Miracle-dz/UniFAR-FTUs huggingface dataset:
Region Quad-Tree Decomposition Based Edge Detection for Medical Images

Edge detection in medical images has generated significant interest in the medical informatics community, especially in recent years. With the advent of imaging technology in biomedical and clinical domains, the growth in medical digital images has exceeded our capacity to analyze and store them for efficient representation and retrieval, especially for data mining applications. Medical decision support applications frequently demand the ability to identify and locate sharp discontinuities in an image for feature extraction and interpretation of image content, which can then be exploited for decision support analysis. However, due to the inherent high dimensional nature of the image content and the presence of ill-defined edges, edge detection using classical procedures is difficult, if not impossible, for sensitive and specific medical informatics-based discovery. In this paper, we propose a new edge detection technique based on the regional recursive hierarchical decomposition using quadtree and post-filtration of edges using a finite difference operator. We show that in medical images of common origin, focal and/or penumbral blurred edges can be characterized by an estimable intensity gradient. This gradient can further be used for dismissing false alarms. A detailed validation and comparison with related works on diabetic retinopathy images and CT scan images show that the proposed approach is efficient and accurate.
Supercomputing in plain English : teaching high performance computing to inexperienced programmers

Although the field of High Performance Computing (HPC) has been evolving rapidly, the development of standardized software systems – MPI, OpenMP, LAPACK, PETSc and others – has in principle made HPC accessible to a wider community. However, relatively few scientists and engineers take advantage of computational science and engineering (CSE) in their research, in part because of the considerable degree of sophistication about computing that HPC appears to require. Yet the fundamental concepts of HPC are fairly straightforward and have remained relatively stable over time. These facts raise an important question: can scientists and engineers with relatively modest computing experience learn HPC concepts well enough to take advantage of them in their research? To answer this question, HPC educators must address several issues. First, what are the fundamental issues and concepts in CSE? Second, what are the fundamental issues and concepts in HPC? Third, how can these ideas be expressed in a manner that is clear to a person with relatively modest computing experience? Finally, is classroom exposure sufficient, or is guidance required to assist investigators in incorporating HPC into their research codes? We discuss an effort, now underway, to develop materials that express sophisticated scientific computing concepts in a manner accessible to a broad audience. These materials, now partially completed, will address many of the above questions, employing plain English, analogies and narratives to target this population. In addition, we examine a programmatic approach that incorporates not only the use of these materials but also the crucial contribution of followup. Send correspondence to Henry Neeman ( hneeman@ou.edu )
An approach for handling risk and uncertainty in multiarmed bandit problems

A composite material composed of a non-oxide type ceramic and iron or an alloy thereof is disclosed, wherein the non-oxide type ceramic is formed with a copper metallized surface and bonded to the iron or alloy thereof with an intermediate layer of Invar steel, Kovar or copper disposed between the copper metallized surface and the iron or alloy thereof.
Formation of a novel phagosome by the Legionnaires' disease bacterium (Legionella pneumophila) in human monocytes

Previous studies have shown that L. pneumophila multiplies intracellularly in human monocytes and alveolar macrophages within a membrane-bound cytoplasmic vacuole studded with ribosomes. In this paper, the formation of this novel vacuole is examined. After entry into monocytes, L. pneumophila resides in a membrane-bound vacuole. During the first hour after entry, vacuoles containing L. pneumophila are found surrounded by smooth vesicles fusing with or budding off from the vacuolar membrane and by mitochondria closely apposed to the vacuolar membrane. By 4 h, vacuoles are found less frequently surrounded by these cytoplasmic organelles, but now ribosomes and rough vesicles are found gathered about the vacuole. By 8 h, the ribosome- lined vacuole has formed. Erythromycin, at concentrations that completely inhibit the intracellular multiplication of L. pneumophila, has no effect on vacuole formation. Formalin-killed L. pneumophila also reside in a membrane-bound vacuole after entry into monocytes. In contrast to the situation with live L. pneumophila, cytoplasmic organelles are not found surrounding vacuoles containing formalin- killed L. pneumophila at any time after entry. Formalin-killed bacteria are rapidly digested, and by 4 h, few remain intact. The L. pneumophila- containing vacuole has certain features in common with other intracellular organisms that inhibit phagosome-lysosome fusion; these organisms may share a common mechanism for vacuole formation and inhibition of phagosome-lysosome fusion.
Mutations of the beta subunit of RNA polymerase alter both transcription pausing and transcription termination in the trp operon leader region in vitro.

