Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating Graph Features for Predicting Protein-Protein Interactions

This chapter presents applications of machine learning to predicting protein-protein interactions (PPI) in Saccharomyces cerevisiae. Several supervised inductive learning methods have been developed that treat this task as a classification problem over candidate links in a PPI network – a graph whose nodes represent proteins and whose arcs represent interactions. Most such methods use feature extraction from protein sequences (e.g., amino acid composition) or associated with protein sequences directly (e.g., GO annotation). Others use relational and structural features extracted from the PPI network, along with the features related to the protein sequence. Topological features of nodes and node pairs can be extracted directly from the underlying graph. This chapter presents two approaches from the literature (Qi et al., 2006; Licamele & Getoor, 2006) that construct features on the basis of background knowledge, an approach that extracts purely topological graph features (Paradesi et al., 2007), and one that combines knowledge-based and topological features (Paradesi, 2008). Specific graph features that help in predicting protein interactions are reviewed. This study uses two previously published datasets (Chen & Liu, 2005; Qi et al., 2006) and a third dataset (Paradesi, 2008) that was created by combining and augmenting three existing PPI databases. The chapter includes a comparative study of the impact of each type of feature (topological, protein sequence-based, etc.) on the sensitivity and specificity of classifiers trained using specific types of features. The results indicate gains in the area under the sensitivity-specificity curve for certain algorithms when topological graph features are combined with other biological features such as protein sequence-based features.
Assessing the Anatomical and Functional Efficacy of Aflibercept on Wet ARMD: An OCT and Mferg Recording

Objective: To investigate the therapeutic efficacy of aflibercept on sub-foveal choroidal neovascularization due to Age-Related Macular Degeneration (ARMD). Methods: Fifteen patients (15 eyes) with sub-foveal choroidal neovascularization due to ARMD were treated with intravitreal aflibercept. The doses were monthly for the first three months, being repeated every three months after for one year, using 2 mg of intravitreal aflibercept. A total of six aflibercept injections were, finally, performed during the 12-month study. All patients underwent a complete ophthalmic examination, including the measurement of bestcorrected visual acuity, fundus examination, intraocular pressure measurement, fluorescein angiography, optical coherence tomography (OCT) scan and multifocal electroretinography (mfERG) recording, at the baseline and at the first, second, third, sixth, ninth and 12th month after the first injection of aflibercept. Two masked examiners evaluated the visual acuity based on standard Snellen charts. Results: Fifteen patients (15 eyes), of mean age 69.2 ± 4.9 years old, with sub-foveal choroidal neovascularization due to ARMD were participated in this study. The mean BCVA was 0.12 ± 0.08, 0.20 ± 0.10, 0.25 ± 0.1, 0.28 ± 0.1, 0.34 ± 0.14, 0.36 ± 0.14 and 0.40 ± 0.14 decimal, at presentation, 1st, 2nd, 3rd, 6th, 9th and 12th month, respectively. Significant differences in amplitudes but not in latencies of three rings were observed over time. Significant reductions were noted among the central retinal thickness measurements before intravitreal aflibercept and at 1st, 2nd, 3rd, 6th, 9th and 12th month (465.0 ± 161.4, 374.9 ± 139.5, 323.3 ± 113.8, 290.3 ± 85, 263.3 ± 69, 243.0 ± 60.6 and 226.9 ± 63.5, respectively). Conclusion: This is the first time that anatomical and functional improvement of the macula in patients with subfoveal choroidal neovascularization due to ARMD was shown objectively, based on OCT and mfERG recordings. In addition, the improvement of visual acuity was noted over time. Our study supports the fact that intravitreal use of aflibercept is safe and effective in treating sub-foveal choroidal neovascularization observed in patients with ARMD
Real-Time Euclid: A language for reliable real-time systems

