Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Essential Genes based on Machine Learning and Information Theoretic Features

Computational tools have enabled a relatively simple prediction of essential genes (EGs), which would otherwise be done by costly and tedious gene knockout experimental procedures. We present a machine learning based predictor using information-theoretic features derived exclusively from DNA sequences. We used entropy, mutual information, conditional mutual information, and Markov chain models as features. We employed a support vector machine (SVM) classifier and predicted the EGs in 15 prokaryotic genomes. A fivefold cross-validation on the bacteria E. coli, B. subtilis, and M. pulmonis resulted in AUC score of 0.85, 0.81, and 0.89, respectively. In cross-organism prediction, the EGs of a given bacterium are predicted using a model trained on the rest of the bacteria. AUC scores ranging from 0.66 to 0.9 and averaging 0.8 were obtained. The average AUC of the classifier on a one-to-one prediction among E. coli, B. subtilis, and Acinetobacter is 0.85. The performance of our predictor is comparable with recent and state-of-the art predictors. Considering that we used only sequence information on a problem that is much more complicated, the achieved results are very
A flexible robot control solution for hip resurfacing surgery

Robots are becoming more common in our lives. Nowadays we observe robots working in houses, pharmacies, stores, and even in operating rooms. This evolution to become more human friendly and easier to interact cannot assume industrial robots, due to their heavy weight. In order to be well accepted by humans, when a robot is inserted into a room, we have to consider human safety and space limitations, which is critical in medical procedures, therefore, the use lightweight robots is required. This implies some non-standard control techniques in order to remove robot flexible links vibrations that may occur. In this work, a flexible manipulator robot control methodology is presented with the aim to perform a Hip Resurfacing Arthroplasty Surgery.
Rates of Convergence for a Class of Global Stochastic Optimization Algorithms

Inspired and motivated by the recent advances in simulated annealing algorithms, this paper analyzes the convergence rates of a class of recursive algorithms for global optimization via Monte Carlo methods. By using perturbed Liapunov function methods, stability results of the algorithms are established. Then the rates of convergence are ascertained by examining the asymptotic properties of suitably scaled estimation error sequences.
Mixed-Metal Tungsten Oxide Photoanode Materials Made by Pulsed-Laser in Liquids Synthesis.

Globally scalable sunlight-driven devices that convert solar energy into storable fuels will require efficient light absorbers that are made of non-precious elements. Suitable photoanode materials are yet to be discovered. Here we utilised the timesaving nature of pulsed-laser-in-liquids synthesis and prepared a series of neat and mixed-metal tungsten oxide photoanode materials to investigate the effect of ad-metals on optical and photocurrent generation properties. We obtained sub-μm-sized materials with different colours from W, Al, Ta, or first-row transition metal targets in water or aqueous ammonium metatungstate solutions. We observed metastable polymorphs of WO3 and tungsten oxides with varying degrees of oxygen deficiency. Pulsed-laser in liquids synthesis of Ni in ammonium metatungstate solutions produce hollow spheres (with ≤6 % Ni with respect to W). Photocurrent generation in strong aqueous acid is highest in mixed-metal tungsten oxide photoanode materials with around 5 % of iron or nickel.
The Impact of Personality on Virtual Team Creativity and Quality

A series of experiments investigated creativity and quality of work-product solutions in virtual teams (Ocker,2007, 2005; Ocker & Fjermestad, 1998; Ocker, Hiltz, & Johnson, 1998; Ocker, Hiltz, Turoff, & Fjermestad, 1996). Across experiments, small teams with about five graduate students interacted for approximately two weeks to determine the high-level requirements and design for a computerized post office (Goel, 1989; Olson, Olson, Storrosten, & Carter, 1993). The means of interaction was manipulated in these experiments such that teams interacted via one of the following treatments: (1) asynchronous computer-medicated communication (CMC), (2) synchronous CMC, (3) asynchronous CMC interspersed with face-to-face (FtF) meetings, or (4) a series of traditional FtF meetings without any electronic communication. A repeated finding across experiments was that teams interacting only using asynchronous CMC—that is, teams without any FtF or synchronous communication—produced significantly more creative results than teams in the other treatments. Additionally, asynchronous virtual teams rated high in creativity were generally not the same teams that were judged high in terms of the quality of their deliverable. To further examine these findings, this article presents results of an exploratory study designed to investigate the impact of individual personality facets on team outcomes. The objective of this study is to determine whether differences in team outcomes—in terms of the level of creativity versus the quality of the team deliverable—can be predicted by individual member personality. Specifically, two research questions are investigated:
Pathologic margin involvement and the risk of recurrence in patients treated with breast-conserving therapy.

