Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations between Testosterone Levels and Incident Prostate, Lung, and Colorectal Cancer. A Population-Based Study

Background: The relationship between testosterone and cancer is relatively unexplored. We sought to examine whether testosterone and related hormones are associated with incident prostate, lung, and colorectal cancer. Methods: This was a population-based cohort study. Demographic and clinical predictors of cancer, and testosterone, sex hormone-binding globulin (SHBG), and luteinizing hormone (LH) were measured between 2001 and 2004 in 3,635 community-dwelling men aged 70 to 88 years (mean 77 years). Cancer notifications were obtained via electronic record linkage until December 31, 2010. Results: During a mean follow-up period of 6.7 ± 1.8 years, there were 297, 104, and 82 cases of prostate, colorectal, and lung cancer. In adjusted competing risks proportional hazards models, each one SD increase in free testosterone was associated with a 9% increase in prostate cancer risk (95% confidence interval [CI], 1.00–1.18), but other hormones were not significantly associated. No significant associations were observed between hormonal parameters and colorectal cancer. Higher total testosterone was associated with lung cancer. Compared with the mean of 15 nmol/L, men with levels of 20 nmol/L were 1.38 times more likely to be cases (95% CI, 1.21–1.57), whereas those with levels of 30 nmol/L were 3.62 times more likely to be cases (95% CI, 2.53–5.18). Higher free testosterone was also associated with lung cancer, though SHBG and LH were not. Associations were maintained after exclusion of current smokers. Conclusions: Higher free testosterone was associated with incident prostate cancer. Higher testosterone levels may also be associated with lung cancer. Impact: Further studies should investigate whether these risks apply to men receiving testosterone therapy. Cancer Epidemiol Biomarkers Prev; 21(8); 1319–29. ©2012 AACR.
Public-private partnership : new opportunities for meeting social needs

This book is a collection of articles exploring the potential for and limits to an expanded role for private corporations and the possibilities for new modes of business/government cooperation. The contributors' articles are grouped by broad topic: "The Public and Private Sectors", "New Functions for the Corporation? ", "Opportunities for the 1980's", and "Achieving Democratic Legitimacy". Editors Brooks and Liebman are affiliated with Harvard University, and Schelling is with the Academy of Arts and Sciences. The contributors are primarily professors at major universities.
Hepcidin Levels and Their Determinants in Different Types of Myelodysplastic Syndromes

Iron overload may represent an additional clinical problem in patients with Myelodysplastic Syndromes (MDS), with recent data suggesting prognostic implications. Beyond red blood cells transfusions, dysregulation of hepcidin, the key iron hormone, may play a role, but studies until now have been hampered by technical problems. Using a recently validated assay, we measured serum hepcidin in 113 patients with different MDS subtypes. Mean hepcidin levels were consistently heterogeneous across different MDS subtypes, with the lowest levels in refractory anemia with ringed sideroblasts (RARS, 1.43 nM) and the highest in refractory anemia with excess blasts (RAEB, 11.3 nM) or in chronic myelomonocytic leukemia (CMML, 10.04 nM) (P = 0.003 by ANOVA). MDS subtypes remained significant predictors of hepcidin in multivariate analyses adjusted for ferritin and transfusion history. Consistently with current knowledge on hepcidin action/regulation, RARS patients had the highest levels of toxic non-transferrin-bound-iron, while RAEB and CMML patients had substantial elevation of C-Reactive Protein as compared to other MDS subtypes, and showed lost of homeostatic regulation by iron. Growth differentiation factor 15 did not appear as a primary hepcidin regulator in this series. If confirmed, these results may help to calibrate future treatments with chelating agents and/or hepcidin modulators in MDS patients.
An improved FOCUSS-based learning algorithm for solving sparse linear inverse problems