Real-Time Euclid, a language designed specifically to address reliability and guaranteed schedulability issues in real-time systems, is introduced. Real-Time Euclid uses exception handlers and import/export lists to provide comprehensive error detection, isolation, and recovery. The philosophy of the language is that every exception detectable by the hardware or the software must have an exception-handler clause associated with it. Moreover, the language definition forces every construct in the language to be time- and space-bounded. Consequently, Real-Time Euclid programs can always be analyzed for guaranteed schedulability of their processes. Thus, it is felt that Real-Time Euclid is well-suited for writing reliable real-time software.
Outliers and data descriptions

In previous research the support vector data description (SVDD) is proposed to solve the problem of one-class classification. In one-class classification, one set of data, called the target set, has to be distinguished from the rest of the feature space. In the original optimization of the support vector data description, two parameters have to be given beforehand by the user. In this paper a new, heuristic, error is defined. Minimizing this error, both free parameters in the SVDD can be determined without the use of example outlier objects. This paper shows under what circumstances the heuristic error correlates well with the true error.
Survival and prognostic factors in malignant pleural mesothelioma: a retrospective study of 314 patients in the west part of Japan.

OBJECTIVE The objective in our study was to examine baseline and other characteristics associated with survival in patients with malignant pleural mesothelioma in Japan. METHODS Three hundred and fourteen patients with an adjudicated diagnosis of mesothelioma were examined. Survival was evaluated by the Kaplan-Meier method with the log-rank test. The Cox model was used to estimate the hazard ratio for the possible prognostic factors. RESULTS Of 314 patients, 223 (71%) died and only 40 (13%) were still alive at the end of the observation period starting from the day of diagnosis, while 51 (16%) were transferred to other hospitals or had the last health service contact before the end of the study period yielding the median survival of 308 days. In the multivariate analysis, age older than 70 years (hazard ratio = 2.17; 95% confidence interval, 1.36-3.46), non-epithelioid type (hazard ratio = 1.58; 95% confidence interval, 1.15-2.18), poor performance status (hazard ratio = 3.22; 95% confidence interval, 1.19-8.74), high white blood cell count (hazard ratio = 1.49; 95% confidence interval, 0.99-2.26) and high C-reactive protein level (hazard ratio = 1.80; 95% confidence interval, 1.06-3.06) were negatively associated with survival, after adjustment for other factors. CONCLUSIONS Some baseline conditions including old age, poor performance status, non-epithelioid type, high white blood cell count and high C-reactive protein level were determinants of poor survival of patients with malignant mesothelioma.
The Role of Cytidine Deaminases on Innate Immune Responses against Human Viral Infections

The APOBEC family of proteins comprises deaminase enzymes that edit DNA and/or RNA sequences. The APOBEC3 subgroup plays an important role on the innate immune system, acting on host defense against exogenous viruses and endogenous retroelements. The role of APOBEC3 proteins in the inhibition of viral infection was firstly described for HIV-1. However, in the past few years many studies have also shown evidence of APOBEC3 action on other viruses associated with human diseases, including HTLV, HCV, HBV, HPV, HSV-1, and EBV. APOBEC3 inhibits these viruses through a series of editing-dependent and independent mechanisms. Many viruses have evolved mechanisms to counteract APOBEC effects, and strategies that enhance APOBEC3 activity constitute a new approach for antiviral drug development. On the other hand, novel evidence that editing by APOBEC3 constitutes a source for viral genetic diversification and evolution has emerged. Furthermore, a possible role in cancer development has been shown for these host enzymes. Therefore, understanding the role of deaminases on the immune response against infectious agents, as well as their role in human disease, has become pivotal. This review summarizes the state-of-the-art knowledge of the impact of APOBEC enzymes on human viruses of distinct families and harboring disparate replication strategies.
Una propuesta metodológica para estimar los cambios sobre el valor de la propiedad: estudio de caso para Bogotá aplicando propensity score matching y

