Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Frequent Substructures in Chemical Compounds

The discovery of the relationships between chemical structure and biological function is central to biological science and medicine. In this paper we apply data mining to the problem of predicting chemical carcinogenicity. This toxicology application was launched at IJCAI'97 as a research challenge for artificial intelligence. Our approach to the problem is descriptive rather than based on classification; the goal being to find common substructures and properties in chemical compounds, and in this way to contribute to scientific insight. This approach contrasts with previous machine learning research on this problem, which has mainly concentrated on predicting the toxicity of unknown chemicals. Our contribution to the field of data mining is the ability to discover useful frequent patterns that are beyond the complexity of association rules or their known variants. This is vital to the problem, which requires the discovery of patterns that are out of the reach of simple transformations to frequent itemsets. We present a knowledge discovery method for structured data, where patterns reflect the one-to-many and many-to-many relationships of several tables. Background knowledge, represented in a uniform manner in some of the tables, has an essential role here, unlike in most data mining settings for the discovery of frequent patterns.
A Survey of Dynamic Epistemic Logic

Dynamic Epistemic Logic is the study of how to reason about knowledge, belief, and communication. This paper surveys this fast-growing field, covering syntax, semantics, axiomatics, bisimulation and action emulation, expressivity results, extension and embedding results, and issues of truth persistence and paradox that result from doxastic change. Along the way, we identify a number of open problems and areas for further work.
Segmentation of pelvic structures for planning CT using a geometrical shape model tuned by a multi-scale edge detector

Accurate segmentation of the prostate and organs at risk in computed tomography (CT) images is a crucial step for radiotherapy planning. Manual segmentation, as performed nowadays, is a time consuming process and prone to errors due to the a high intra- and inter-expert variability. This paper introduces a new automatic method for prostate, rectum and bladder segmentation in planning CT using a geometrical shape model under a Bayesian framework. A set of prior organ shapes are first built by applying principal component analysis to a population of manually delineated CT images. Then, for a given individual, the most similar shape is obtained by mapping a set of multi-scale edge observations to the space of organs with a customized likelihood function. Finally, the selected shape is locally deformed to adjust the edges of each organ. Experiments were performed with real data from a population of 116 patients treated for prostate cancer. The data set was split in training and test groups, with 30 and 86 patients, respectively. Results show that the method produces competitive segmentations w.r. t standard methods (averaged dice = 0.91 for prostate, 0.94 for bladder, 0.89 for rectum) and outperforms the majority-vote multi-atlas approaches (using rigid registration, free-form deformation and the demons algorithm).
An Archaeometallurgical Investigation on Metal Samples from the Chiaravalle Cross

The production and manufacturing techniques of metals involve expertise, and the study of ancient artifacts relies on interdisciplinary skills. Metalworking processes used in the production of jewelry masterpieces can, for example, give indications on the provenance of an ancient object of an unknown origin and the techniques used. In this regard, metallic samples from the Chiaravalle Cross (a beautiful processional cross with a complex structure, dating to the 13th century) have been studied, combining bulk and point measurements. Neutron-based experiments (like Prompt Gamma Activation Analysis and neutron diffraction) provide the bulk of the elemental and mineralogical composition, while particle induced X-ray emission analyses evidenced important details on its manufacturing techniques.
A Multilevel Model for Comorbid Outcomes: Obesity and Diabetes in the US

Multilevel models are overwhelmingly applied to single health outcomes, but when two or more health conditions are closely related, it is important that contextual variation in their joint prevalence (e.g., variations over different geographic settings) is considered. A multinomial multilevel logit regression approach for analysing joint prevalence is proposed here that includes subject level risk factors (e.g., age, race, education) while also taking account of geographic context. Data from a US population health survey (the 2007 Behavioral Risk Factor Surveillance System or BRFSS) are used to illustrate the method, with a six category multinomial outcome defined by diabetic status and weight category (obese, overweight, normal). The influence of geographic context is partly represented by known geographic variables (e.g., county poverty), and partly by a model for latent area influences. In particular, a shared latent variable (common factor) approach is proposed to measure the impact of unobserved area influences on joint weight and diabetes status, with the latent variable being spatially structured to reflect geographic clustering in risk.
Nanoimmunotherapy – cloaked defenders to breach the cancer fortress

