Miracle-dz/UniFAR-FTUs huggingface dataset:
Online Bayesian Collaborative Topic Regression

Collaborative Topic Regression (CTR) combines ideas of probabilistic matrix factorization (PMF) and topic modeling (e.g., LDA) for recommender systems, which has gained increasing successes in many applications. Despite enjoying many advantages, the existing CTR algorithms have some critical limitations. First of all, they are often designed to work in a batch learning manner, making them unsuitable to deal with streaming data or big data in real-world recommender systems. Second, the document-specific topic proportions of LDA are fed to the downstream PMF, but not reverse, which is sub-optimal as the rating information is not exploited in discovering the low-dimensional representation of documents and thus can result in a sub-optimal representation for prediction. In this paper, we propose a novel scheme of Online Bayesian Collaborative Topic Regression (OBCTR) which is efficient and scalable for learning from data streams. Particularly, we {\it jointly} optimize the combined objective function of both PMF and LDA in an online learning fashion, in which both PMF and LDA tasks can be reinforced each other during the online learning process. Our encouraging experimental results on real-world data validate the effectiveness of the proposed method.
T315I-mutated Bcr-Abl in chronic myeloid leukemia and imatinib: insights from a computational study

The early stage of chronic myeloid leukemia is triggered by the tyrosine kinase Bcr-Abl. Imatinib mesylate, a selective inhibitor of Bcr-Abl, has been successful in chronic myeloid leukemia clinical trials, but short-lived remissions are usually observed in blast crisis patients. Sequencing of the BCR-ABL gene in relapsed patients revealed a set of mutants that mediate drug resistance. Previously reported work postulated that the missense T315I mutation both alters the three-dimensional structure of the protein binding site, thus decreasing the protein sensitivity for the drug, and does not feature a fundamental hydrogen bond that is critical for binding with imatinib. These speculations, however, were not supported by investigations at the molecular modeling level. Here, we present the results obtained from the application of molecular dynamics simulations to the study of the interactions between T315I Bcr-Abl and imatinib. For the first time, we show that, with respect to the wild-type system, the absence of the supposedly critical H-bond is not the only cause for the failure of receptor inhibition by imatinib, but also a plethora of other protein/drug interactions are drastically and unfavorably changed in the mutant protein.
Feedback Allocation for OFDMA Systems With Slow Frequency-Domain Scheduling

We study the problem of allocating limited feedback resources across multiple users in an orthogonal-frequency-division-multiple-access downlink system with slow frequency-domain scheduling. Many flavors of slow frequency-domain scheduling (e.g., persistent scheduling, semi-persistent scheduling), that adapt user-sub-band assignments on a slower time-scale, are being considered in standards such as 3GPP Long-Term Evolution. In this paper, we develop a feedback allocation algorithm that operates in conjunction with any arbitrary slow frequency-domain scheduler with the goal of improving the throughput of the system. Given a user-sub-band assignment chosen by the scheduler, the feedback allocation algorithm involves solving a weighted sum-rate maximization at each (slow) scheduling instant. We first develop an optimal dynamic-programming-based algorithm to solve the feedback allocation problem with pseudo-polynomial complexity in the number of users and in the total feedback bit budget. We then propose two approximation algorithms with complexity further reduced, for scenarios where the problem exhibits additional structure.
Imaging and Clinicopathologic Characteristics of Breast Cancers in Younger Group Compared to in Old Group.

Although the incidence of breast cancer in Korea remains much lower than that in Western countries, it has been continuously increased. Recently, breast cancer has been reported highest incidence among the women’s cancer in Korea. The breast cancer incidence reported in United States is 6.5% occurs by the age of 40 yr where as 11.3-17.3% of the incidence occurs in women younger than 35 yr of age according to the Korean Breast Cancer Society which is much higher. (1-3) Previous studies have shown mammography (MMG) to be ineffective as a diagnostic modality in young women, Ultrasound (US) would be the method of choice in the evaluation of young aged breast cancer. (4,5) However, there has not been a world consensus of US used as a screening tool for breast cancer. Also many reports suggested that in young age breast cancer is more aggressive and carries a higher mortality in younger women. (6-8) Whether a poorer prognosis is caused by a diagnostic delay or different characteristics of the tumor is still controversial. Most of the studies were limited to the young age cancer without comparison to old age group. (9-13) In this study, we evaluated the difference of imaging features on MMG and US, clinical and pathologic characteristics of young age breast cancer compared to older patients in Korean women.
Optimal utilization of a cognitive shared channel with a rechargeable primary source node

