Miracle-dz/UniFAR-FTUs huggingface dataset:
GNOMICS: A one-stop shop for biomedical and genomic data

The World Wide Web is an indispensable tool for biomedical researchers who are striving to understand the molecular basis of phenotype. However, it presents challenges in the form of proliferation of data resources, with heterogeneity ranging from their content to functionality to interfaces. This often frustrates researchers who must visit multiple sites, become familiar with their interfaces, and learn how to use them to extract knowledge. Even then, one may never feel sure that they have tracked down all needed information. We envision addressing this challenge with GNOMICS (Genomic Nomenclature Omnibus and Multifaceted Informatics and Computational Suite), a suite with both a programmatic interface and a GUI. GNOMICS allows for extensible biomedical functionality, including identifier conversion, pathway enrichment, sequence alignment, and reference gathering, among others. It combines usage of other biological and chemical database application programming interfaces (APIs) to deliver uniform data which can be further manipulated and parsed.
A FAST DIRECT IMAGING METHOD FOR THE INVERSE OBSTACLE SCATTERING PROBLEM WITH NONLINEAR POINT SCATTERERS

Consider the scattering of a time-harmonic plane wave by heterogeneous media consisting of linear or nonlinear point scatterers and extended obstacles. A generalized Foldy–Lax formulation is developed to take fully into account of the multiple scattering by the complex media. A new imaging function is proposed and an FFT-based direct imaging method is developed for the inverse obstacle scattering problem, which is to reconstruct the shape of the extended obstacles. The novel idea is to utilize the nonlinear point scatterers to excite high harmonic generation so that enhanced imaging resolution can be achieved. Numerical experiments are presented to demonstrate the effectiveness of the proposed method.
Innovative Exploratory Clinical Approaches for Relapsed and / or Refractory Metastatic Ewing ’ s Sarcoma

Relapsed and/or refractory Ewing’s Sarcoma is a devastating pediatric disease with rapid progression and oftentimes severe side effects related to generally ineffective high dose multi-agent chemotherapy. Eighty five percent of diagnosed Ewing’s Sarcoma is characterized by EWS/FLI1 fusion gene expression that provides a unique opportunity for targeted therapeutics development. The EWS/FLI1 gene is a “driver gene” with transformative potential and integral to Ewing’s cancer progression. Although encoding a transcription factor, which is pharmacologically “undruggable”, it connects with potentially targetable molecular signals and, in addition, as a fusion gene along with accompanying tumor specific mutations provides unique neoantigens some of which process into immunogenic epitope. Very few cutting edge advances for the management and control of Ewing’s Sarcoma have been made in the last 20 years due, in part, to low incidence (one case per million people), a narrow therapeutic window, and a limited availability of tissue suitable for biomarker studies. However, recent advances in DNA/RNA manipulation [CRISPR and RNA interference (siRNA)] as well as in molecular and immune technologies have transformed both the understanding of signaling pathways and molecular mechanisms of actions and, consequently, the approach to target identification. We review the innovative exploratory approaches to five unique therapies (a EWS-FLI1 co-activator, the EWS-FLI1 fusion gene itself, a signaling receptor, a DNA damage repair component, and the antigenic matrix) currently undergoing clinical assessment in Ewing’s Sarcoma for which preliminary preclinical and clinical results suggest therapeutic benefit. Ghisoli M1,2,3, Manning L4, Senzer N1,4,5 and Nemunaitis J1,2,3,4,5* 1Mary Crowley Cancer Research Centers, USA 2Medical Oncology and Hematology, Texas Oncology, USA 3Medical City Dallas Hospital, USA 4Gradalis, Inc., USA
Etiology of oesophageal cancer ( C 15 ) in Central and South America

