Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of Barium-Based Fecal Tagging for CT Colonography: a Comparison between the Use of High and Low Density Barium Suspensions in a Korean Population - a Preliminary Study

Objective This preliminarily study was designed to determine and to compare the efficacy of two commercially available barium-based fecal tagging agents for CT colonography (CTC) (high-density [40% w/v] and low-density [4.6% w/v] barium suspensions) in a population in Korea. Materials and Methods In a population with an identified with an average-risk for colorectal cancer, 15 adults were administered three doses of 20 ml 40% w/v barium for fecal tagging (group I) and 15 adults were administered three doses of 200 ml 4.6% w/v barium (group II) for fecal tagging. Excluding five patients in group I and one patient in group II that left the study, ten patients in group I and 14 patients in group II were finally included in the analysis. Two experienced readers evaluated the CTC images in consensus regarding the degree of tagging of stool pieces 6 mm or larger. Stool pieces were confirmed with the use of standardized CTC criteria or the absence of matched lesions as seen on colonoscopy. The rates of complete fecal tagging were analyzed on a per-lesion and a per-segment basis and were compared between the patients in the two groups. Results Per-lesion rates of complete fecal tagging were 52% (22 of 42; 95% CI, 37.7-66.6%) in group I and 78% (28 of 36; 95% CI, 61.7-88.5%) in group II. The difference between the two groups did not reach statistical significance (p = 0.285). The per-segment rates of complete tagging were 33% (6 of 18; 95% CI, 16.1%-56.4%) in group I and 60% (9 of 15; 95% CI, 35.7%-80.3%) in group II; again, the difference between the two groups did not reach statistical significance (p = 0.171). Conclusion Barium-based fecal tagging using both the 40% w/v and the 4.6% w/v barium suspensions showed moderate tagging efficacy. The preliminary comparison did not demonstrate a statistically significant difference in the tagging efficacy between the use of the two tagging agents, despite the tendency toward better tagging with the use of the 4.6% w/v barium suspension.
Prospective Analysis of Traffic Exposure as a Risk Factor for Incident Coronary Heart Disease: The Atherosclerosis Risk in Communities (ARIC) Study

Background For people living close to busy roads, traffic is a major source of air pollution. Few prospective data have been published on the effects of long-term exposure to traffic on the incidence of coronary heart disease (CHD). Objectives In this article, we examined the association between long-term traffic exposure and incidence of fatal and nonfatal CHD in a population-based prospective cohort study. Methods We studied 13,309 middle-age men and women in the Atherosclerosis Risk in Communities study, without previous CHD at enrollment, from 1987 to 1989 in four U.S. communities. Geographic information system–mapped traffic density and distance to major roads served as measures of traffic exposure. We examined the association between traffic exposure and incident CHD using proportional hazards regression models, with adjustment for background air pollution and a wide range of individual cardiovascular risk factors. Results Over an average of 13 years of follow-up, 976 subjects developed CHD. Relative to those in the lowest quartile of traffic density, the adjusted hazard ratio (HR) in the highest quartile was 1.32 [95% confidence interval (CI), 1.06–1.65; p-value for trend across quartiles = 0.042]. When we treated traffic density as a continuous variable, the adjusted HR per one unit increase of log-transformed density was 1.03 (95% CI, 1.01–1.05; p = 0.006). For residents living within 300 m of major roads compared with those living farther away, the adjusted HR was 1.12 (95% CI, 0.95–1.32; p = 0.189). We found little evidence of effect modification for sex, smoking status, obesity, low-density lipoprotein cholesterol level, hypertension, age, or education. Conclusion Higher long-term exposure to traffic is associated with incidence of CHD, independent of other risk factors. These prospective data support an effect of traffic-related air pollution on the development of CHD in middle-age persons.
A distributed auction algorithm for the assignment problem