This paper considers the scenario in which a set of nodes share a common channel. Some nodes have a rechargeable battery and the others are plugged to a reliable power supply and, thus, have no energy limitations. We consider two source-destination pairs and apply the concept of cognitive radio communication in sharing the common channel. Specifically, we give high-priority to the energy-constrained source-destination pair, i.e., primary pair, and low-priority to the pair which is free from such constraint, i.e., secondary pair. In contrast to the traditional notion of cognitive radio, in which the secondary transmitter is required to relinquish the channel as soon as the primary is detected, the secondary transmitter not only utilizes the idle slots of primary pair but also transmits along with the primary transmitter with probability p. This is possible because we consider the general multipacket reception model. Given the requirement on the primary pair's throughput, the probability p is chosen to maximize the secondary pair's throughput. To this end, we obtain two-dimensional maximum stable throughput region which describes the theoretical limit on rates that we can push into the network while maintaining the queues in the network to be stable. The result is obtained for both cases in which the capacity of the battery at the primary node is infinite and also finite.
Space Use and Movement of a Neotropical Top Predator: The Endangered Jaguar

Accurately estimating home range and understanding movement behavior can provide important information on ecological processes. Advances in data collection and analysis have improved our ability to estimate home range and movement parameters, both of which have the potential to impact species conservation. Fitting continuous-time movement model to data and incorporating the autocorrelated kernel density estimator (AKDE), we investigated range residency of forty-four jaguars fit with GPS collars across five biomes in Brazil and Argentina. We assessed home range and movement parameters of range resident animals and compared AKDE estimates with kernel density estimates (KDE). We accounted for differential space use and movement among individuals, sex, region, and habitat quality. Thirty-three (80%) of collared jaguars were range resident. Home range estimates using AKDE were 1.02 to 4.80 times larger than KDE estimates that did not consider autocorrelation. Males exhibited larger home ranges, more directional movement paths, and a trend towards larger distances traveled per day. Jaguars with the largest home ranges occupied the Atlantic Forest, a biome with high levels of deforestation and high human population density. Our results fill a gap in the knowledge of the species’ ecology with an aim towards better conservation of this endangered/critically endangered carnivore—the top predator in the Neotropics.
Eecient Progressive Sampling

Having access to massive amounts of data does not necessarily imply that induction algorithms must use them all. Samples often provide the same accuracy with far less computational cost. However, the correct sample size is rarely obvious. We analyze methods for progressive sampling|starting with small samples and progressively increasing them as long as model accuracy improves. We show that a simple, geometric sampling schedule is e cient in an asymptotic sense. We then explore the notion of optimal e ciency: what is the absolute best sampling schedule? We describe the issues involved in instantiating an \optimally e cient" progressive sampler. Finally, we provide empirical results comparing a variety of progressive sampling methods. We conclude that progressive sampling often is preferable to analyzing all data instances.
Perfusion and diffusion MR imaging of thromboembolic stroke

A carotid embolic stroke model in rats was studied with a combination of diffusion‐ and perfusion‐sensitive magnetic resonance (MR) imaging at 4.7 T. Capillary blood deoxygenation changes were monitored during formation of focal ischemia by acquiring multisection magnetic susceptibility‐weighted echo‐planar images. A signal intensity decrease of 7% ± 3 in ischemic brain (1% ± 2 in normal brain) was attributable to a T2* decrease due to increased blood deoxygenation, which correlated well with subsequently measured decreases in the apparent diffusion coefficient. The same multisection methods were used to track the first‐pass transit of a bolus of dysprosium‐DTPA‐BMA [diethylenetriaminepentaacetic acid‐bis(methylam‐ide)] to assess relative tissue perfusion before and after stroke and after treatment with a thrombolytic agent. Analysis of contrast agent transit profiles suggested a total perfusion deficit in ischemic tissue and essentially unchanged perfusion in normal brain tissue after stroke.
Significance of stromal-1 and stromal-2 signatures and biologic prognostic model in diffuse large B-cell lymphoma