BACKGROUND The relationship between the microscopic margins of resection and ipsilateral breast recurrence (IBR) after breast-conserving therapy for carcinomas with or without an extensive intraductal component (EIC) has not been adequately defined. METHODS Of 1,790 women with unilateral clinical Stage I or II breast carcinoma treated with radiation therapy as part of breast-conserving therapy, 343 had invasive ductal histology evaluable for an extensive intraductal component (EIC), had inked margins that were evaluable for an review of their pathology slides, and received > or = 60 Gray to the tumor bed; these 343 women constitute the study population. The median follow-up was 109 months. All available slides were reviewed by one of the study pathologists. Final inked margins of excision were classified as negative > 1 mm (no invasive or in situ ductal carcinoma within 1 mm of the inked margin); negative-1 mm, or close carcinoma < or = 1 mm from the inked margin but not at the margin); or positive (carcinoma at the inked margin). A focally positive margin was defined as invasive or in situ ductal carcinoma at the margin in three or fewer low-power fields. The first site of recurrent disease was classified as either ipsilateral breast recurrence (IBR) or distant metastasis/regional lymph node failure. RESULTS Crude rates for the first site of recurrence were calculated first for all 340 patients evaluable at 5 years, then separately for the 272 patients with EIC-negative cancers and the 68 patients with EIC-positive cancers. The 5-year rate of IBR for all patients with negative margins was 2%; and for all patients with positive margins, the rate was 16%. Among patients with negative margins, the 5-year rate of IBR was 2% for all patients with close margins (negative < or = 1 mm) and 3% for those with negative > 1 mm margins. For patients with close margins, the rates were 2% and 0% for EIC-negative and EIC-positive tumors, respectively; the corresponding rates for patients with negative margins > 1 mm were 1% and 14%. The 5-year rate of IBR for patients with focally positive margins was 9% (9% for EIC-negative and 7% for EIC-positive patients). The 5-year crude rate of IBR for patients with greater than focally positive margins was 28% (19% for EIC-negative and 42% for EIC-positive patients). CONCLUSIONS Patients with negative margins of excision have a low rate of recurrence in the treated breast, whether the margin is > 1 mm or < or = 1 mm and whether the carcinoma is EIC-negative or EIC-positive. Among patients with positive margins, those with focally positive margins have a considerably lower risk of local recurrence than those with more than focally positive margins, and could be considered for breast-conserving therapy.
A novel random projection model for Linear Discriminant Analysis based face recognition

Linear Discriminant Analysis (LDA) is one of the commonly used statistical methods for feature extraction in face recognition tasks. However, LDA often suffers from the Small Sample Size (3S) problem, which occurs when the total number of training data is smaller than the dimension of input feature space. To deal with 3S problem, this paper proposes a novel approach for LDA-based face recognition using Random Projection (RP) technique. The advantages of random projection mainly include three aspects such as data-independent, dimensionality reduction and approximate distance preservation. So, based on the Johnson-Lindenstrauss theory, a new RP model is proposed for dimensionality reduction and simultaneously for learning the structure of the manifold with high accuracy. If the within-class scatter matrix is nonsingular in the randomly mapped feature space, LDA can be performed directly. Otherwise, RP will be followed by our previous Regularized Discriminant Analysis (RDA) approach for face recognition. Two public available databases, namely FERET and CMU PIE databases, are selected for evaluation. Comparing with PCA, DLDA and Fisherface approaches, our proposed method gives the best performance.
Number Versus Contour Length in Infants' Discrimination of Small Visual Sets