Este estudio comparo los resultados obtenidos mediantes Propensity Score Matching (PSM, nombre y sigla en ingles) y un modelo de precios hedonico espaciales (PHE) para estimar elcambio en el valor de la propiedad en Bogota, cuando un predio se encuentra ubicado cerca auna estacion de TransMilenio (TM). Asi, en 2008, las viviendas colindantes a una estacion deTM en promedio obtienen un precio mayor entre $117.500 (PHE) y $115.403 (PSM) por metro cuadrado, cuando es contrastado con el valor por metro cuadrado de los predios alejados del area de influencia del sistema TM y que potencialmente hubiesen podido estar afectados directamente por el proyecto.
Methods for Joint Imaging and RNA-seq Data Analysis

Emerging integrative analysis of genomic and anatomical imaging data which has not been well developed, provides invaluable information for the holistic discovery of the genomic structure of disease and has the potential to open a new avenue for discovering novel disease susceptibility genes which cannot be identified if they are analyzed separately. A key issue to the success of imaging and genomic data analysis is how to reduce their dimensions. Most previous methods for imaging information extraction and RNA-seq data reduction do not explore imaging spatial information and often ignore gene expression variation at genomic positional level. To overcome these limitations, we extend functional principle component analysis from one dimension to two dimension (2DFPCA) for representing imaging data and develop a multiple functional linear model (MFLM) in which functional principal scores of images are taken as multiple quantitative traits and RNA-seq profile across a gene is taken as a function predictor for assessing the association of gene expression with images. The developed method has been applied to image and RNA-seq data of ovarian cancer and KIRC studies. We identified 24 and 84 genes whose expressions were associated with imaging variations in ovarian cancer and KIRC studies, respectively. Our results showed that many significantly associated genes with images were not differentially expressed, but revealed their morphological and metabolic functions. The results also demonstrated that the peaks of the estimated regression coefficient function in the MFLM often allowed the discovery of splicing sites and multiple isoform of gene expressions.
Modified Fuzzy K-mean clustering using MapReduce in Hadoop and cloud

Apache Hadoop is an open source software framework which structures Big data (both structured and unstructured). It is nowadays one of the biggest motivator in market as data storage is inexpensive in it. The storage method of Hadoop uses a distributed file system which lets the user store large amount of data by simply adding more nodes to a Hadoop cluster. Clustering a large amount of data is a point of concern. MapReduce, a programming model used by Hadoop allows a parallelization technique by decomposing a larger problem involving large dataset to smaller portion of data and then executing it. A scalable machine learning library named as Mahout is an approach to clustering which runs on Hadoop. In this paper, the Hadoop multi-node cluster is formed using Amazon EC2. This paper focuses on Fuzzy k-mean clustering algorithm which is modified by centroid generation method using MapReduce in Hadoop. Experimental results depict a decrease in the number of iterations thereby leading to a decrease in the execution time when modification of Fuzzy K-mean clustering algorithm is done using Canopy generation in MapReduce in Hadoop.
Product differentiation and state promotion of farm produce: an analysis of the Jersey fresh tomato.

Product differentiation, a prerequisite for successful state promotion of state branded farm products, may be reflected by differences in the own-price, cross-price and income elasticties of demand between a state's brand and other products. This paper tests for such differentiation by estimating demand functions for tomatoes available at the retail level in New Jersey. The "Jersey Fresh" brand is shown to have higher own-price and income elasticities of demand. It is thus perceived to be of higher quality than others. Consumers are also found to be origin biased. Promotion based on the Jersey Fresh's unique attributes and on encouraging further origin bias may have a good chance of success.
With a little help from a friend: a shower calendar to save water

This design case presents and discusses the Shower Calendar, a "persuasive" concept for reducing the con-sumption of water for showering. It starts from a dis-cussion of different types of feedback employed by earlier design cases. Based on this, we designed the Calendar concept as an ambient, persistent and indi-vidualized feedback. A field study with two families (6 individuals) revealed that the Calendar fosters goal setting, comparison, competition, and communication. In addition, quantitative data showed one family to have been more successful in translating the Calendar's offer into actual behavior change, i.e., saving water. This highlights that change is not achieved by the product itself (as in automation or regulation), but by the people involved.
Schooling and Labor Market Consequences of School Construction in Indonesia: Evidence from an Unusual Policy Experiment