We develop an improved algorithm for solving blind sparse linear inverse problems where both the dictionary (possibly overcomplete) and the sources are unknown. The algorithm is derived in the Bayesian framework by the maximum a posteriori method, with the choice of prior distribution restricted to the class of concave/Schur-concave functions, which has been shown previously to be a sufficient condition for sparse solutions. This formulation leads to a constrained and regularized minimization problem which can be solved in part using the FOCUSS (focal underdetermined system solver) algorithm for vector selection. We introduce three key improvements in the algorithm: an efficient way of adjusting the regularization parameter; column normalization that restricts the learned dictionary; reinitialization to escape from local optima. Experiments were performed using synthetic data with matrix sizes up to 64/spl times/128; the algorithm solves the blind identification problem, recovering both the dictionary and the sparse sources. The improved algorithm is much more accurate than the original FOCUSS-dictionary learning algorithm when using large matrices. We also test our algorithm on natural images, and show that a learned overcomplete representation can encode the data more efficiently than a complete basis at the same level of accuracy.
Teaching Mathematics as Deliberate Practice through Public Lessons

In this article we examine the activities of 2 public lessons prepared and conducted by a group of elementary school teachers in China. We employ the conceptual lens of deliberate practice to understand how the public lesson activities possibly contributed to improvement of the teachers' knowledge and instructional performance. We found that teaching mathematics as deliberate practice through public lessons gave the teachers an opportunity to refine their instruction in 3 core aspects that included designing appropriate mathematical tasks for students, teaching the difficult mathematical idea, and using mathematically, pedagogically appropriate language.
Toward Formalizing A Validation Methodology Using Simulation Coverage

The biggest obstacle in the formal verification of large designs istheir very large state spaces, which cannot be handled even bytechniques such as implicit state space traversal. The only viablesolution in most cases is validation by functional simulation. Unfortunately, this has the drawbacksof high computationalrequirementsdue to the large number of test vectors needed, and the lack of adequate coverage measures to characterize the quality of a given testset. To overcome these limitations, there has been recent interest inhybrid techniques which combine the strengths of formal verification and simulation. Formal verification-based techniques are usedon a test model (usually much smaller than the design) to derive a setof functional test vectors, which are then used for design validationthrough simulation. The test set generated typically satisfies somecoverage measure on the test model. Recent research has proposedthe use of state or transition coverage. However, no effort has beenmade to relate these measures to the coverage of design errors. Furthermore, the derivation of the test model remains largely ad-hoc,with few formal guidelines.We demonstrate that under a given set of assumptions, transitiontours on test models can be used for complete validation of an implementation against a specification, for a large and important classof designs that includes many programmable/hardwired, general-purpose processors/DSPs. A by-product of this study is specificguidelines for deriving the test model, motivated by the requirement of providing complete coverage of all errors. We illustrate theapplication of our methodology on a pipelined implementation of the DLX processor.
Partially parallel imaging with phase‐sensitive data: Increased temporal resolution for magnetic resonance temperature imaging

Magnetic resonance temperature imaging can be used to monitor the progress of thermal ablation therapies, increasing treatment efficacy and improving patient safety. High temporal resolution is important when therapies rapidly heat tissue, but many approaches to faster image acquisition compromise image resolution, slice coverage, or phase sensitivity. Partially parallel imaging techniques offer the potential for improved temporal resolution without forcing such concessions. Although these techniques perturb image phase, relative phase changes between dynamically acquired phase‐sensitive images, such as those acquired for MR temperature imaging, can be reliably measured through partially parallel imaging techniques using reconstruction filters that remain constant across the series. Partially parallel and non‐accelerated phase‐difference‐sensitive data can be obtained through arrays of surface coils using this method. Average phase differences measured through partially parallel and fully Fourier encoded images are virtually identical, while phase noise increases with g$\sqrt{\rm L}$ as in standard partially parallel image acquisitions. Magn Reson Med 53:658–665, 2005. © 2005 Wiley‐Liss, Inc.
The ultrastructure of the integument of the frog lung‐fluke, Haematoloechus medioplexus (Trematoda: Plagiorchiidae)