RNA polymerase was purified from rifampicin-resistant mutants of Escherichia coli which exhibit altered transcription termination at the trp operon attenuator in vivo. These mutant polymerases were used to investigate transcription pausing at the trp leader pause site and transcription termination at the trp attenuator. The mutant polymerases examined in vitro mimic their in vivo termination responses; i.e. RNA polymerase isolated from a mutant which displays high transcriptional read-through of the trp operon in vivo allows greater transcriptional read-through in vitro, while RNA polymerase prepared from a mutant which has reduced read-through in vivo exhibits greater termination of transcription in vitro. The observed differences are not due to the presence of--or response to--alternate secondary structures in the trp leader transcript since deletion of the DNA segment corresponding to some of these alternate structures does not affect termination efficiency. The mutant polymerases also have comparable effects on the kinetics of transcription pausing at the trp leader pause site; the termination-deficient polymerase exhibits diminished pausing while the termination-proficient polymerase displays enhanced pausing. We suggest that this correlation reflects polymerase recognition of similar features of RNA secondary structures in the pause and termination events. In addition, since single mutational changes in RNA polymerase affect two activities, pausing and termination, it is likely that a single site or region of the polymerase is involved in both events.
A mobile robot: Sensing, planning and locomotion

A mobile robot architecture must include sensing, planning, and locomotion which are tied together by a model or map of the world based on sensor information, apriori knowledge and generic models. The architecture of a Stanford's autonomous mobile robot is described including its distributed computing system, locomotion, and sensing. Additionally, some of the issues in the representation of a world model are explored. Sensor models are used to update the world model in a uniform manner, and uncertainty reduction is discussed.
EMAGEN: An Efficient Approach to Multiple Whole Genome Alignment

Following advances in biotechnology, many new whole genome sequences are becoming available every year. A lot of useful information can be derived from the alignment and comparison of different genomes. However, most of the current research focuses on pairwise genome alignment, and only a few available applications can efficiently align multiple genomes. In this paper, we present an efficient approach to align closely related multiple whole genomes, combining suffix arrays, graph theoretic formulation and existing tools for gap (short sequence) alignment. Our approach first finds a maximum set of aligned conserved regions among multiple whole genomes, then aligns the gaps between consecutive conserved regions with Clustal W. We present two methods to find the maximum set of aligned conserved regions among whole genomes. In first method, called Direct Matching (DM), multiple whole genomes are aligned with their DNA sequences. However, because most parts of prokaryotic genomes are encoded regions, we introduce second method, Functional Matching (FM), to especially align multiple prokaryotic genomes with their concatenated protein sequences. We present experimental results for both methods and give the analysis of the results. The FM method generates much better results for less closely related prokaryotic genomes than DM method. It outputs more and longer conserved regions, which conveys more accurate and detailed information about the conservation and inheritance of genomes, and generates more detailed alignments.
Routing Protocols