This study examined infants' use of contour length in number discrimination tasks. We systematically varied number and contour length in a visual habituation experiment in order to separate these two variables. Sixteen 6- to 8-month-old infants were habituated to displays of either two or three black squares on a page. They were then tested with alternating displays of either a familiar number of squares with a novel contour length or a novel number of squares with a familiar contour length. Infants dishabituated to the display that changed in contour length, but not to the display that changed in number. We conclude that infants base their discriminations on contour length or some other continuous variable that correlates with it, rather than on number.
Bit Loading Algorithm Based on a Probabilistic Approach for HomePlug AV

In this paper bit loading algorithms that try to maximize the throughput, guaranteeing the overall BER below a fixed target, are investigated. In particular,the optimal solution is given and an approximation based on a probabilistic approach is detailed, providing a very simple implementation with negligible loss. The proposed solution is tested in the HPAV system, using a realistic power line channel model. Numerical results, in terms of throughput and complexity, show that the proposed solution is a good trade-off between performance and complexity.
Do Insulin‐treated Diabetic Patients Use an Injection‐meal‐interval in Daily Life?

The usefulness of routine screening for islet cell antibodies (ICA) in late-onset diabetes is still a matter for debate. Gregory and Tattersall reported that ICA status knowledge did not significantly contribute to the management of the disease, in particular for deciding to initiate insulin therapy. ’ Yet, ICA determination i s thought to help identify latent Type 1 (insulin-dependent) diabetes in subjects presenting with late-onset diabetes, in particular in lean female subjects with HLA-DR3/DR4 haplotype excess and associated th yrogastri c auto i m m u n i ty . In this group, the combination of ICA with (sub)normal weight at diagnosis and Type 1 diabetes epidemiology predicts insulin-dependency, and sustains the clinical diagnosis of latent Type 1 diab e t e ~ . ~ , ~ On the other hand, late-onset diabetes occurring in obese subjects strongly points toward Type 2 (non-insulin dependent) diabetes, and ICA determination i s often not performed at diagnosis. In previous studies on the prognostic value of ICA in late-onset diabetes, obese subjects were not included or poorly represented, and therefore the predictive value of ICA positivity in this sizeable cohort of diabetic subjects was not properly addressed. 5,h We did a retrospective analysis of the epidemiological, clinical, and autoimmune status of all consecutive obese (>120 % ideal body weight, IBW) subjects presenting with late-onset (>45 years) diabetes and ICA positivity (ICA+), over a 3-year period (1 987-90). ICA+ was detected by a semi-quantitative indirect irnmunofluorescence method. ICA+ subjects (n=14) were all white Caucasians, and represented 8 % of all ICA+ adult patients screened at St Luc Academic Hospital (Brussels) over that period. These 14 ICA+ patients had a long-term history of obesity (mean maximum IBW (*SEMI 144 2 7 %) and were still obese/overweight at diagnosis of diabetes (125 & 9 % IBW). At diagnosis, their mean age was 62 ? 3 (range: 45-80) years, and 93 % were female. A family history for diabetes was found in half the subjects (n=7). HLA-DR3/DR4 haplotypes were: HLA-DR3 (n=2), HLA-DR4(n=l), and HLA-DR3/DR4 (n=3). These patients combined some characteristics of Type 2 diabetes epidemiology with latent Type 1 diabetes, since all patients eventually developed frank insulin-dependency within 1-36 months. Eleven ICA+ subjects
Classifying Out-of-vocabulary Terms in a Domain-Specific Social Media Corpus

In this paper we consider the problem of out-of-vocabulary term classification in web forum text from the automotive domain. We develop a set of nine domain- and application-specific categories for out-of-vocabulary terms. We then propose a supervised approach to classify out-of-vocabulary terms according to these categories, drawing on features based on word embeddings, and linguistic knowledge of common properties of out-of-vocabulary terms. We show that the features based on word embeddings are particularly informative for this task. The categories that we predict could serve as a preliminary, automatically-generated source of lexical knowledge about out-of-vocabulary terms. Furthermore, we show that this approach can be adapted to give a semi-automated method for identifying out-of-vocabulary terms of a particular category, automotive named entities, that is of particular interest to us.
Microwave methods of ferroelectrics and related materials investigation