The typical trematode worm is covered with a protective surface layer which has been regarded as a somewhat dense, nonliving structure secreted by certain glandular parenchymal cells. In many trematodes the body covering is provided with spines, hooks, or scaIes serving to secure the parasite in the tissues of the host. For a description of controversies dealing with the origin and nature of the “cuticle” of trematodes and cestodes, the reader is referred to Hyman (’51). Odlaug (’48) reviewed the early literature dealing with the body wall of trematodes and studied the parenchyma and body wall of the frog lung-fluke, Haematoloechus ( ~ Pneumonoeces) medioplexus. He noted general cytological features based on studies with the light microscope. The present paper is part of a broad research program dealing with the ultrastructure of both free-living and parasitic flatworms. Evidence will be presented showing that the integument of the lungfluke is syncytial and is not composed of extracellular material. The syncytium can be divided into two main regions: (1) the perinuclear cytoplasm (= certain “parenchymal cells”) lying beneath a basement membrane and two layers of muscle, and (2), the distal cytoplasm which forms the surface layer (= “cuticle”) of the worm’s body. The two regions are connected by narrow cytoplasmic processes.
On the eigenvalue distribution of preconditioned nonsymmetric saddle point matrices

In this paper, we derive bounds for the complex eigenvalues of a nonsymmetric saddle point matrix with a symmetric positive semidefinite (2,2) block, that extend the corresponding previous bounds obtained by Bergamaschi. For the nonsymmetric saddle point problem, we propose a block diagonal preconditioner for the conjugate gradient method in a nonstandard inner product. Numerical experiments are also included to test the performance of the presented preconditioner. Copyright © 2013 John Wiley & Sons, Ltd.
PCR detection of potentially pathogenic aeromonads in raw and cold‐smoked freshwater fish

Aims: Development of a PCR assay for detection of aeromonads carrying the hlyA and/or aerA genes in fish. Methods and Results: The protocol involves an overnight selective enrichment step in tryptic soy broth yeast extract containing 10 µg ml‐1 of ampicillin followed by extraction of DNA and PCR amplification of two haemolysin genes that contribute to the virulence of Aer. hydrophila. This procedure can detect initial populations of 1–10 cfu g−1 within 24 h in artificially contaminated samples. In naturally contaminated fish, both genes were detected in 13 out of 14 fresh fish lots (aeromonads levels between < 1 and 5·42 log cfu g−1) and in 4 out of 16 lots of vacuum‐packed cold‐smoked fish (aeromonads levels between < 1 and 3·37 log cfu g−1). Before enrichment, dominant species were Aer. hydrophila HG1 (aerA+hlyA+), Aer. bestiarum HG2 (aerA+hlyA+) and Aer. caviae HG4 (aerA–hlyA–). After enrichment, Aer. hydrophila HG1 (aerA+hlyA+) was dominant. Conclusions: Fresh fish and even smoked fish carry hlyA+ and/or aerA+ aeromonads that can be detected by PCR within 24 h. Significance and Impact of the Study: The PCR assay described offers considerable potential as a rapid method with specificity, sensitivity and simplicity.
Language barriers to learning science

This article draws on a study done in 1996 by Jordaan and Mangu which sought to determine how well pupils understand concepts which appear frequently in their textbooks and also to establish whether support material would facilitate learning. This article is not as much interested in the performance level of the students as the underlying reasons for the poor performance. The article explores some of the responses made by students in order to define their difficulties more precisely and concludes by making recommendations for learning and teaching. Hierdie artikel bou voort op 'n studie wat in 1996 deur Jordaan en Mangu gedoen is wat probeer het om te bepaal hoe goed leerders konsepte wat gereeld in hulle handboeke voorkom, verstaan en ook om vas te stel of ondersteunende materiaal die leerproses fasiliteer. Hierdie artikel is nie soseer gerig op die prestasievlakke van die leerders nie, maar eerder op die onderliggende redes vir hulle swak prestasie. Die artikel ondersoek sekere van die response van die leerders en poog daardeur om van die struikelblokke wat wetenskaplike diskoers aan die leerders hied me er presies te omskryf Die artikel sluit af met voorstelle vir verbeterings aan die leerproses en aan onderriglewering.
3-(2-hydroxyphenyl)catechol as substrate for proximal meta ring cleavage in dibenzofuran degradation by Brevibacterium sp. strain DPO 1361