Cohort studies conducted in China, Japan, the Republic of Korea, the United Kingdom, and the USA (as cited in [4]) showed that smokers have an increased risk of developing oesophageal cancer than never-smokers and that the risk increases with the intensity of smoking (duration and number of packs per day). In a cohort study in the USA, Freedman et al. [5] reported that current smokers had a significantly increased risk of developing AC (hazard ratio [HR], 3.7; 95% confidence interval [CI], 2.20–6.22) and SCC (HR, 9.27; 95% CI, 4.04–21.29) than non-smokers. They also found strong positive associations between alcohol consumption (> 3 drinks per day vs 1 drink per day) and the risk of SCC (HR, 4.93; 95% CI, 2.69– 9.03), but found no association with AC (HR, 1.10; 95% CI, 0.69–1.74). Pandeya et al. [6] estimated that 49% (95% CI, 38–60%) and 32% (95% CI, 25–40) of the oesophageal SCCs diagnosed in Australia between 2002 and 2005 were due to smoking and heavy alcohol consumption, respectively. Furthermore, more than 75% of the SCC burden in men could be attributed to smoking with heavy alcohol consumption; 36% (95% CI, 29–44%) of the SCCs in men but only 5% (95% CI, 2– 10%) of those in women were due to smoking more than 30 pack–years and the consumption of more than 17 alcoholic drinks per week.
Impact of Sales Promotion Technique Used by Online Dealers on Consumers

Online promotions are one of the least utilized showcasing instruments on a site not on account of they are insufficient, but since they are not well caught on. If the online dealers know the parameters influencing online Indian consumers behavior and the connection between the different promotional tools and types of consumers they can develop the marketing strategies in order to convert potential customers into active customers and increase the sales as this is new need of the present era. This study majorly focusses upon the factors affecting the behavior of the consumers while shopping online due to different sales promotion techniques used by the online dealers. In this paper it was found that Promotional emails,Promotional SMS, Discounts, User friendly Interface, Promotional Pop ups, Convience and Sales Promtion Influences are the seven major factors , which have very important role in the online consumer behavior. It has also been found that the sales promotion does not only have positive impact but also negative on the consumers as they feel that they have been cheated number of times due to diffrent promotional tools and it had worsely effected the brand loyalty among the consumers which not only lead to decline in the sales but also lack of trust which overall hampers the brand image.
An overfilled cavity problem for Maxwell's equations

This paper is concerned with the mathematical analysis of the scattering of a time‐harmonic electromagnetic plane wave by an open and overfilled cavity that is embedded in a perfect electrically conducting infinite ground plane, where the electromagnetic wave propagation is governed by the Maxwell equations. Above the flat ground surface and the open aperture of the cavity, the space is assumed to be filled with a homogeneous medium with a constant permittivity and permeability, whereas the interior of the cavity is filled with some inhomogeneous medium with a variable permittivity and permeability. The scattering problem is modeled as a boundary value problem over a bounded domain, with transparent boundary condition proposed on the hemisphere enclosing the inhomogeneity represented by the cavity. The existence and uniqueness of the weak solution for the model problem are established by using a variational approach. The perfectly matched layer (PML) method is investigated to truncate the unbounded electromagnetic cavity scattering problem. It is shown that the truncated PML problem attains a unique solution. An explicit error estimate is given between the solution of the original scattering problem and that of the truncated PML problem. The error estimate implies that the PML solution converges exponentially to the original cavity scattering problem by increasing either the PML medium parameter or the PML layer thickness. The convergence result is expected to be useful for determining the PML medium parameter in the computational electromagnetic scattering problem. Copyright © 2012 John Wiley & Sons, Ltd.
Geodiversity and endemism in the iconic Australian Pilbara region: a review of landscape evolution and biotic response in an ancient refugium

We review the biogeography of the Pilbara, synthesize information on the geological and landscape history of this region and surrounds, and assess fine‐scale genetic structure across multiple taxa to examine hypotheses concerning the distribution of genetic lineages. We use this to provide a baseline for future biological studies in an ancient area of endemism.
Development of Mobile-Interfaced Machine Learning-Based Predictive Models for Improving Students Performance in Programming Courses