The assignment problem constitutes one of the fundamental problems in the context of linear programming. Besides its theoretical significance, its frequent appearance in the areas of distributed control and facility allocation, where the problems¿ size and the cost for global computation and information can be highly prohibitive, gives rise to the need for local solutions that dynamically assign distinct agents to distinct tasks, while maximizing the total assignment benefit. In this paper, we consider the linear assignment problem in the context of networked systems, where the main challenge is dealing with the lack of global information due to the limited communication capabilities of the agents. We address this challenge by means of a distributed auction algorithm, where the agents are able to bid for the task to which they wish to be assigned. The desired assignment relies on an appropriate selection of bids that determine the prices of the tasks and render them more or less attractive for the agents to bid for. Up to date pricing information, necessary for accurate bidding, can be obtained in a multi-hop fashion by means of local communication between adjacent agents. Our algorithm is an extension to the parallel auction algorithm proposed by Bertsekas et al to the case where only local information is available and it is shown to always converge to an assignment that maximizes the total assignment benefit within a linear approximation of the optimal one.
Closing the Loop for Edge Detection and Object Proposals

Edge grouping and object perception are unified procedures in perceptual organization. However the computer vision literature classifies them as independent tasks. In this paper, we argue that edge detection and object proposals should benefit one another. To achieve this, we go beyond bounding boxes and extract closed contours that represent potential objects within. A novel objectness metric is proposed to score and rank the proposal boxes by considering the sizes and edge intensities of the closed contours. To improve the edge detector given the top-down object proposals, we group local closed contours and construct global object hierarchies and segmentations. The edge detector is retrained and enhanced using these hierarchical segmentations as additional feature channels. In the experiments we show that by closing the loop for edge detection and object proposals, we observe improvements for both tasks. Unifying edges and object proposals is valid and useful.
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task—a result that approaches the human inter-annotator agreement (0.8875)—and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system’s ability to return real-time results: the average response time for each team’s DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction. Database URL: http://www.biocreative. org/tasks/biocreative-v/track-3-cdr/
NSOM the fourth dimension: Integrating nanometric spatial and femtosecond time resolution

Photonic devices are becoming the cornerstone of next generation systems for computing and information processing. This paper reports on the first steps in the development of methods to understand these devices with nanometric (10−7 cm) spatial and femtosecond (10−15 s) time resolution. The basis of this achievement is the dramatic developments that have occurred in the past few years in a new area of optics called near-field optics. Near-field optics is a form of lensless optics with a resolution that is subwavelength and which is independent of the wavelength of the light being employed. We report in this paper the transmission of pulses with tens of femtosecond duration through subwavelength, near-field optical elements. We also report on a femtosecond near-field optical light source with cross-correlating capabilities and on the growth of GaAs in the tip of micropipettes for use as an ultra-fast electro-optical switch which can cross-correlate optical, electrical, and electro-optical effects. These developments are especially relevant in the investigation of photonic devices since such devices can alter their characteristics as a function of size in the mesoscopic regime from just below lens-based optical resolutions to dimensions that approach atomic scales of ∼1 nm (10−7 cm). In view of the fact that these devices and the processes that govern them also exhibit ultrafast speeds, the combination of state of the art femtosecond laser spectroscopy with the unique features of near-field optics is a critical step in advancing our next generation understandings of such materials and structures so that their full potential in information processing can be achieved.
Systemic therapy for unresectable, mixed hepatocellular-cholangiocarcinoma: treatment of a rare malignancy.

BACKGROUND Combined hepatocellular-cholangiocarcinoma (HCC-CC) has a reported incidence of less than 5% of primary hepatic malignancies. The treatment approach to this malignancy is undefined. Our objective of this case series is to provide some insight into chemotherapy and/or targeted therapy in this setting. METHODS Pathologic and radiographic review confirmed seven combined HCC-CC patients during a 5-year time frame [2009-2014]. Data points were demographics, chemotherapy and/or targeted therapy given in the first and second-line setting, localized treatment if given, first radiographic result, progression-free survival (PFS), and overall survival (OS). RESULTS Seven patients were identified. Front-line treatment showed a median PFS of 3.4 months. Total median OS was 8.3 months. Regimens given included gemcitabine alone +/- bevacizumab, gemcitabine + platinum (GP) +/- bevacizumab, and sorafenib. Front-line treatment with these regimens showed progressive disease in 71% (5 patients) on first radiographic scan with all patients who received sorafenib front-line progressing at that restaging. Disease-control (complete response + partial response + stable disease) was seen in 29% of patients (2 patients) with 1 patient receiving GP and 1 patient receiving gemcitabine + bevacizumab. Of note, 2 patients that received GP +/- bevacizumab in the second-line setting had disease control on first radiographic scan. CONCLUSIONS Our retrospective review speaks to the rarity of this malignancy and challenges that are associated with its diagnosis and treatment. GP +/- bevacizumab showed disease control in first or second-line treatment in 3 patients. Treatment with this regimen in this rare malignancy subgroup warrants further investigation.
Biology of human papillomaviruses