Brevibacterium sp. strain DPO 1361 oxygenates dibenzofuran in the unusual angular position. The 3-(2-hydroxyphenyl)catechol thus generated is subject to meta ring cleavage in the proximal position, yielding 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienoic acid, which is hydrolyzed to 2-oxo-4-pentenoate and salicylate by 2-hydroxy-6-oxo-6-phenyl-2,4-hexadienoic acid hydrolase. The proximal mode of ring cleavage is definitely established by isolation and unequivocal structural characterization of a cyclization product of 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienoic acid, i.e., 3-(chroman-4-on-2-yl)pyruvate.
Polymorphisms in Autophagy Genes and Susceptibility to Tuberculosis

Recent data suggest that autophagy is important for intracellular killing of Mycobacterium tuberculosis, and polymorphisms in the autophagy gene IRGM have been linked with susceptibility to tuberculosis (TB) among African-Americans, and with TB caused by particular M. tuberculosis genotypes in Ghana. We compared 22 polymorphisms of 14 autophagy genes between 1022 Indonesian TB patients and 952 matched controls, and between patients infected with different M. tuberculosis genotypes, as determined by spoligotyping. The same autophagy polymorphisms were studied in correlation with ex-vivo production of TNF, IL-1β, IL-6, IL-8, IFN-γ and IL-17 in healthy volunteers. No association was found between TB and polymorphisms in the genes ATG10, ATG16L2, ATG2B, ATG5, ATG9B, IRGM, LAMP1, LAMP3, P2RX7, WIPI1, MTOR and ATG4C. Associations were found between polymorphisms in LAMP1 (p = 0.02) and MTOR (p = 0.02) and infection with the successful M. tuberculosis Beijing genotype. The polymorphisms examined were not associated with M. tuberculosis induced cytokines, except for a polymorphism in ATG10, which was linked with IL-8 production (p = 0.04). All associations found lost statistical significance after correction for multiple testing. This first examination of a broad set of polymorphisms in autophagy genes fails to show a clear association with TB, with M. tuberculosis Beijing genotype infection or with ex-vivo pro-inflammatory cytokine production.
High-Accuracy Phrase Translation Acquisition Through Battle-Royale Selection

In this paper, we report on an unsupervised greedy-style process for acquiring phrase translations from sentence-aligned parallel corpora. Thanks to innovative selection strategies, this process can acquire multiple translations without size criteria, i.e. phrases can have several translations, can be of any size, and their size is not considered when selecting their translations. Even though the process is in an early development stage and has much room for improvements, evaluation shows that it yields phrase translations of high precision that are relevant to machine translation but also to a wider set of applications including memory-based translation or multi-word acquisition.
How to Choose Successful Losers in Error-Driven Phonotactic Learning

An error-driven phonotactic learner is trained on a stream of licit phonological forms. Each piece of training data counts as a winner in terms of Optimality Theory. In order to test its current grammar, the learner needs to compare the current winner with a properly chosen loser. This paper advocates a new subroutine for the choice of the loser, based on the idea of minimizing the “distance” from the given winner.
Detailed Shape Representation with Parallax Mapping

Although texture mapping is a common technique for adding apparent surface detail to 3-D objects, it lacks the capability to represent the motion parallax effect. So the mesh to which it is applied limits its realism. In this paper, we propose Parallax Mapping, a simple method to motion parallax effects on a polygon. This method has very fast per-pixel shape representation and can be performed in real-time with current hardware.
A Fast Factorization-Based Approach to Robust PCA

