester termination of pregnancy. METHODS From 1990-97 an audit was carried out, on the 3283 cases personally operated on by the author, using the information routinely obtained during pre-operative counselling. RESULTS Two sets of figures were obtained. The first (minimum figures) were restricted to those who used condoms on every occasion of coitus (746 or 22.7% of all women seen). The second (maximum figures) included all of these plus those who did not use condoms on every occasion or who used condoms in conjunction with another method (1494 or 45.5% of all women seen). In this expanded group, there was no obvious cause for the failure in 446 (29.9% of condom users). The main reason for failure was not using condoms every time (736 or 49.3% of condom failures). Leakage of semen occurred in 321 cases (21.5% of condom failures) and 104 of these had used emergency contraception which had also failed (7.0% of condom failures). Condoms failed more often in women under 25 years of age. CONCLUSIONS There is a need for better education on correct condom use and improved availability of emergency contraception. There is also a need for greater standardisation in reporting contraceptive failure.
Detection of Residents’ Abnormal Behaviour by Analysing Energy Consumption of Individual Households

As average life expectancy continuously rises, assisting the elderly population with living independently is of great importance. Detecting abnormal behaviour of the elderly living at home is one way to assist the eldercare systems with the increase of the elderly population. In this study, we perform an initial investigation to identify abnormal behaviour of household residents using energy consumption data. We conduct an experiment in two parts, the first to identify a suitable prediction algorithm to model energy consumption behaviour, and the second to detect abnormal behaviour. This approach allows for an initial step for the elderly care that has a low cost, is easily deployable, and is non-intrusive.
Computer-based drug-utilization review--risk, benefit, or boondoggle?

On October 28, 1990, with little debate, Congress passed the Omnibus Budget Reconciliation Act, requiring the states to provide claims-based drug-utilization review to approximately 34 million Medicaid enrollees.1,2 The provisions of the program were borrowed from the ill-fated Medicare Catastrophic Coverage Act of 1988, repealed in 1990; the stated goals were to reduce potentially inappropriate prescribing and dispensing of medications, enhance the counseling of patients, and reduce growth in expenditures for drugs.1 Drug-utilization review is a structured, ongoing program that interprets patterns of drug use in relation to predetermined criteria and attempts to prevent or minimize inappropriate prescribing.3, .
Specificity of the neutralizers as the cause of errors in evaluating disinfectant efficacy: an assessment of triclosan

One of the most commonly used methods for assessing disinfectants in vitro is the dilution‐neutralization test. Although it is known that using an effective neutralizer is essential for obtaining reliable results, in the case of disinfectants like triclosan, whose neutralization is more complicated, an adequate neutralizer is not always used. Here, we compare the efficacy of different neutralizers described previously, and others that have been modified, against several antiseptic formulations of triclosan. The strains of reference used were Pseudomonas aeruginosa, Enterococcus faecium, Staphylococcus aureus and Escherichia coli. The solutions of antiseptic were triclosan 2% aqueous solution, and three alcoholic solutions containing 2, 0·068 and 0·5% triclosan, respectively. In the dilution‐neutralization test, six neutralizers with different degrees of complexity were assayed. Our results show that the antiseptic solutions studied are effective against the strains of reference, with the exception of triclosan 2% aqueous solution against Ps. aeruginosa. Most neutralizers proved ineffective, depending on the antiseptic solution and the bacterial species, particularly in the case of Staph. aureus. These findings confirm a need to test every neutralizer specifically for each disinfectant, at the maximum concentration used, and for every specific bacterial strain.
Human Bocavirus in Very Young Infants Hospitalized with Acute Respiratory Infection in Northeast Brazil

Abstract A cross-sectional study was carried out over a period of 12 months to investigate the occurrence of human bocavirus (HBoV) infection in infants hospitalized for respiratory infections in a teaching hospital in Salvador, Brazil, and to describe the clinical manifestations of this infection. Nasopharyngeal aspirates were collected from the children and immunofluorescence and polymerase chain reaction were performed to investigate the presence of respiratory viruses. HBoV was detected in 4 out of 66 patients. Two of the HBoV-positive infants were co-infected with other viruses. The principal clinical findings in HBoV-positive children were: nasal obstruction, catarrh, cough, fever and dyspnea. This study revealed HBoV infection in children aged <2 months, suggesting that the infection may occur at a very early age.
Multivariate Non-Linear Feature Selection with Kernel Multiplicative Updates and Gram-Schmidt Relief

We address problems of classification in which the number of input components (variables, features) is very large compared to the number of training samples. In this setting, it is often desirable to perform a feature selection to reduce the number of inputs, either for efficiency, performance, or to gain understanding of the data and the classifiers. We compare a number of methods on mass-spectrometric data of human protein sera from asymptomatic patients and prostate cancer patients. We show empirical evidence that, in spite of the high danger of overfitting, non-linear methods can outperform linear methods, both in performance and number of features selected.
Production of New T Cells by Thymus in Children: Effect of HIV Infection and Antiretroviral Therapy

