Miracle-dz/UniFAR-FTUs huggingface dataset:
Polarization tensor: between biology and engineering

There has been a lot of interest over recent years in the study of mathematical aspects and applications of the polarization tensor. This promising terminology appears widely in electric and electromagnetic inverse problems. Our main purpose in this paper then is to review the polarization tensor biologically in electro-sensing by a weakly electric fish and in the engineering problems which are based on the Eddy current principle. Here, the mathematical formulations of the polarization tensor for both cases are firstly presented. At the same time, a few related applications will also be briefly explained.
Characterization Microencapsul Pepton from Spoiled By Catch Fish Using Spray Drying Methods

Spoiled by catch fish is one of catch produce that have low economic value. Utilization and how to increase the selling value of byproducts by making peptone. Peptone fish is a derivative product or derivative of a water-soluble protein hydrolyzate and does not undergo any coagulation process in hot water. This research aim is to produce peptone with spoiled by catch fish as raw materials using microencapsulation technique and maltodextrin as coating ingredients. Microencapsulate of peptone has a chemical composition with moisture content 8.95%, ash content 5.26%, protein content 62.79%, Fat content 0.44% and carbohydrate content 21.48%. The chemical characteristic peptone by-catch rotten fish indicate that product has solubility 98.87%, nitrogen total 10.05%, α amino nitrogen 1.22%, AN/TN 12.14%, salt content 8.04% and pH 6.69. Microencapsulate peptone has a physical characteristic with lightness value 60.01, whiteness value 57.44 and dominated red color value 1.70 and yellow color value 10.33. The water activity of microencapsulating spoiled by catch fish peptone at room temperature of storage after 5 hours was lower than peptone spoiled by catch fish without micro encapsulation and product of commercial peptone. Amino acid analysis results indicate that microencapsulate spoiled by catch fish peptone arginine, serine, tyrosine, histidine and threonine amino acids higher than peptone spoiled by catch fish without microencapsulation and commercial product of peptone. Microorganism growth curve with Optical Density (OD). That indicates microencapsulate spoiled by catch fish peptone has bacterial growth curve more good than a commercial product of peptone and peptone spoiled by catch fish without micro encapsulation.
Distribution and relative abundance of Tennessee Cave Salamanders (Gyrinophilus palleucus and Gyrinophilus Gulolineatus) with an emphasis on Tennessee populations

—The Tennessee Cave Salamander complex (Gyrinophilus palleucus and G. gulolineatus) consists of three obligate cave-dwelling taxa inhabiting subterranean waters of east and central Tennessee, north Alabama, and northwest Georgia. Although ranges of these taxa are poorly understood, their populations are reportedly small and declining. The IUCN lists G. gulolineatus as "Endangered" and G. p. necturoides as "Vulnerable"; whereas, NatureServe lists G. gulolineatus (G1) and G. p. necturoides (G2G3T1) as Critically Imperiled. To better determine the distribution and relative abundance of extant populations, we searched 113 cave streams in middle and east Tennessee, seven in northwest Georgia, 13 in north Alabama and two in southern Kentucky. We found 1183 salamanders, including 63 G. gulolineatus, 681 G. palleucus, and 439 G. porphyriticus (Spring Salamanders), during 229 surveys of 135 caves. Gyrinophilus palleucus and G. gulolineatus were observed in more caves (30) than G. porphyriticus (17 caves). Members of the complex were found at 52% (12 of 23) of historic caves and at 16% (18 of 110) of non-historic caves. We extended the known distribution of G. palleucus in the Collins, Elk, Duck, and lower Tennessee River watersheds of central Tennessee, and the distribution of G. gulolineatus into the Clinch River watershed of east Tennessee. We found robust populations at historic sites thought to be declining; therefore, our data do not support previous claims of range-wide declines. However, the fragile ecosystems of subterranean environments make populations vulnerable to habitat alteration. In particular, Knox Co. populations of G. gulolineatus and Rutherford and Wilson cos. populations of G. palleucus are located in areas of rampant urban development associated with significant surface habitat and concomitant groundwater alteration.
ANTIMICROBIAL CHARACTERIZATION AND THERAPEUTIC APPLICATIONS OF NOVEL SYNTHETIC THIAZOLE COMPOUNDS AGAINST MULTIDRUG-RESISTANT STAPHYLOCOCCI AND ENTEROCOCCI