Robust principal component analysis (RPCA) has been widely used for recovering low-rank matrices in many data mining and machine learning problems. It separates a data matrix into a low-rank part and a sparse part. The convex approach has been well studied in the literature. However, state-of-the-art algorithms for the convex approach usually have relatively high complexity due to the need of solving (partial) singular value decompositions of large matrices. A non-convex approach, AltProj, has also been proposed with lighter complexity and better scalability. Given the true rank r of the underlying low rank matrix, AltProj has a complexity of O(r2dn), where d × n is the size of data matrix. In this paper, we propose a novel factorization-based model of RPCA, which has a complexity of O(kdn), where k is an upper bound of the true rank. Our method does not need the precise value of the true rank. From extensive experiments, we observe that AltProj can work only when r is precisely known in advance, however, when the needed rank parameter r is specified to a value different from the true rank, AltProj cannot fully separate the two parts while our method succeeds. Even when both work, our method is about 4 times faster than AltProj. Our method can be used as a light-weight, scalable tool for RPCA in the absence of the precise value of the true rank.
Detection of Recombination in DNA Multiple Alignments with Hidden Markov Models

Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected.
Non-linear reading for a structured web indexation

The growth of the Web has posed new challenges for Information Retrieval (IR). Most of the current systems are based on traditional models, which have been developed for atomic and independents documents and are not adapted to the Web. A promising research orientation consists of studying the impact of the Web structure on indexing. The HyperDocument model presented in this article is based on essential aspects of information comprehension: content, composition and linear/non-linear reading.
Formaldehyde exposure and leukemia : a new meta-analysis and potential mechanisms

Smith MT. Formaldehyde exposure and leukemia: a new meta-analysis and potential mechanisms. Current evaluation Conclusion from the previous Monograph: Acetaldehyde is possibly carcinogenic to humans (Group 2B) because there is inadequate evidence in humans for the carcinogenicity of acetaldehyde, and there is sufficient evidence in experimental animals for the carcinogenicity of acetaldehyde. Exposure and biomonitoring Acetaldehyde is primarily used as an intermediate in the manufacturing of acetic acid, flavorings, aniline dyes, plastics and synthetic rubber, in some fuel compounds and in the manufacture of numerous other products (Muttray et al., 2009). Acetaldehyde is also a ubiquitous indoor and outdoor air pollutant. Sources of acetaldehyde are industrial burning processes, traffic emissions or emissions emerging from the combustion of wood. It is also a component of tobacco smoke. Acetaldehyde is also an endogenous metabolite produced from ethanol. During alcohol consumption, acetaldehyde is formed in the digestive system by microbes in normal gut and flora. Ethanol oxidation also occurs, to a limited extent, in nearby tissues. As ethanol is distributed to the aqueous phase of the human body, it is metabolized continuously to acetaldehyde as long as it remains in the blood and saliva, leading to its accumulation in the saliva and intestinal contents during and after the consumption of alcohol (Lachenmeier et al., 2009a). Lachenmeier and Sohnius (2008) analyzed and evaluated a large sample of different alcoholic beverages. Beer (9 ± 7 mg/l, range 0–63 mg/l) had significantly lower acetaldehyde contents than wine (34 ± 34 mg/l, range 0–211 mg/l), or spirits (66 ± 101 mg/l, range 0–1159 mg/l). The highest acetaldehyde concentrations were generally found in fortified wines (118 ± 120 mg/l, range 12–800 mg/l). Foods and beverages produced or preserved by fermentation may contain small amounts of ethanol and mutagenic (>100 µM) concentrations of acetaldehyde. These include dairy products (i.e. yogurts), fermented soy products (e.g., soy sauces), tofu products, fermented vegetables (e.g., Chinese pickles and kimchi), vinegar and homemade beers. Many fruits, such as apples, may have their own metabolic pathways for acetaldehyde production. In addition, acetaldehyde is used widely as a food additive and aroma agent (Salaspuro 2009a).