The decrease in the number of CD4+ T cells during HIV infection is the result of both peripheral destruction of cells by the virus and inadequate replacement of these cells. Aging and HIV infection lead to lower production of new T cells by the thymus, and, therefore, a complete restoration of the immune system is not generally achieved in infected adults after antiretroviral therapy. Because children have a completely functional thymus, we addressed the effects of HIV-1 infection on the production of new T cells in vertically infected children and whether the decrease of viral load after therapy results in a restoration of thymic function. To analyze the thymic function, T-cell receptor rearrangement excision circles were measured by quantitative PCR. Our results indicate that HIV-infected children have lower T-cell receptor rearrangement excision circle levels than age-matched uninfected children, likely due to an inhibitory effect of HIV on thymic function. Additionally, in some patients, the decrease in viral load after retroviral therapy allows the generation of new T cells by the thymus, thus recovering the normal number of CD4 cells.
A Novel Method for Protein Subcellular Localization Based on Boosting and Probabilistic Neural Network

Subcellular localization is a key functional characteristic of proteins. An automatic, reliable and efficient prediction system for protein subcellular localization is needed for large-scale genome analysis. In this paper, we introduce a novel subcellular prediction method combining boosting algorithm with probabilistic neural network algorithm. This new approach provided superior prediction performance compared with existing methods. The total prediction accuracy on Reinhardt and Hubbard's dataset reached up to 92.8% for prokaryotic protein sequences and 81.4% for eukaryotic protein sequences under 5-fold cross validation. On our new dataset, the total accuracy achieved 83.2%. This novel method provides superior prediction performance compared with existing algorithms based on amino acid composition and can be a complementing method to other existing methods based on sorting singals.
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis

MOTIVATION DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers using DNA fragments that are specific to individual open reading frames (ORFs). RESULTS PRIMEGENS first carries out a BLAST search for each target ORF against all other ORFs of the genome to quickly identify possible homologous sequences. Then it performs optimal sequence alignment between the target ORF and each of its homologous ORFs using dynamic programming. PRIMEGENS uses the sequence alignments to select gene- specific fragments, and then feeds the fragments to the Primer3 program to design primer pairs for PCR amplification. PRIMEGENS can be run from the command line on Unix/Linux platforms as a stand-alone package or it can be used from a Web interface. The program runs efficiently, and it takes a few seconds per sequence on a typical workstation. PCR primers specific to individual ORFs from Shewanella oneidensis MR-1 and Deinococcus radiodurans R1 have been designed. The PCR amplification results indicate that this method is very efficient and reliable for designing specific probes for microarray analysis.
Do psychological and physiological stressors alter the acute pain response to castration and tail docking in lambs?

OBJECTIVE To investigate whether events that may be stressful to young lambs, including simulated infection or social isolation, modulate pain experienced by lambs following castration and tail docking (C/D). STUDY DESIGN Randomised, controlled, prospective study. ANIMALS Fifty male lambs born to 46 second-parity Mule ewes. METHODS Lambs were allocated randomly to one of four groups, experiencing either a potential stressor or handling on day 2 after birth, followed by C/D or handling only on day 3. Quantitative sensory testing (QST) data [mechanical nociceptive thresholds (MNT), Semmes Weinstein filaments (SW), response to cold] and serum cortisol concentration were measured at time points after application of treatments to lambs on days 2 and 3 after birth. The treatment groups were LPS, injection of bacterial lipopolysaccharide IV on day 2, C/D on day 3; ISOL, isolation from the dam for 10 minutes on day 2, C/D on day 3; CAST, handling only on day 2, C/D on day 3; CONT, handled only on days 2 and 3. RESULTS Castration and tail docking caused transient hypoalgesia as measured by MNT and SW. Simulated infection and isolation caused hyperalgesia 3 hours after application, indicated by a reduction in MNT, however they did not alter the pain response to C/D compared to lambs in the CAST group. Injection of LPS and C/D caused increased serum cortisol concentration. The magnitude of the cortisol response to C/D was not altered by prior exposure to either LPS or isolation. CONCLUSIONS AND CLINICAL RELEVANCE LPS and isolation did not modulate the response to C/D but did cause hyperalgesia. This highlights the importance of flock health management and husbandry techniques to reduce the incidence of either systemic infection or psychological stressors in young lambs.
Clinical Relevance of VPAC1 Receptor Expression in Early Arthritis: Association with IL-6 and Disease Activity