Multicast Routing Instabilities Native multicast is critical for scaling the delivery of high-bandwidth data, such as audio and video, to multiple receivers. Until recently, however, multicast routing has been unstable, thus making it difficult to ensure robust data delivery.The authors' in-depth analysis of routing instabilities in the multicast infrastructure seeks to identify underlying inconsistencies among routing views at different routers and characterize instabilities by evaluating temporal and spatial variations in these views. Results are based on multiprotocol border gateway protocol (MBGP) routing tables. M ulticast 1 is one of the best available service models for scalable, many-to-many delivery of data on the Internet. Multicast achieves scalability by letting sources send a packet only once, regardless of the number of receivers. In network-layer multicast, network elements (routers, switches, and so on) replicate packets at network branching points, delivering copies to all interested receivers. Replicating each packet as close to the receiver as possible improves efficiency. Multicast uses range from the delivery of conventional multimedia streams such as audio and video to emerging services such as desktop streaming, whiteboards, and collaborative distance learning. As the multicast infrastructure has matured, several limitations have come to light. Although the infrastructure has recently become more robust, 2 weaknesses in the underlying protocols have historically resulted in poor connectivity and significant routing instabilities. Although the severity of multicast routing problems is well known, little research toward solving them exists. Consequently, researchers know little about how the multicast infrastructure operates, how to solve existing problems, and what other problems exist. This article seeks to remedy this lack of knowledge by analyzing multicast routing instabilities at individual routers and comparing views between them. Our goal is to present a network-layer view of multicast routing stability and to characterize instabilities by evaluating temporal and spatial variations in the routing views. We also explore potential causes of these instabilities. In the early 1990s, multicast existed as a tunnel-based infrastructure — the multi-cast backbone (MBone) — that used the Distance-Vector Multicast Routing Protocol (DVMRP). In 1997, advancements in protocol development and subsequent deployment had considerably diminished DVMRP's use at the interdomain level, and
Top-k Aggressors Sets in Delay Noise Analysis

We present, in this paper, novel algorithms to compute the set of "top-k" aggressors in a design. We show that the computation of the set of top-k "aggressors is non-trivial, since we must consider all per mutations of aggressors that are coupled to a critical path. Also, different sets of aggressors contribute different amounts of noise to each critical path and a brute-force enumeration to obtain the set of top-k aggressors has impractical runtime. Our proposed approach uses two key techniques to reduce the runtime complexity: Firstly, we model the delay noise propagated from a victim net to its fanout net by a so-called pseudo aggressor, which simplifies our problem formulation significantly. Secondly, we define a dominance property for aggressor sets, which imposes a partial ordering on the aggressor sets and allows us to efficiently prune the enumeration space. We then demonstrate the effectiveness of our proposed algorithm on benchmark circuits.
Two courses, two problems, and Project E-xchange: International collaboration to enhance cross-cultural communication

In two academic years (from December 2007—March 2008, and December 2008—March 2009), students studying English at a Japanese university and about Japanese culture at an American university exchanged messages in small groups through electronic media to improve their communication skills and knowledge of culture. This paper reviews the project, outcomes, improvements, and its possible future application.
OSAS-Related Inflammatory Mechanisms of Liver Injury in Nonalcoholic Fatty Liver Disease

Obstructive sleep apnoea syndrome (OSAS) is a common sleep disorder, affecting over 4% of the general population, and is associated with metabolic syndrome and cardiovascular disease, independent of obesity and traditional risk factors. OSAS has been recently connected to nonalcoholic fatty liver disease (NAFLD), the most common chronic liver disease in the world, which can be found in 30% of the general adult population. Several studies suggest that the chronic intermittent hypoxia (CIH) of OSAS patients may per se trigger liver injury, inflammation, and fibrogenesis, promoting NAFLD development and the progression from steatosis to steatohepatitis, cirrhosis, and hepatocellular carcinoma. In NAFLD patients, liver disease may be caused by hypoxia both indirectly by promoting inflammation and insulin resistance and directly by enhancing proinflammatory cytokine production and metabolic dysregulation in liver cells. In this review, we focus on molecular mechanisms linking OSAS to NAFLD, including hypoxia inducible factor (HIF), nuclear factor kappa B (NF-κB), YKL-40, unfolded protein response, and hypoxic adipose tissue inflammation, which all could provide novel potential therapeutic approaches for the management of NAFLD patients with OSAS.
Re: "occupational risk factors for esophageal and stomach cancers among female textile workers in Shanghai, China".