Abstract Cancer continues to be ranked among the top causes of mortality in the world despite the advances made in science and technology. The sub-par performance of cancer therapeutic strategies is due to the transformation of the cancer from a proliferating mass of cells into an impregnable fortress that manipulates and controls the microenvironment to prevent access to any potential cytotoxic factor as well as circumvent the innate immune surveillance processes. Recruitment of the native immune cells to selectively recognize and kill cancer cells can serve to augment the cytotoxic effects of conventional cancer therapeutic approaches. In addition to annihilation of the cancer cells, the induction of memory in the immune cells prevents the possibility of cancer recurrence. However, despite the apparent benefits of cancer immunotherapy, there are several pitfalls that need to be addressed in order to extend these benefits to the clinic. In this context, engineered nanostructured carrier systems can be effectively employed for an activation and priming of the host immune system selectively against the target cancer cells. This has led to the emergence of “nanoimmunotherapy” as an important therapeutic approach against cancer. The use of multi-functional nanomaterials in combination with immunotherapy offers possible solutions to overcome the current limitations in cancer therapy and represents the next generation of “smart therapeutics,” which forms the prime focus of discussion in this review.
Bilateral internal mammary artery grafting: are BIMA better?

Current evidence supports a policy of increasing use of arterial grafts during CABG, in particular bilateral internal mammary arteries The clinical and prognostic benefits of coronary artery bypass grafting (CABG) are well accepted for certain subgroups of patients with ischaemic heart disease,1 and as many as one million patients undergo this operation annually on a worldwide basis. Most CABG patients require grafting of the three main native coronary arteries; for the last 15 years the “standard” operation has achieved this using a single internal mammary artery (SIMA) and supplemental vein grafts performed with cardiopulmonary bypass. Although this procedure achieves excellent short and medium term outcome, and over 70% of patients are alive 12 years after surgery,2 the long term results are limited by progressive vein graft failure.3 Off pump coronary artery bypass (OPCAB) surgery and the increasing use of arterial conduits are now changing the nature of the standard CABG. This article reviews evidence for the routine use of bilateral internal mammary artery (BIMA) grafts in CABG patients. Large observational studies, 4,5 rather than randomised trials, have established the internal mammary artery (IMA) as the “gold standard” graft in CABG. These studies have shown that the use of an IMA graft to the left anterior descending (LAD) coronary artery improves survival and reduces the incidence of late myocardial infarction, recurrent angina, and the need for further cardiac interventions.1,4,5 The evidence is so persuasive that in the UK over 90% of CABG patients now receive a SIMA graft.6 There have been no randomised trials comparing SIMA and BIMA grafts. Nevertheless, the possibility that BIMA grafts may offer additional clinical and survival benefits to that observed with a SIMA graft has been addressed in several observational studies over the last decade (reviewed in Taggart …
Preconception Cardiovascular Risk Factors and Pregnancy Outcome

Background: Pregnancy-related cardiovascular conditions are associated with both poorer pregnancy outcomes and cardiovascular disease later in life. Little is known about the relationship between preconception cardiovascular risk factor levels and pregnancy complications. Methods: Data from the Cardiovascular Risk in Young Finns Study were linked with birth registry data for 1142 primiparous women. Age-standardized levels of total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglycerides, blood pressure, insulin, and glucose from the study visit prior to last menstrual period were calculated. These factors were examined as predictors of gestational age, preterm birth (<37 weeks), birthweight, low birthweight (<2500 g), small-for-gestational-age (weight <10th percentile for gestational age), hypertensive disorders of pregnancy, and gestational diabetes, using linear and Poisson regression with adjustment for age, body mass index, smoking, and socioeconomic status. Results: Higher triglycerides were associated with a higher risk of hypertensive disorders (adjusted risk ratio [aRR] = 1.42 [95% confidence interval (CI) = 0.90-2.23]), preeclampsia (1.70 [1.08-2.65]), and gestational diabetes (1.68 [1.25-2.25]). After removing women with pregnancy complications (n = 30), the estimated aRR for the association between systolic blood pressure and preterm birth was 1.23 (95% CI = 0.99-1.54); for HDL-c and low birthweight, 0.97 (0.73-1.28); for diastolic blood pressure and small-for-gestational-age, 0.98 (0.81-1.20); and for systolic blood pressure and small-for-gestational-age, 1.18 (0.97-1.45). Conclusions: High lipid levels before pregnancy predict an increased risk of preeclampsia and gestational diabetes. Reported associations between these pregnancy complications and later cardiovascular disease of the mother are probably explained, at least in part, by maternal conditions that precede pregnancy. Interventions to improve cardiovascular health before pregnancy may reduce risk of pregnancy complications.
Crystal Structure of a Nucleocapsid-Like Nucleoprotein-RNA Complex of Respiratory Syncytial Virus