Background The vasoactive intestinal peptide (VIP) receptors VPAC1 and VPAC2 mediate anti-inflammatory and immunoregulatory responses in rheumatoid arthritis (RA). Data on the expression of these receptors could complement clinical assessment in the management of RA. Our goal was to investigate the correlation between expression of both receptors and the 28-Joint Disease Activity Score (DAS28) in peripheral blood mononuclear cells (PBMCs) from patients with early arthritis (EA). We also measured expression of IL-6 to evaluate the association between VIP receptors and systemic inflammation. Methods We analyzed 250 blood samples collected at any of the 5 scheduled follow-up visits from 125 patients enrolled in the Princesa Early Arthritis Register Longitudinal study. Samples from 22 healthy donors were also analyzed. Sociodemographic, clinical, and therapeutic data were systematically recorded. mRNA expression levels were determined using real-time PCR. Then, longitudinal multivariate analyses were performed. Results PBMCs from EA patients showed significantly higher expression of VPAC2 receptors at baseline compared to healthy donors (p<0.001). With time, however, VPAC2 expression tended to be significantly lower while VPAC1 receptor expression increased in correlation with a reduction in DAS28 index. Our results reveal that more severe inflammation, based on high levels of IL-6, is associated with lower expression of VPAC1 (p<0.001) and conversely with increased expression of VPAC2 (p<0.001). A major finding of this study is that expression of VPAC1 is lower in patients with increased disease activity (p = 0.001), thus making it possible to differentiate between patients with various degrees of clinical disease activity. Conclusion Patients with more severe inflammation and higher disease activity show lower levels of VPAC1 expression, which is associated with patient-reported impairment. Therefore, VPAC1 is a biological marker in EA.
Development of a conservation-oriented precision agriculture system: Crop production assessment and plan implementation

From site-specific crop and soil information collected from a Missouri claypan soil field for over a decade (1993 to 2003), we implemented a precision agriculture system in 2004 with a goal of using site-specific management practices to improve farming profitability and conserve soil and water resources. The objectives of this study were to: 1) show how precision crop and soil information was used to assess productivity, and 2) document the development of the precision agriculture system plan for implementation on the field, relying on this productivity assessment and conservation opportunities. The study field was uniformly managed from 1991- 2003, during which time variability in soil and landscape parameters and yield were measured, and causes of yield variation were determined. Profitability maps were created from yield maps and production records. Because erosion has degraded the topsoil on shoulder and side slope positions of major portions of this field, corn-soybean management practices have rarely been profitable in these shallow topsoil areas. We prioritized these and other results, and developed the precision agriculture system plan. The plan, described in detail, is aimed at increasing profitability while improving water and soil quality.
Effectiveness of two Arthritis Foundation programs: Walk With Ease, and YOU Can Break the Pain Cycle

Objective: To evaluate the effectiveness of two Arthritis Foundation programs: Walk With Ease (WWE) and YOU Can Break The Pain Cycle (PC). Design: Quasi-experimental, repeated measures design. Retested at six weeks and four months. Setting: Community based intervention. Participants: Volunteer sample of 163 adults with arthritis recruited through mailings, newspapers, and flyers. Interventions: Subjects participated in a 90 minute seminar (PC, Group A), a six-week walking program (WWE, Group B), or both programs (Group C). Main outcome measures: Survey assessment of arthritis knowledge, general health, self-management activities, confidence, physical abilities, depression, health distress, and how arthritis affects their life. A Squat Test, a Six Minute Walk test, and a Timed Functional Walk Test were also administered. Results: Subjects in Group B were more confident, less depressed, had less health distress, and less pain than subjects in Group A. Scores of Group C were between Group A and B scores. Differences in groups over time indicated that the WWE resulted in increased confidence, physical abilities, time spent in self-management activities and decreased pain and fatigue. All groups increased in walking endurance at six weeks, and increased in health distress at four months. Conclusion: Subjects in different programs differed on impact of arthritis. These programs provide effective arthritis management opportunities.
Induction: Processes of Inference, Learning, and Discovery

Two psychologists, a computer scientist, and a philosopher have collaborated to present a framework for understanding processes of inductive reasoning and learning in organisms and machines. Theirs is the first major effort to bring the ideas of several disciplines to bear on a subject that has been a topic of investigation since the time of Socrates. The result is an integrated account that treats problem solving and induction in terms of rule-based mental models. Induction is included in the Computational Models of Cognition and Perception Series. A Bradford Book.
Hepatitis B virus X protein induces expression of alpha-fetoprotein and activates PI3K/mTOR signaling pathway in liver cells

The hepatitis B virus (HBV)-X protein (HBx) induces malignant transformation of liver cells, and elevated expression of alpha-fetoprotein (AFP) is a significant biomarker of hepatocarcinogenesis. However, the role of AFP in HBV-related hepatocarcinogenesis is unclear. In this study, we investigated the regulatory impact of AFP expression on HBx-mediated malignant transformation of human hepatocytes. We found that HBV induced the expression of AFP before that of oncogenes, e.g., Src, Ras and chemokine (C-X-C motif) receptor 4 (CXCR4), and AFP activated protein kinase B (AKT) and mammalian target of rapamycin (mTOR) in HBV-related HCC tissues and in human liver cells transfected with HBx. Cytoplasmic AFP interacted with and inhibited phosphatase and tensin homolog deleted on chromosome 10 (PTEN), activating the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway and promoting mTOR-mediated stimulation of the transcription factor hypoxia inducible factor-1α (HIF-1α), and therefore led to the activation of the promoters of Src, CXCR4, and Ras genes. On the contrary, reduced expression of AFP by siRNA resulted in the repression of p-mTOR, pAKT, Src, CXCR4, and Ras in human malignant liver cells. Taken together, for the first time our study indicates that HBx-induced AFP expression critically promote malignant transformation in liver cells through the activation of PI3K/mTOR signaling.