Student performance modelling (SPM) is a critical step to assessing and improving students performances in their learning discourse. However, most existing SPM are based on statistical approaches, which on one hand are based on probability, depicting that results are based on estimation; and on the other hand, actual influences of hidden factors that are peculiar to students, lecturers, learning environment and the family, together with their overall effect on student performance have not been exhaustively investigated. In this paper, Student Performance Models (SPM) for improving students performance in programming courses were developed using M5P Decision Tree (MDT) and Linear Regression Classifier (LRC). The data used was gathered using a structured questionnaire from 295 students in 200 and 300 levels of study who offered Web programming, C or JAVA at Federal University, Oye-Ekiti, Nigeria between 2012 and 2016. Hidden factors that are significant to students performance in programming were identified. The relevant data gathered, normalized, coded and prepared as variable and factor datasets, and fed into the MDT algorithm and LRC to develop the predictive models. The evaluation results obtained indicate that the variable-based LRC produced the best model in terms of MAE, RMSE, RAE and the RRSE having yielded the least values in all the evaluations conducted. Further results obtained established the strong significance of attitude of students and lecturers, fearful perception of students, erratic power supply, university facilities, student health and students attendance to the performance of students in programming courses. The variable-based LRC model presented in this paper could provide baseline information about students performance thereby offering better decision making towards improving teaching/learning outcomes in programming courses.
Mutations close to a hub residue affect the distant active site of a GH1 β-glucosidase

The tertiary structure of proteins has been represented as a network, in which residues are nodes and their contacts are edges. Protein structure networks contain residues, called hubs or central, which are essential to form short connection pathways between any pair of nodes. Hence hub residues may effectively spread structural perturbations through the protein. To test whether modifications nearby to hub residues could affect the enzyme active site, mutations were introduced in the β-glycosidase Sfβgly (PDB-ID: 5CG0) directed to residues that form an α-helix (260–265) and a β-strand (335–337) close to one of its main hub residues, F251, which is approximately 14 Å from the Sfβgly active site. Replacement of residues A263 and A264, which side-chains project from the α-helix towards F251, decreased the rate of substrate hydrolysis. Mutation A263F was shown to weaken noncovalent interactions involved in transition state stabilization within the Sfβgly active site. Mutations placed on the opposite side of the same α-helix did not show these effects. Consistently, replacement of V336, which side-chain protrudes from a β-strand face towards F251, inactivated Sfβgly. Next to V336, mutation S337F also caused a decrease in noncovalent interactions involved in transition state stabilization. Therefore, we suggest that mutations A263F, A264F, V336F and S337F may directly perturb the position of the hub F251, which could propagate these perturbations into the Sfβgly active site through short connection pathways along the protein network.
Enhancing Citizenship Learning with International Comparative Research: Analyses of IEA Civic Education Datasets

Large-scale international databases provide valuable resources for scholars, educators and policy-makers interested in civic engagement and education in nations that are democracies or striving towards democracy. However, the multidisciplinary nature of secondary analysis of these data has created a fragmentary picture that limits educators’ awareness of relevant findings. We present a summary of research conducted across disciplines using datasets from two large-scale crossnational studies of civic education conducted by the International Association for the Evaluation of Educational Achievement (CIVED:99 and ICCS:09). The IEA studies KeywoRds citizenship education civic engagement political attitudes ICCS:09 CIVED:99
Emotional aftereffects of stereotype suppression.