Objective : Diffuse Large B Cell Lymphoma (DLBCL) is a heterogeneous group of tumors with different biological and clinical characteristics that have diverse clinical outcomes and response to therapy. Stromal-1 signature of tumor microenvironment of DLBCL represents extracellular matrix deposition and histiocytic infiltrate, whereas stromal-2 represents angiogenesis that could affect tumor progression. Methods : The aim of the present study is to assess the significance of stromal-1 signature using SPARC-1 and stromal-2 signature using CD31 expression and then finally to construct biologic prognostic model (BPM) in 60 cases of DLBCL via immunohistochemistry. Results : Microvessel density (P<0.05) and SPARC percentage of expression (P<0.001) were higher in DLBCL, including germinal and nongerminal cases, compared with reactive follicular hyperplasia. High microvessel density was significantly associated with splenic involvement (P=0.008), high mitotic count (P=0.045), and presence of capsular invasion (P=0.035). Percentage of SPARC expression was significantly associated with splenic involvement (P=0.03). Constructing BPM showed that 42 cases (70%) were of low biologic score (0–1) and 18 cases (30%) were of high biologic score (2–3). Low BPM cases showed less probability for splenic involvement (P=0.04) and a higher rate of complete response to therapy compared with high score cases (P=0.08). Conclusions : The DLBCL microenvironment could modulate tumor progression behavior since angiogenesis and SPARC positive stromal cells promote dissemination by association with spleen involvement and capsular invasion. Biologic prognostic models, including modified BPM, which considered cell origin of DLBCL and stromal signature pathways, could determine DLBCL progression and response to therapy.
Chagas disease and the US blood supply

Purpose of review To describe new developments in blood-bank screening and management of patients with chronic Trypanosoma cruzi infection in the United States. Recent findings The first US Food and Drug Administration licensed serological test for T. cruzi blood screening went into widespread usage in January 2007. More than 500 confirmed T. cruzi-infected donations were detected by mid-June 2008. Until recently, drug therapy was recommended for acute and congenital infections, but seldom for chronic infections, which were believed to respond poorly. However, in the 1990s, efficacy was demonstrated in two placebo-controlled trials of benznidazole in children with chronic T. cruzi infection. In 2006, a nonrandomized, nonblinded trial demonstrated that benznidazole treatment may slow progression of cardiomyopathy and decrease mortality risk in infected adults. Summary Blood-bank screening will continue to detect T. cruzi-infected donors. Based on recent data, antitrypanosomal treatment is recommended for all acute and congenital T. cruzi infections, reactivated infection, and chronically infected children. In adults aged 19–50 years without advanced heart disease, treatment should generally be offered; management should be individualized for older adults. Less toxic, more effective drugs, a sensitive, specific assay for response to treatment, and improved healthcare access would promote more effective management.
Comprehensive Genomic Characterization of Cutaneous Malignant Melanoma Cell Lines Derived from Metastatic Lesions by Whole-Exome Sequencing and SNP Array Profiling