Human papillomaviruses (HPVs) cause squamous cancers of epithelial surfaces, of which genital cancers are the most common. In this article we have attempted to describe the properties and functions of the viral proteins of HPV type 16, a common cause of genital cancers, and have tried to suggest how their expression may lead to a dysregulated cell which may become malignant. These viruses are attempting to replicate in terminally differentiating keratinocytes and must stimulate G1 to S‐phase progression for the replication of their genome. As part of the successful completion of replication and assembly of infectious virus particles, the virus needs at least partial differentiation to occur. Therefore, at the same time as differentiation is occurring, the nuclei of infected cells are in S‐phase. While the mechanisms of action of the viral proteins are not completely understood, researchers are making progress and this article strives to bring together the conclusions from some of this work.
Nanotextured super-hydrophobic transparent poly(methyl methacrylate) surfaces using high-density plasma processing

We present an environmentally friendly, rapid, no-rinse and mass-production amenable plasma process for the fabrication of super-hydrophobic (SH) poly(methyl methacrylate) (PMMA) surfaces using only a one load/unload step in a low-pressure, high-density plasma reactor. First, oxygen plasma is applied to nanotexture the PMMA surface via etching processes leading to high aspect ratio (HAR) topography, with dual-roughness characteristics for short process durations, as evidenced by AFM analysis. The duration of the process may range from 1 min to several min depending on the roughness amplitude and on the degree of transparency desired. The significance of the ion-bombardment is revealed and discussed. After this first step, the gas chemistry is changed to a fluorocarbon one which leads to a few nanometres-thick Teflon-like film deposition, thus altering the PMMA surface chemistry within a few seconds. Following this process, a very large area (depending on the reactor scale) of the PMMA may become SH in less than 1.5 min (total process duration) with a transparency as desired (from fully transparent to milky and antireflective). The contact angles (CA) measured are approximately 152° with 5° hysteresis. For short process durations, the dual-roughness character of PMMA surfaces favours the SH formation, despite the low roughness factor. Furthermore, the dry and low-temperature character of the process ensures the intactness of PMMA’s shape and bulk mechanical properties.
Decreased Blood Flow with Increased Metabolic Activity: A Novel Sign of Pancreatic Tumor Aggressiveness

Purpose: To study blood flow (BF) and metabolism in normal pancreas and in different pancreatic lesions. We then determined the effect of these biomarkers on outcome in patients with pancreatic cancer. Experimental Design: Oxygen-15–labeled water and fluorodeoxyglucose positron emission tomography/computed tomography scans were used in 26 patients with a suspicion of pancreatic cancer to measure pancreatic BF and metabolism. In addition, the ratio of standardized uptake value to BF (SUV/BF) was calculated. Patients were divided into three groups: patients with a finding of normal pancreas (n = 7), benign lesions (n = 8), and malignant tumors (n = 11). Results: Patients with benign and malignant pancreatic tumors had decreased BF of the lesion by 48% and 60%, respectively, compared with patients with normal pancreatic tissue. SUVmax was 3-fold higher in malignant tumors compared with both benign lesions and normal pancreas (P < 0.05). In contrast, the SUVmax of patients with benign lesions and normal pancreas did not differ. The SUV/BF ratio was significantly higher in malignant lesions than in benign lesions or in patients with normal pancreas (P < 0.05). In patients with cancer, high SUV/BF ratio was a stronger predictor of poor survival compared with high metabolism or lower-than-normal pancreatic BF. Conclusions: BF in pancreatic cancer is significantly reduced compared with the normal pancreas, which may in part explain the poor success of both radiotherapy and chemotherapy. We suggest that the composite measurement of BF and metabolism in pancreatic cancer could serve as a novel tool in the planning of treatments targeting vasculature. (Clin Cancer Res 2009;15(17):5511–7)
Benefits, Adoption Barriers and Myths of Open Data and Open Government

In this article, based on data collected through interviews and a workshop, the benefits and adoption barriers for open data have been derived. The results suggest that a conceptually simplistic view is often adopted with regard to open data, which automatically correlates the publicizing of data with use and benefits. Also, five “myths” concerning open data are presented, which place the expectations within a realistic perspective. Further, the recommendation is provided that such projects should take a user's view.
Simulation-based distributed fuzzy control for WIP in a multi-variety and small-batch discrete production system with one tightly coupled cell