EMOTIONAL AFTEREFFECTS OF STEREOTYPE SUPPRESSION MAY 2006 KATHLEEN C. BURNS, B.A., GRINNELL COLLEGE M.S., UNIVERSITY OF MASSACHUSETTS AMHERST Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Linda M. Isbell Two studies established that there are previously unexamined negative consequences of stereotype suppression beyond the traditional stereotype rebound effect. It is suggested that stereotype suppression has more in common with the literature on the suppression of emotionally arousing thoughts than the general thought suppression literature. Suppressing emotionally arousing thoughts often leads to emotional aftereffects (i.e. emotional rebound), but limited cognitive rebound. Both studies established the presence of emotional aftereffects following stereotype suppression using both direct and indirect measures of emotion. In addition. Study 1 found reduced stereotype activation following suppression relative to the control condition, whereas Study 2 attempted to determine whether these emotional aftereffects influenced the desire for intergroup contact. Future research involving people’s attempts to correct for emotional aftereffects is suggested.
Humans matching fingerprints: Sequence and Size

Television shows like ‘CSI’ can give the impression that matching crime-scene fingerprints is fully automated. But it is actually humans (fingerprint experts) who ultimately decide whether a crime-scene print belongs to a suspect or not. Despite this fact, there have been no published, peer-reviewed studies directly examining the extent to which experts can correctly match fingerprints to one another. In two experiments presented here we aim to determine the factors affecting accuracy using non-expert participants and test (1) whether the advantage found for the sequential presentation of faces applies to prints and (2) whether the amount of information in a print matters.
Microbiological Etiology of Prosthetic Joint Infections

Introduction: Infection of the prosthesis remains one of the most devastating complications of arthroplasty surgery. Identification of the likely cause of early-onset PJI is particularly important given that these infections are more frequently treated with a debridement procedure where the implant is not removed. Aim and objectives: To identify the microbiological aetiology of prosthetic joint infections and to identify the antimicrobial susceptibility pattern in order to propose the treatment guidelines of PJI based on the duration of onset of symptoms. Material and methods: Synovial fluid collected preoperatively, periprosthetic tissue and the removed prosthesis were processed following standard laboratory protocols set up by the Mayo Clinic. Results:The primary gram stain from culture positive samples was positive in 81/111 (72.97%) samples. Gram negative bacteria constituted majority of the isolates (57/75) (76%) identified from early onset of infection of which Acinetobacter baumannii was the commonest and was significantly associated with early onset infection, while MRSA was associated significantly with delayed onset infection and CONS was significantly associated with late onset infection. Discussion: This study highlights the importance of gram negative pathogens (76%) in early onset of infection, which showed a high incidence of resistance to β lactam and β lactam inhibitor combinations which might be due to the high incidence of ESBL in both community and hospital acquired infections. Multi-drug resistance among the isolates advocates the case for reconsideration of existing protocols for surgeries involving prosthesis which might potentially decrease the incidence of PJIs and reduce patient morbidity and mortality. Treatment modalities can be determined based upon the database generated in individual institutions
Mutation Status of KRAS, BRAF, PIK3CA and Expression Level of AREG and EREG Identify Responders to Cetuximab in a Large Panel of Patient Derived Colorectal Carcinoma Xenografts of All Four UICC Stages

To advance preclinical testing of novel targeted drugs in colorectal cancer (CRC) we established a panel of 133 mouse xenograft models from fresh tumor specimens of 239 patients with CRC of all four UICC stages. A subgroup of 67 xenograft models was treated with cetuximab, bevacizumab and oxaliplatin as single agents. Mutation status of KRAS (G12, G13, A146T), BRAF (V600E) and PIK3CA (E542K, E545K, H1047R) was assessed in all xenografts by allelespecific real-time PCR. KRAS codon 61 was assessed by conventional sequencing. AREG and EREG expression levels were analyzed by real-time PCR expression assays. In the treatment experiment we observed response rates of 27% (18/67) for cetuximab, 3% (2/67) for bevacizumab, and 6% (4/67) for oxaliplatin. Classification based on KRAS, BRAF and PIK3CA mutation status identified 15 of the responders (sensitivity 83%, confidence interval at p = 0.05 (CI): 59% - 96%), and 38 nonresponders (specificity 78%, CI: 63% - 88%). If any mutation except in KRAS codon 13 were considered, the classifier reached sensitivity of 94% and specificity of 69%. We improved specificity of the classifiers to 90% and 86% respectively by adding AREG and EREG RNA expression thresholds retrospectively. In patient-derived xenograft models, we found a predictive classifier for response to cetuximab that is more accurate than established biomarkers. We confirmed its potential performance in primary human tumors. For patients, the classifier’s sensitivity promises increased response rates and its specificity limits unnecessary toxicity. Given the scope of our xenograft models across all UICC stages, this applies not only to mCRC but also to the adjuvant setting of earlier stages. The xenograft collection allows to mimic randomized phase II trials and to test novel drugs effectively as single agents or in combinations. It also enables the development of highly accurate companion diagnostics as demonstrated by us for cetuximab.
Production of itaconic acid by Ustilago maydis from agro wastes in solid state fermentation