Cutaneous malignant melanoma is the most fatal skin cancer and although improved comprehension of its pathogenic pathways allowed to realize some effective molecular targeted therapies, novel targets and drugs are still needed. Aiming to add genetic information potentially useful for novel targets discovery, we performed an extensive genomic characterization by whole-exome sequencing and SNP array profiling of six cutaneous melanoma cell lines derived from metastatic patients. We obtained a total of 3,325 novel coding single nucleotide variants, including 2,172 non-synonymous variants. We catalogued the coding mutations according to Sanger COSMIC database and to a manually curated list including genes involved in melanoma pathways identified by mining recent literature. Besides confirming the presence of known melanoma driver mutations (BRAFV600E, NRASQ61R), we identified novel mutated genes involved in signalling pathways crucial for melanoma pathogenesis and already addressed by current targeted therapies (such as MAPK and glutamate pathways). We also identified mutations in four genes (MUC19, PAICS, RBMXL1, KIF23) never reported in melanoma, which might deserve further investigations. All data are available to the entire research community in our Melanoma Exome Database (at https://155.253.6.64/MExDB/). In summary, these cell lines are valuable biological tools to improve the genetic comprehension of this complex cancer disease and to study functional relevance of individual mutational events, and these findings could provide insights potentially useful for identification of novel therapeutic targets for cutaneous malignant melanoma.
Robust treatment of simultaneous collisions

Robust treatment of complex collisions is a challenging problem in cloth simulation. Some state of the art methods resolve collisions iteratively, invoking a fail-safe when a bound on iteration count is exceeded. The best-known fail-safe rigidifies the contact region, causing simulation artifacts. We present a fail-safe that cancels impact but not sliding motion, considerably reducing artificial dissipation. We equip the proposed fail-safe with an approximation of Coulomb friction, allowing finer control of sliding dissipation.
Self-localized quasi-particle excitation in quantum electrodynamics and its physical interpretation.

The self-localized quasi-particle excitation of the electron-positron field (EPF) is found for the first time in the framework of a standard form of the quantum electrodynamics. This state is interpreted as the "physical" electron (positron) and it allows one to solve the following problems: i) to express the "primary" charge e0 and the mass m0 of the "bare" electron in terms of the observed values of e and m of the "physical" electron without any infinite parameters and by essentially nonperturbative way; ii) to consider µ-meson as another self-localized EPF state and to estimate the ratio mµ/m; iii) to prove that the self- localized state is Lorentz-invariant and its energy spectrum corresponds to the relativistic free particle with the observed mass m; iv) to show that the expansion in a power of the observed charge e 1 corresponds to the strong coupling expansion in a power of the "primary" charge e 1 0 e when the interaction between the "physical" electron and the transverse electromagnetic field is considered by means of the perturbation theory and all terms of this series are free from the ultraviolet divergence.
Systemic injection of recombinant human erythropoietin after focal cerebral ischemia enhances oligodendroglial and endothelial progenitor cells in rat brain

Erythropoietin (EPO) has been demonstrated the ability of recombinant human erythropoietin (r-Hu-EPO), when administered intracerebro-ventricularly, to improve stroke outcome through the reduction of stroke damage. In a brain ischemic model, however, systemic administration of r-Hu-EPO has not been intensely investigated given that in general, large glycosylated molecules have been deemed incapable of crossing the blood-brain barrier. In this study, administration of r-Hu-EPO for 4 days, intraperitoneally after ischemia-reperfusion (I-R) increased the number of bromodeoxyuridine (BrdU)-positive cells in the penumbra (10.1±1.4, n=5, P<0.05) and in the subventricular zone (SVZ) of the lateral ventricle (LV) (25±2.7, n=5, P<0.05) as compared with those of I-R (penumbra: 2.5±0.7; SVZ of LV: 3.8±1.5). A significant increase of BrdU-positive cells in these areas was coincident with a strong immunoreactivity of oligodendrocyte progenitor cell marker (2', 3'-cyclic nucleotide 3'-phosphodiesterase). Furthermore, r-Hu-EPO administration increased the number of BrdU-positive cells in the choroid plexus (7.8±2.3, n=5, P<0.05) and in cerebral blood vessels (3.5±1.3, n=5, P<0.05) when compared with those of I-R (choroid plexus: 1.2±0.5; cerebral blood vessels: 0.6±0.1). These results suggest that, even when systemically administered, r-Hu-EPO may have therapeutic potential for stroke via the proliferation of oligodendroglial and endothelial progenitor cells.
µCell - Interdisciplinary Research in Modelling and Simulation of Cell Spatial Behaviour