A recent issue of the Journal included an excellent and interesting paper by Wernli et al. (1) supporting the concept that exposure to organic dust that contains endotoxin has beneficial effects against cancer. We would like to comment on the commonly suggested confounder associated with lower rates of cancer in workers exposed to organic dust— smoking—and expand on the mechanism by which endotoxin in dust may be responsible for the observed benefits as related to this exposure. Historically, a few reports suggested that dust reduced the rate of lung cancer (2), although most investigators dismissed this finding and inferred that this was a methodological issue relating to lower smoking rates in exposed populations. However, studies by this research group (3–5) investigating Chinese cotton textile workers, as well as other investigations of textile (6, 7) and agricultural (8) workers, specifically dairy farmers (9, 10), now support the position that this effect of a lower-than-expected rate of cancer is not a result of differences in smoking rates between study and control populations. A 1973 study by Henderson and Enterline (11) collected data on the smoking rates of cotton textile workers and reported that the rates were slightly higher (51.9 percent) than those of the control population (51.2 percent). A recent evaluation of smoking rates of cotton textile workers (12) also suggests that the rate for this population is higher than or similar to that for controls and the general population. This study (1), as have others (2, 9), suggests that the mechanism for the lower rates of cancer is a result of endotoxin, a lipopolysaccharide constituent of the Gram-negative bacterial cell wall. Previous investigations (13, 14) have shown that many occupational groups are exposed to high levels of airborne dust containing endotoxin. Wernli et al. (1) suggest that the endotoxin results in stimulation of the immune system, which causes macrophages to become antitumor/carcinogenic. We previously suggested a mechanism for this antitumor activity through the involvement of toll-like receptors and cytotoxic mediators, such as cytokines Letters to the Editor 233
Association between tumour necrosis factor-α inhibitors and risk of serious infections in people with inflammatory bowel disease: nationwide Danish cohort study

Objective To investigate whether people with inflammatory bowel disease treated with tumour necrosis factor-α (TNF-α) inhibitors are at increased risk of serious infections. Design Nationwide register based propensity score matched cohort study. Setting Denmark, 2002-12. Participants The background cohort eligible for matching comprised 52 392 people with inflammatory bowel disease, aged 15 to 75 years, of whom 4300 were treated with TNF-α inhibitors. To limit confounding, a two stage matching method was applied; firstly matching on age, sex, disease duration, and inflammatory bowel disease subtype, and secondly matching on propensity scores (1:1 ratio); this yielded 1543 people treated with TNF-α inhibitors and 1543 untreated to be included in the analyses. Main outcome measures The main outcome was any serious infection, defined as a diagnosis of infection associated with hospital admission. Cox regression was used to estimate hazard ratios for two risk periods (90 and 365 days after the start of TNF-α inhibitor treatment). Hazard ratios of site specific serious infections were obtained solely for the 365 days risk period. Results Within the 90 days risk period, 51 cases of infection were observed in users of TNF-α inhibitors (incidence rate 14/100 person years), compared with 33 cases in non-users (9/100 person years), yielding a hazard ratio of 1.63 (95% confidence interval 1.01 to 2.63). Within the risk period of 365 days, the hazard ratio was 1.27 (0.92 to 1.75). In analyses of site specific infections, the hazard ratio was above 2 for several of the subgroups but only reached statistical significance for skin and soft tissue infections (2.51, 1.23 to 5.12). Conclusions This nationwide propensity score matched cohort study suggests an increased risk of serious infections associated with use of TNF-α inhibitors within the first 90 days of starting treatment and a subsequent decline in risk. This calls for increased clinical awareness of potential infectious complications among people with inflammatory bowel disease using these drugs, especially early in the course of treatment.
A 12-year experience at a tertiary hospital on patients with multiple primary malignant neoplasms.