Itaconic acid (IA) is one of the hopeful substances within the cluster of organic acids. IA is used in artificial glass, bioactive compounds in pharmacy, medicine, agriculture, for the synthesis of fiber, resin, plastic, rubber, paints, surfactant, ionexchange resins and lubricant. Most recurrently used microorganism for commercial production of IA is Aspergillus terreus. Some filamentous fungi belonging to Ustilaginales also produce IA. In the present work, an attempt was made to produce IA by Ustilago maydis employing Solid State Fermentation (SSF) from various agro wastes like ground nut shells, rice bran, rice husk, orange pulp, ground nut oil cake, orange pulp and sugarcane bagasse as carbon substrates, which were used after pretreatment. 10 g of each substrate was taken in a 500 ml conical flasks separately and supplemented with 20 mL nutrient solution containing glucose, at pH 3. One milliliter inoculum containing 1×10 7 spores was added and moisture was maintained at 60%. After incubation at 32°C for 5 days, the acid production was estimated by spectrophotometric method and by HPLC analysis. Interestingly, the yield of itaconic acid was promising with all the above substrates, where orange pulp, sugarcane bagasse and rice bran supported higher yields.
Un estudio en educación secundaria sobre las representaciones gráficas cartesianas aplicadas a biología de poblaciones.

El uso de las representaciones graficas cartesianas induce en alumnos de Educacion Secundaria dificultades en la interpretacion y en la descripcion de la informacion representada. Se vislumbran puntos de dificultad en la construccion de este tipo de representaciones a partir de datos y conceptos contenidos en un texto. Este estudio analiza estas deficiencias en el area de la Biologia y en particular en su aplicacion a conceptos de Biologia de poblaciones.
Analysis Modification synthesis based Optimized Modulation Spectral Subtraction for speech enhancement

Traditional analysis modification synthesis (AMS) is fairly applied for spectral subtraction along with Short Time Fourier Transform. Based on this AMS method, we proposed an approach for modified modulation spectral subtraction. Results reported in previous studies shows that the modulation spectral subtraction performs better for speech courted by additive white Gaussian noise to improve speech quality. It gives improved speech quality scores in stationary noise, but it fails to give improved speech quality in the real time noise environment. Also, the computational cost of existing modulation domain spectral subtraction methods is high. Thus we propose an approach of applying minimum statistics noise estimation technique on the real modulation magnitude spectrum along with optimized noise suppression factor and spectral floor to improve speech quality in the real time noise environment. Finally, the objective, subjective and intelligibility evaluation metrics of speech enhancement indicates that the proposed method achieves better performance than the existing spectral subtraction algorithms across different input SNR and noise type along with improved computational time. Computation time is improved by 57.13% as compared to traditional modulation domain spectral subtraction method. The modulation frame duration of 128 ms is found to be a good compromise between shorter and longer frame duration, which gives improved results. Keywords—Optimized modulation spectral subtraction, speech enhancement, Analysis modification synthesis, Noise.