Between 1973 and 1978, the Indonesian Government constructed over 61,000 primary schools throughout the country. This is one of the largest school construction programs on record. I evaluate the effect of this program on education and wages by combining differences across regions in the number of schools constructed with differences across cohorts induced by the timing of the program. The estimates suggest that the construction of primary schools led to an increase in education and earnings. Children ages 2 to 6 in 1974 received 0.12 to 0.19 more years of education for each school constructed per 1,000 children in their region of birth. Using the variations in schooling generated by this policy as instrumental variables for the impact of education on wages generates estimates of economic returns to education ranging from 6.8 percent to 10.6 percent.
Evaluating Earnings Management in Taiwan’s Nonprofit Hospitals Using Cross-Sectional Abnormal Items Models

The purpose of this paper is to examine whether earnings management in the non profit hospitals of Taiwan and analyze the earnings management behavior. We developed and tested the standard-Jones, modified-Jones, BD (abnormal bad debt), WCA (abnormal working capital), NORR (abnormal non-operating or non-revenue generating activity expenditure), and NGSP-models (abnormal net gain on the sale of property) to estimate the amount of abnormal accrual items or abnormal real items. Empirical evidence suggested that the BD, NORR and NGSP models may be used to determine levels of earnings management. Thus, these models are ideal for determining how Taiwan’s nonprofit hospitals manage their earnings.
Frequency-Domain Equalization in Single-Carrier Transmission: Filter Bank Approach

This paper investigates the use of complex-modulated oversampled filter banks (FBs) for frequency-domain equalization (FDE) in single-carrier systems. The key aspect is mildly frequency-selective subband processing instead of a simple complex gain factor per subband. Two alternative low-complexity linear equalizer structures with MSE criterion are considered for subband-wise equalization: a complex FIR filter structure and a cascade of a linear-phase FIR filter and an allpass filter. The simulation results indicate that in a broadband wireless channel the performance of the studied FB-FDE structures, with modest number of subbands, reaches or exceeds the performance of the widely used FFT-FDE system with cyclic prefix. Furthermore, FB-FDE can perform a significant part of the baseband channel selection filtering. It is thus observed that fractionally spaced processing provides significant performance benefit, with a similar complexity to the symbol-rate system, when the baseband filtering is included. In addition, FB-FDE effectively suppresses narrowband interference present in the signal band.
The Role of Bone Subtraction Computed Tomographic Angiography in Determining Intracranial Aneurysms in Non-Traumatic Subarachnoid Hemorrhage

Background: The presence of blood in the subarachnoid space is an acute pathology with a serious risk of death and complications. The most common etiology (approximately 80%) is intracranial aneurysm. Objectives: The aim of this study was to assess the role of bone subtracted computed tomographic angiography (BSCTA), a novel and noninvasive method for determining and characterizing intracranial aneurysms. Patients and Methods: Sixty consecutive patients with clinically suspected non-traumatic subarachnoid hemorrhage (SAH) were considered to enter the study. The subtraction quality was inadequate in ten patients; thus, they were excluded, leaving 50 patients (84.4%) in the study. Bone subtracted and non-subtracted 3D images were obtained from the BSCTA raw data sets. All images obtained by digital subtraction angiography (DSA), BSCTA, and computed tomographic angiography (CTA) were evaluated for the presence or absence of an aneurysm and the location, minimal sac diameter, and neck size ratio of the aneurysm. DSA was considered as the gold standard during the evaluation of the data. Results: Of the 50 patients who participated in this study, 11 had no aneurysms as determined by both CTA and DSA. Examination of the remaining 39 patients revealed the presence of 51 aneurysms. While 3D-CTA could not detect six aneurysms that were located in the base of the skull, 3D-BSCTA easily detected them. Moreover, five aneurysms were only partially detected by 3D-CTA. According to this data, the sensitivity of 3D-BSCTA and 3D-CTA was calculated as 98% and 86.3%, respectively; the specificity was calculated as 100% and 90.9%, respectively, per aneurysm; and the sensitivity of 100% for 3D-BSCTA and 98% for 3D-CTA was achieved by using combined images with multi-planar reconstruction (MPR) and maximum intensity projection (MIP). BSCTA detected and characterized the aneurysms as well as DSA, and BSCTA and DSA gave concordant results in detecting aneurysms. Conclusions: BSCTA is easily accessible, less time consuming, and most importantly, a non-invasive technique for detecting intracranial aneurysms. It is also suitable for patients who have been referred to emergency services. Therefore, it can be used in emergency conditions and as a first-line diagnostic method in patients with non-traumatic SAH.
A Maternal–Offspring Coadaptation Theory for the Evolution of Genomic Imprinting