PURPOSE The incidence of multiple primary malignant neoplasms (MPMN) has dramatically increased. The purpose of this retrospective study was to present the 12-year experience at a University Hospital in patients with MPMN and to investigate the role of genetic factors in their pathogenesis. METHODS The medical records of 7516 cancer patients, treated in our Institution from 2000 to 2012, were reviewed. Diagnosis of MPMN was based on the Warren and Gates' criteria. RESULTS Among 7516 patients, 39 (0.5%) (10 men, mean age 70.0±6.98 years, and 29 women, mean age 64.7±8.24 years) presented with MPMN. Eighty-two percent of them developed 2 primary malignant neoplasms (PMNs), whereas 3 PMNs were developed in 7 patients. Breast cancer was the most common cancer type diagnosed among female patients (59%); 14 and 3 had 2 and 3 PMNs, respectively. Eight had a family history of breast cancer while in 3 genetic testing revealed mutations in BRCA1 and BRCA2 genes. The second most common type of malignancy was colorectal cancer (24%); 5 developed 2 PMNs, whereas 2 developed 3 PMNs. Five patients had a family history of colorectal cancer. Colon cancer was the most frequent neoplasm among male patients (50%; 3 developed 2 and 2 3 PMNs. In 2 patients the family history was positive for colorectal cancer. CONCLUSIONS Although many factors may contribute to MPMN development, positive family history and inherent mutations significantly predispose to MPMN appearance. Thus, management of MPMN patients should be based on a detailed family history and genetic testing.
A specific exercise strategy reduced the need for surgery in subacromial pain patients

Background and purpose A programme based on eccentric exercises for treating subacromial pain was in a previous study found effective at 3-month follow-up. The purposes of the present study were to investigate whether the results were maintained after 1 year and whether the baseline Constant-Murley score, rotator cuff status and radiological findings influenced the outcome. Patients and methods 97 patients on the waiting list for arthroscopic subacromial decompression had been randomised to a specific exercise programme or unspecific exercises (controls). After 3 months of exercises, the patients were asked whether they still wanted surgery and this option was available until a 1-year follow-up. 1 year after inclusion or 1 year after surgery, the number of patients who decided to have surgery in each group was compared. The choice of surgery was related to the baseline Constant-Murley score, ultrasound and radiographs taken at inclusion. Results All patients had improved significantly (p<0.0001) in the Constant-Murley score at the 1-year follow-up. Significantly more patients in the control group decided to have surgery (63%) than those in the specific exercise group (24%; p<0.0001). Patients who decided to have surgery had a significantly lower baseline Constant-Murley score and more often a full-thickness tear. Patients with partial tears did not differ from those with intact tendons. Interpretation The positive short-term results of specific exercises were maintained after 1 year, and this exercise strategy reduces the need for surgery. Full-thickness tear and a low baseline Constant-Murley score appear to be a predictive marker for a less good outcome. Trial registration number Clinical trials NCT01037673.
Microstrip Patch versus Dielectric Resonator Antenna Bearing All Commonly Used Feeds: An experimental study to choose the right element.

Microstrip patches and dielectric resonators (DRs) are two low-profile variants of modern microwave and wireless antennas. However, the DR antenna (DRA) is relatively new and still passing through the stages of development. Both variants are quite similar in terms of performance and characteristics. This article focuses on a meaningful comparative study where we have considered all commonly used feed mechanisms such as coaxial probe, microstrip line, and rectangular aperture for both antennas operating near the same frequency. Circular geometry, i.e., cylindrical DRA (CDRA) and circular microstrip patch antenna (CMPA), have been chosen, and a systematic investigation based on thorough experiments has been executed. Multiple sets of prototypes have been fabricated and measured at 4 GHz. All available data have been furnished and compared, indicating relative advantages and disadvantages. This comparative study should provide qualitative and quantitative instructions to a designer for choosing the right element and corresponding feed based on design requirement and feasibility.