RSV in 3D Respiratory syncytial virus (RSV) causes pneumonia and bronchiolitis in infants. RSV is an RNA virus in which the genomic RNA forms part of a nuclease-resistant helical ribonucleoprotein complex. Tawar et al. (p. 1279) now use x-ray and electron microscopy data to model the structure of this nucleocapsid complex and show how it can template RNA synthesis. The crystal structure shows RNA wrapped around a decameric ring of nucleocapsid protein. Combining this structure with electron microscopy data gives a model that shows how polymerase might read out the RNA bases without disassembling the nucleocapsid helix. In negative-strand RNA viruses, viral RNA wraps around a nucleocapsid helix with the bases accessible to the viral polymerase. The respiratory syncytial virus (RSV) is an important human pathogen, yet neither a vaccine nor effective therapies are available to treat infection. To help elucidate the replication mechanism of this RNA virus, we determined the three-dimensional (3D) crystal structure at 3.3 Å resolution of a decameric, annular ribonucleoprotein complex of the RSV nucleoprotein (N) bound to RNA. This complex mimics one turn of the viral helical nucleocapsid complex, which serves as template for viral RNA synthesis. The RNA wraps around the protein ring, with seven nucleotides contacting each N subunit, alternating rows of four and three stacked bases that are exposed and buried within a protein groove, respectively. Combined with electron microscopy data, this structure provides a detailed model for the RSV nucleocapsid, in which the bases are accessible for readout by the viral polymerase. Furthermore, the nucleoprotein structure highlights possible key sites for drug targeting.
Ocean and climate modeling

high-definition global climate model for hypothetical January conditions in eastern Africa, an area that has experienced severe rainfall in recent months. The wispy streamers show high concentrations of water vapor (which contributes to the formation of clouds associated with weather systems); the larger bright white patches are typically associated with such phenomena as thunderstorm clusters. This prototype simulation on a 45-mile grid was done with a large parallel computer at Los Alamos National Laboratory by Steve Hammond of the National Center for Atmospheric Research using a custom parallel version of NCAR's Community Climate Model, Version 2. (Visualization created by Don Middleton of NCAR using the GeoSphere image)
Scatter correction using a primary modulator on a clinical angiography C‐arm CT system

Purpose Cone beam computed tomography (CBCT) suffers from a large amount of scatter, resulting in severe scatter artifacts in the reconstructions. Recently, a new scatter correction approach, called improved primary modulator scatter estimation (iPMSE), was introduced. That approach utilizes a primary modulator that is inserted between the X‐ray source and the object. This modulation enables estimation of the scatter in the projection domain by optimizing an objective function with respect to the scatter estimate. Up to now the approach has not been implemented on a clinical angiography C‐arm CT system. Methods In our work, the iPMSE method is transferred to a clinical C‐arm CBCT. Additional processing steps are added in order to compensate for the C‐arm scanner motion and the automatic X‐ray tube current modulation. These challenges were overcome by establishing a reference modulator database and a block‐matching algorithm. Experiments with phantom and experimental in vivo data were performed to evaluate the method. Results We show that scatter correction using primary modulation is possible on a clinical C‐arm CBCT. Scatter artifacts in the reconstructions are reduced with the newly extended method. Compared to a scan with a narrow collimation, our approach showed superior results with an improvement of the contrast and the contrast‐to‐noise ratio for the phantom experiments. In vivo data are evaluated by comparing the results with a scan with a narrow collimation and with a constant scatter correction approach. Conclusions Scatter correction using primary modulation is possible on a clinical CBCT by compensating for the scanner motion and the tube current modulation. Scatter artifacts could be reduced in the reconstructions of phantom scans and in experimental in vivo data.
Impact of the approximated on-line centering and whitening in OL-JADE on the quality of the estimated fetal ECG

OL-JADE is an on-line method for fetal ECG extraction from non-invasive potential recordings, able to work in real-time on a DSP. With respect to the original JADE algorithm, it exploits a recursive sample-by-sample approximated centering and whitening stage that partially violates the requirements of the subsequent JADE stage. In this paper this aspect is investigated showing a comparison with another similar algorithm, tracking BLISS, on artificial mixtures of real signals. OL-JADE presents a reduced complexity and, in case of time variances in the mixing process, permutations are confined to the involved sources. The imperfect centering and whitening have limited consequences in terms of signal distortions in presence of time variances, restricted to the time span of such variations.
AGELI: An integrated platform for the Assessment of national Genetic Evaluation results by Learning and Informing