A central aim of systems biology is the strengthening of quantitative and qualitative knowledge of biological systems by studying the interactions between components and processes that lead to emerging properties and behaviours. Systems biology proliferated over the latter half of the twentieth century with the aid of technological advances and subsequent interdisciplinary research between natural scientists, computer scientists, and mathematicians. In this paper we present μCell, an interdisciplinary research project undertaken by undergraduates at the University of Warwick, seeking to aid systems biology intuition. The project's main contribution is a modelling and simulation tool for multi-cellular environments aimed at simulating higher-level cellular behaviours based on the interoperation of biochemical signalling pathway models and procedural models of cell components and structures, such as flagella. Based on these interoperated models, μCell is able to simulate spatial properties and behaviours of cells, such as chemotaxis. This paper introduces μCell, gives a case study model and simulation of flagella-based chemotaxis in E. coli, and discusses the pedagogical outcomes of the project for the students.
Instabilities and flame speeds in large-scale premixed gaseous explosions

The instability of spherical flames in quiescent premixtures is considered using the linear theory developed by Bechtold and Matalon, which includes hydrodynamic and thermodiffusive instabilities. Ranges of unstable wavenumbers are presented for different Markstein numbers as the flame propagates, characterized by the flame Peclet number. Hydrodynamic instabilities arise at the larger wavelengths and cascade down through a range of ever–decreasing wavelengths to be stabilized at the smallest wavelength by thermodiffusive effects. It would appear that, in practice, the associated cell formation lags somewhat behind what is predicted by the theory and an attempt is made to allow for this. With it, a fractal analysis is employed with the two limiting unstable wavelengths as inner and outer cut–offs. The ever–increasing surface wrinkling as the flame propagates creates a larger surface area and consequent flame acceleration. The analysis yields an expression for the flame speed after a critical Peclet number has been attained. The flame speed increases as the square root of elapsed time and the analytical expression is in agreement with the results of measurements of large explosions. The fractal analysis is probably valid because of the large length–scales and small flame stretch rates, unlike those in many turbulent flames in engineering applications, where the flame stretch rate usually reduces the burning rate. The mechanisms for the creation of turbulence are discussed, including a brief speculation of the repercussions for deflagration to detonation transitions in large–scale explosions, including supernovae.
Prevalence of Cigarette Smoking among Adult Cancer Survivors in Korea

Purpose Cigarette smoking is associated not only with increased risk of cancer incidence, but also influences prognosis, and the quality of life of the cancer survivors. Thus, smoking cessation after cancer diagnosis is necessary. However, smoking behavior among Korean cancer-survivors is yet unknown. Materials and Methods We investigated the smoking status of 23770 adults, aged 18 years or older, who participated in the Health Interview Survey of the Korea National Health and Nutrition Examination Survey from 2007 to 2010. Data on the cancer diagnosis and smoking history were obtained from an interview conducted by trained personals. "Cancer-survivor" was defined as anyone who has been diagnosed with cancer by a physician regardless of time duration since diagnosis. Smoking status was classified into "never-smoker", "former-smoker", and "current-smoker". Former-smoker was further divided into "cessation before diagnosis" and "cessation after diagnosis". Results Overall, 2.1% of Korean adults were cancer-survivors. The smoking rate of Korean cancer-survivors was lower than that of non-cancer controls (7.8±1.3% vs. 26.4±0.4%, p<0.001). However, 53.4% of the cancer-survivors continued to smoke after their cancer diagnosis. In multivariate analysis, male gender [odds ratio (OR), 6.34; 95% confidence interval (CI), 2.62-15.31], middle-aged group (OR, 2.74; 95% CI, 1.12-6.72), the lowest income (OR, 4.10; 95% CI, 1.19-14.15), living with smoking family member(s) (OR, 5.49; 95% CI, 2.42-12.48), and the poor self-perceived health status (OR, 2.78; 95% CI, 1.01-7.71) were independently associated with persistent smoking among Korean cancer-survivors. Conclusion The smoking rate among Korean cancer survivors is low. However, the smoking cessation rate after the cancer diagnosis is also low. This mandates comprehensive and systematic intervention for smoking cessation among cancer-survivors.