Imprinted genes are expressed either from the maternally or paternally inherited copy only, and they play a key role in regulating complex biological processes, including offspring development and mother–offspring interactions. There are several competing theories attempting to explain the evolutionary origin of this monoallelic pattern of gene expression, but a prevailing view has emerged that holds that genomic imprinting is a consequence of conflict between maternal and paternal gene copies over maternal investment. However, many imprinting patterns and the apparent overabundance of maternally expressed genes remain unexplained and may be incompatible with current theory. Here we demonstrate that sole expression of maternal gene copies is favored by natural selection because it increases the adaptive integration of offspring and maternal genomes, leading to higher offspring fitness. This novel coadaptation theory for the evolution of genomic imprinting is consistent with results of recent studies on epigenetic effects, and it provides a testable hypothesis for the origin of previously unexplained major imprinting patterns across different taxa. In conjunction with existing hypotheses, our results suggest that imprinting may have evolved due to different selective pressures at different loci.
Dynamics of the Segre varieties of a real submanifold in complex space

Let M ⊂ C be a smooth (C∞) real submanifold of codimension d with 0 ∈ M . We choose smooth real-valued functions r = (r1, . . . , rd), with differentials dr1, . , drd linearly independent at 0, so thatM is defined by r = 0 near the origin. If the complex differentials ∂r1, . , ∂rd are also linearly independent at 0, thenM is called generic (near the origin). If M is a real-analytic, generic submanifold, there is a family of complex submanifolds of C , called the Segre varieties associated to M , which carry a great deal of information about the local geometry of M . The Segre varieties have been used by many mathematicians to study mappings between generic submanifolds. (See the end of this introduction for some specific references.) In this paper, we shall consider an algebraic substitute for these varieties for the case of smooth manifolds by introducing a formal mapping which, in the realanalytic case, parametrizes the Segre varieties. Our main objective is to study iterations of this mapping and relate these iterations to the local CR geometry of the manifold. If r is a local defining function of a smooth generic submanifold M as above, then we denote by ρj(Z, Z) the Taylor series of rj at 0. We write ρ = (ρ1, . . . , ρd). We consider ρj(Z, ζ) as a formal power series in the 2N indeterminates (Z, ζ). We shall denote the ring of such power series with complex coefficients by C[[Z, ζ]]. By a formal mapping F : (C, 0) → (C, 0), we shall mean a p-tuple F (x) = (F1(x), . , Fp(x)), where x = (x1, . . . , xk), of formal power series Fj ∈ C[[x]] without constant terms. The rank of F , RkF , is defined as the rank of the Jacobian matrix ∂F/∂x regarded as a Kx-linear mapping Kx → Kx, where Kx denotes the field of fractions of C[[x]]. Hence RkF is the largest integer s such that there is an s× s minor of the matrix ∂F/∂x which is not 0 as a formal power series in x. Let γ(ζ, t), where ζ = (ζ1, . . . ζN), t = (t1, . . . , tn), and n = N − d, be a formal mapping (C × C, 0)→ (C , 0) such that