Ferroelectric materialspsila distinct feature is large dielectric permittivity epsiv which sometimes is accompanied by the large loss tangent tandelta. Often this becomes an obstacle to conduct their accurate characterization despite of variety of techniques available. This report is devoted to the selection of proper method for specific cases of bulk or film materials investigation to obtain reliable data of their epsiv and tandelta.
A 90-nm CMOS embedded low power SRAM compiler

In this paper a highly flexible low power single port Static Random Access Memory (SRAM) compiler design is presented. The Divided Word Line (DWL) and Divided Bit Line (DBL) scheme were implemented for reducing active power. Particular emphasis was put to decrease standby power consumption in word line driver. The forced-stack devices as pulse generation element was introduced for sensing enable. This guarantees SRAM can work in low voltage without losing design margin. A test-chip with 17 embedded SRAMs has been fabricated in UMC 90-nm low leakage CMOS logic process1.
Evaluation of shielded Rogowski coil for measuring partial discharge signals

In this paper, the performance of constructed shielded Rogowski coil for measuring partial discharge signals is investigated under different conditions of terminating impedance and the deviation of current carrying conductor (CCC) from central position. The studies are made in both frequency and time domain. Also the Rogowski coil model is brought and its verification is done.
Function of Semliki Forest virus E3 peptide in virus assembly: replacement of E3 with an artificial signal peptide abolishes spike heterodimerization and surface expression of E1

The Semliki Forest virus spike glycoproteins E1 and p62 form a heterodimeric complex in the endoplasmic reticulum (ER) and are transported as such to the cell surface. In the mature virus particle, the heterodimeric association of E1 and E2 (the cleavage product of p62) is maintained, but as a more labile and acid-sensitive oligomer than the E1-p62 complex. The E3 peptide forms the N-terminal part of the p62 precursor and carries the signal for the translocation of p62 into the lumen of the ER. The question of whether E3 is also important in the formation and stabilization of the E1-p62 heterodimer has been addressed here with the aid of an E3 deletion mutant cDNA. In this construct, the entire E3 was replaced with a cleavable, artificial signal sequence which preserved the membrane topology of an authentic E2. The E3 deletion, when expressed via a recombinant vaccinia virus, abolished heterodimerization of the spike proteins. It also resulted in the complete retention of E1 in the ER and almost total inhibition of E2 transport to the plasma membrane. The oligomerization and transport defect of E1 expressed from the E3 deletion mutant could be complemented with a wild-type p62 provided from a separate coding unit in double infections. These results point to a central role of E3 in complex formation and transport of the viral structural components to the site of budding. In conjunction with earlier work (M. Lobigs and H. Garoff, J. Virol. 64:1233-1240, 1990; J. Wahlberg, W. A. M. Boere, and H. Garoff, J. Virol. 63:4991-4997, 1989), the data support a model of spike protein oligomerization control of Semliki Forest virus assembly and disassembly which may be mediated by the presence of E3 in the uncleaved p62 precursor and release of E3 after cleavage.
Molecular epidemiology of a household outbreak of Shiga-toxin-producing Escherichia coli in Poland due to secondary transmission of STEC O104:H4 from Germany.

We characterized two STEC O104 : H4 clinical isolates collected in Poland from a 7-year-old boy with haemolytic uraemic syndrome (HUS) and his nanny. This household outbreak began on 29 May 2011. Because of its time-frame, the outbreak was assumed to be part of the international STEC O104 : H4 outbreak that arose in Germany in May 2011. The two Polish isolates were Shiga-toxin-producing Escherichia coli (stx2 lpf) with enteroaggregative E. coli pathotype (aggR aap aggA), thereby sharing the unique virulence properties of the epidemic STEC O104 : H4 strain from the international outbreak. The Polish isolates were multi-drug resistant and carried bla(TEM), strA, strB, tetA, sul1 and sul2 markers together with the bla(CTX-M-15) gene for CTX-M-15 extended-spectrum β-lactamase. PFGE patterns and plasmid profiles of the Polish isolates and the epidemic STEC O104 : H4 strain corresponded closely. This finding suggested an epidemiological link between the Polish STEC O104 : H4 isolates and the international outbreak. Retrospective serological investigations proved person-to-person transmission of the epidemic STEC O104 : H4 strain from a father who had visited Dortmund, Germany, to his 7-year-old son in Giżycko, Poland. To the best of our knowledge, this is the first report of household transmission of Shiga-toxin-producing E. coli in Poland.
Hit To Lead Optimization, And 3D QSAR Modeling of Imidazolopiperazines Derivatives against Malaria Based On PLSR Machine Learning Technique