This paper examines a multi-variety and small-batch production system with a tightly coupled cell. Using production data analysis, various random factors and constraints in a system with a tightly coupled bottleneck cell caused higher work-in-process (WIP) inventory levels and longer cycle times. Aiming to resolve these production problems, a two-dimensional distributed fuzzy controller with two correction factors has been developed. This heuristic approach is used to supervise the dynamic WIP inventory level changes and regulate the processing rate of each workstation with simple representations and linguistic IF-THEN rules. Based on consideration of certain major stochastic factors, a simulation model is explored with a control objective to maintain the WIP and cycle time at a low level. Simulation results show that this optimized control policy avoids system imbalances and eliminates bottlenecks. By comparison, the proposed approach significantly improves the system's performance and robustness.
NSP 5a3a: A Potential Novel Cancer Target in Head and Neck Carcinoma

NSP 5a3a along with three other distinct though similar splice variants were initially identified corresponding to locus HCMOGT-1 on chromosome 17p11.2 [1]. Secondary structure analysis of the novel structural protein (NSP) isoforms revealed similarity to Spectrin like proteins containing coiled coil domains [1]. The NSP 5a3a isoform had been found to be highly expressed in-vitro in particular cancer cell lines while very low to un-detectable levels in normal body tissues [1]. Subsequent investigation of this isoform revealed its novel interaction with B23 [2], a multifunctional nucleolar protein involved in ribosome biogenesis, rRNA transcription, mitosis, cell growth control, and apoptosis [3]. Subsequent investigation, elucidated NSP 5a3a's potential involvement in cellular processes such as ribosome biogenesis and rRNA processing by validating NSP 5a3a's novel interaction with B23 and ribonuclear protein hnRNP-L possibly implicating NSP 5a3a's involvement in cellular activities such as RNA metabolism and processing [4]. In this preliminary investigation, we wanted to observe the effect that over-expressing NSP 5a3a may have on cell cycle and its potential application in cancer treatment in aggressive cancers such as head and neck carcinomas. Over-expressed NSP 5a3a in HN30 cells induced a significant degree of apoptosis, an average of a 10.85 fold increase compared to controls 3 days post-transfection. This effect was more significant then the apoptosis observed between Fadu cells over-expressing NSP 5a3a and its controls. Though, the apoptosis induced in the WI38 control cell line showed an average of a 13.2 fold increase between treated and controls comparable to the HN30 cell line 3 days post-transfection. Molecular analysis indentified a novel p73 dependent mechanism independent of p53 and caspase 3 activity through which NSP 5a3a is inducing apoptosis. We propose NSP 5a3a as a potential therapeutic target for site directed cancer treatment in perhaps certain head and neck carcinomas by induction of apoptosis.
MOMMOP: Multiobjective Optimization for Locating Multiple Optimal Solutions of Multimodal Optimization Problems

In the field of evolutionary computation, there has been a growing interest in applying evolutionary algorithms to solve multimodal optimization problems (MMOPs). Due to the fact that an MMOP involves multiple optimal solutions, many niching methods have been suggested and incorporated into evolutionary algorithms for locating such optimal solutions in a single run. In this paper, we propose a novel transformation technique based on multiobjective optimization for MMOPs, called MOMMOP. MOMMOP transforms an MMOP into a multiobjective optimization problem with two conflicting objectives. After the above transformation, all the optimal solutions of an MMOP become the Pareto optimal solutions of the transformed problem. Thus, multiobjective evolutionary algorithms can be readily applied to find a set of representative Pareto optimal solutions of the transformed problem, and as a result, multiple optimal solutions of the original MMOP could also be simultaneously located in a single run. In principle, MOMMOP is an implicit niching method. In this paper, we also discuss two issues in MOMMOP and introduce two new comparison criteria. MOMMOP has been used to solve 20 multimodal benchmark test functions, after combining with nondominated sorting and differential evolution. Systematic experiments have indicated that MOMMOP outperforms a number of methods for multimodal optimization, including four recent methods at the 2013 IEEE Congress on Evolutionary Computation, four state-of-the-art single-objective optimization based methods, and two well-known multiobjective optimization based approaches.