We present an integrated platform for preprocessing, analysis, alarm issuing and presentation of national genetic evaluation data based on data-mining. Our goal is the integrated qualitative description of national genetic evaluation results, concerning three milk yield traits that constitute a critical issue in the range of services provided by Interbull. Although the standard method for quality assurance appears sufficiently functional (Klei et al., 2002), during the last years there has been a progress concerning an alternative validation method of genetic evaluation results using data-mining (Banos et al., 2003; Diplaris et al., 2004; Han and Kamber, 2000), potentially leading to inference on data quality. A new alarming technique based on multiple criteria was recently established in order to assess and assure data quality (Diplaris et al., 2004). The whole idea was to exploit datamining techniques, i.e. decision trees, and then apply a goodness of fit test to individual tree nodes and an F-test in corresponding nodes from consecutive evaluation runs, aiming at discovering possible abnormalities in bull proof distributions at various regions. In a previous report (Banos et al., 2003) predictions led to by associations discovered had been qualitatively compared to actual proofs and discrepancies had been confirmed using a data set with known errors.
Thalamic Shape Abnormalities in Antipsychotic Naïve Schizophrenia

Background: Neurodevelopmental hypothesis of schizophrenia states abnormal pruning as one of the pathogenetic mechanism in schizophrenia. Though thalamic volume abnormalities have been documented, the shape differences of thalamus in antipsychotic-free schizophrenia in comparison with age- and sex-matched healthy volunteers need validation. Materials and Methods: We examined antipsychotic naïve schizophrenia patients (n=60) and age- and sex-matched healthy volunteers (n=44). The thalamic shape abnormalities were analyzed from their coded structural magnetic resonance imaging (MRI) data using three-dimensional automated image analysis software, FMRIB's (Oxford Center for the functional MRI of the brain) tools-FIRST (FMRIB's Integrated Registration and Segmentation Tool) by creating deformable mesh model. Correlation with the psychopathology scores was carried out using F-statistics. Results: Patients with schizophrenia showed significant inward deformations in the regions corresponding to anterior, ventromedial, mediodorsal, and pulvinar nuclei. There was a direct correlation between negative syndrome score and the deformation in the right mediodorsal and right pulvinar nuclei. Conclusion: The inward deformations of thalamus in antipsychotic naive schizophrenia patients correspond to those nuclei which have reciprocal connections with frontal, superior temporal, and anterior cingulate regions and support the neurodevelopmental hypothesis of schizophrenia.
Is it important to measure or reduce C-reactive protein in people at risk of cardiovascular disease?

Systemic and local vascular inflammation is implicated in atherogenesis. High-sensitivity (hs) assays detecting low concentrations of C-reactive protein (CRP) in healthy individuals have delineated associations of this inflammation marker with cardiovascular events years later. A 160 309-person participant level meta-analysis of 54 prospective studies found the relationship between log-CRP concentration and cardiovascular disease (CVD) events to be linear, with a 2.5-fold risk difference in individuals at opposite extremes of the CRP distribution.1 In vitro studies and animal experiments point to potentially atherogenic actions of CRP,2 and statins lower both CRP and low-density lipoprotein cholesterol (LDL-C). 3 The Justification for the Use of statins in Primary prevention: an Intervention Trial Evaluating Rosuvastatin (JUPITER),4 designed to ‘assess the effect of rosuvastatin on first ever cardiovascular events in apparently healthy men and women who do not qualify for statin therapy due to low levels of LDL-C, but who are at increased cardiovascular risk due to elevated levels of hs-CRP’, was halted because of ‘unequivocal evidence of a reduction in cardiovascular morbidity and mortality among patients who received CRESTOR (rosuvastatin) when compared to placebo’ (http://clinicaltrials.gov/ct2/show/[NCT00239681][1]). Consequently, the US Food and Drug Administration approved an amended license for rosuvastatin for the primary prevention of CVD events in men and women over 50 and 60 years, respectively, with one other risk factor and a CRP concentration of >2 mg/L. Even before the publication of this trial, the estimated 5 million ‘hs-CRP’ tests were being ordered annually in the USA,5 and updated Canadian guidance on CVD prevention6 now recommends the consideration of ‘hs-CRP’ measurement in those at intermediate risk. The 2010 American College of Cardiology Foundation/American Heart Association Guidelines stated that in ‘men 50 years of age or older and women 60 years of age or older with an LDL-C < 130 … [1]: /lookup/external-ref? link_type=CLINTRIALGOV&access_num=NCT00239681&atom=%2Fehj%2F33%2F18%2F2258.atom