Malaria is a mosquito-borne life-threatening disease. Though it is treatable but due to emerging resistance against well-known drugs like 8-aminoquinolines and artemisinin analogs, it is urgent need to develop novel drugs for the treatment of malaria. In order to develop a new drug, imidazolopiperazine derivatives have been shown antimalarial efficacy against wild-type as well as drug resistant malarial parasites. Hence, the experimental dataset (AID: 605733) of imidazolopiperazine series is a valuable resource to develop novel leads for antimalarial drug discovery. In this study, we conducted lead optimization using above dataset. For that, we carried out machine learning 3D QSAR modeling based on partial least square regression. For 3D QSAR modeling, firstly molecular descriptors were calculated using VLife Software followed by PLSR model evaluation by calculating statistical parameters. The value of correlation coefficient (r2 =0.9290) of 3D QSAR PLSR model indicated a strong positive correlation between biological activity and descriptors with high significance level. The high F test value (F= 69.83) suggested a low probability of the model’s failure. The regression model showed that steric (S_292) and electrostatic (E_284, and E_676) interactions play an important role in determining antimalarial activity. After that, we generated a computational library of imidazolopiperazine compounds using the template of core molecule i.e. imidazolopiperazine. The 3D QSAR PLSR model was applied on a computational library of compounds resulting top 10 novel antimalarial lead molecules. This work was extended by carrying out pharmacophore modeling of imidazolopiperazine scaffold which revealed that 5 pharmacophoric features: two aromatic, two aliphatic and one hydrogen bond donor are essential features for antimalarial activity. The Computational lead optimization may help in the design of novel antimalarial molecules. The information obtained from this could be applied for the future development of potent drugs against malaria.
Monocyte and Macrophage Activation by Lipoteichoic Acid Is Independent of Alanine and Is Potentiated by Hemoglobin1

Lipoteichoic acids (LTAs) are Gram-positive bacterial cell wall components that elicit mononuclear cell cytokine secretion. Cytokine-stimulating activity is thought to be dependent on retaining a high level of ester-linked d-alanine residues along the polyglycerol phosphate backbone. However, Streptococcus pyogenes LTA essentially devoid of d-alanine caused human and mouse cells to secrete as much IL-6 as LTA with a much higher d-alanine content. Furthermore, hemoglobin (Hb) markedly potentiates the stimulatory effect of various LTAs on mouse macrophages or human blood cells, regardless of their d-alanine content. LTA and Hb appear to form a molecular complex, based on the ability of each to affect the other’s migration on native acrylamide gels, their comigration on these gels, and the ability of LTA to alter the absorption spectra of Hb. Because S. pyogenes is known to release LTA and secrete at least two potent hemolytic toxins, LTA-Hb interactions could occur during streptococcal infections and might result in a profound alteration of the local inflammatory response.
Sequential Representation of Clinical Data for Full-Fitting Survival Prediction

Survival prediction on time-to-event data associated with patients is crucial in clinical research. Cox-type regression models are widely used for such prediction, but their performance for practical survival prediction suffers due to their use of a maximum partial likelihood estimator, which undermines the effectiveness and robustness of such models. To address this problem, we propose to maximize a new full likelihood that fits the model to all of the data for both failed and censored patients. We also represent time-to-event data by a new sequencing structure, which allows the proposed likelihood to be estimated by predicting event occurrence across the unit time intervals in practice. Furthermore, the likelihood is regularized to prevent overfitting from arising in the model learning step. We investigate the new approach via experimental studies on real-life clinical data and its superior performance compared to other popular state-of-the-art models reveals the great promise of our approach for clinical prediction.