Author: Mohammad, Haroon. Ph.D. Institution: Purdue University Degree Received: December 2016 Title: Antimicrobial Characterization and Therapeutic Applications of Novel Synthetic Thiazole Compounds against Multidrug-Resistant Staphylococci and Enterococci Major Professor: Mohamed Seleem. For more than a century, antibiotics have been valuable allies in combating an array of bacterial infections. However, each year nearly 23,000 people in the United States of America and 25,000 people in Europe die due to infections that are recalcitrant to currently available antimicrobials. The emergence of drug-resistant bacterial species, namely methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), has limited the efficacy of several classes of antibiotics. Compounding this problem further is that many large pharmaceutical companies have left the field of antibacterial drug discovery given the high cost of innovation and low return on investment. Collectively, this highlights an urgent, unmet need to identify and develop new antibacterial agents that attack unique molecular targets in bacterial pathogens. Here, we investigate the antibacterial activity of a new series of phenylthiazole antibiotics against a panel of clinically-relevant ‘ESKAPE’ pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). The lead compound 1 was identified through whole-cell screening of libraries of substituted thiazoles and thiadiazoles. Subsequent derivatives were constructed in an attempt to enhance potency, decrease toxicity to host tissues, and improve the lead compound’s drug-like properties. Broth microdilution assay results show that the lead 1 and two derivatives (2 and 3) possess potent activity against Gram-positive bacterial pathogens including MRSA, methicillin-resistant Staphylococcus pseudintermedius (an emerging pathogen of importance in veterinary medicine) and VRE, inhibiting the growth of clinical isolates at concentrations as low as 0.5 μg/mL. The presence of the outer membrane and efflux pumps appears to impede the antibacterial activity of the phenylthiazoles against Gram-negative bacteria. MRSA and VRE mutants resistant to the phenylthiazoles could not be isolated, both via single-step and multi-step resistance
Testing the moderation of quantitative gene by environment interactions in unrelated individuals

The environment can moderate the effect of genes – a phenomenon called gene-environment (GxE) interaction. There are two broad types of GxE modeled in human behavior – qualitative GxE, where the effects of individual genetic variants differ depending on some environmental moderator, and quantitative GxE, where the additive genetic variance changes as a function of an environmental moderator. Tests of both qualitative and quantitative GxE have traditionally relied on comparing the covariances between twins and close relatives, but recently there has been interest in testing such models on unrelated individuals measured on genomewide data. However, to date, there has been no ability to test quantitative GxE effects in unrelated individuals using genomewide data because standard software cannot solve nonlinear constraints. Here, we introduce a maximum likelihood approach with parallel constrained optimization to fit such models. We use simulation to estimate the accuracy, power, and type I error rates of our method and to gauge its computational performance, and then apply this method to IQ data measured on 40,172 individuals with whole-genome SNP data from the UK Biobank. We found that the additive genetic variation of IQ tagged by SNPs increases as socioeconomic status (SES) decreases, opposite the direction found by several twin studies conducted in the U.S. on adolescents, but consistent with several studies from Europe and Australia on adults.
Die Analyse von genomweiten Re-Sequenzierungsdaten zur Identifizierung kausaler DNA-Variation beim Rind

Ziel dieser Arbeit war die Genom-Re-Sequenzierung von Grundertieren verschiedener Rinderpopulationen und die damit verbundene zuverlassige Aufdeckung der genomischen Variation. Die funktionelle Annotation und populationsweite Imputation sequenzbasierter Varianten, sowie deren Anwendung in genomweiten Assoziationsstudien ermoglichten die Identifizierung potentiell kausaler Kandidaten fur genetisch bedingte Defekte und Merkmale. Mit Hilfe dieser Informationen kann eine optimierte Anpaarung der Tiere bei gleichzeitiger Vermeidung von Erbfehlern erfolgen.
Optimizing guide RNA selection and CRISPR/Cas9 methodology for efficient generation of deletions in C. elegans

The Caenorhabditis elegans Gene Knockout (KO) Consortium is tasked with obtaining null mutations in each of the more than 20,000 open reading frames (ORFs) of this organism. To date, approximately15,000 ORFs have associated putative null alleles. A directed approach using CRISPR/Cas9 methodology is the most promising technique to complete the task. While there has been substantial success in using CRISPR/Cas9 in C. elegans, there has been little emphasis on optimizing the method for generating large insertions/deletions in this organism. To enhance the efficiency of using CRISPR/Cas9 to generate gene knockouts in C. elegans we have developed an online species-specific guide RNA selection tool (http://genome.sfu.ca/crispr). When coupled with previously developed selection vectors, optimization for homology arm length, and the use of purified Cas9 protein, we demonstrate a robust, efficient and effective protocol for generating deletions. Debate and speculation in the larger scientific community about off- target effects due to non-specific Cas9 cutting has prompted us to investigate through whole genome sequencing the occurrence of single nucleotide variants and indels accompanying targeted deletions. We did not detect any off-site variants above the natural spontaneous mutation rate and therefore conclude this modified protocol does not generate off-target events to any significant degree in C. elegans.
Spatial and temporal incidence of insect pests in farmers’ cabbage fields in Senegal

In Senegal, damage caused by insect pests is a major obstacle to seasonal stability and an increase in cabbage production. Little is known about the spatial and temporal distribution of cabbage pests, which makes the design of management recommendations to small-scale farmers challenging. The objectives of this study were to: (i) evaluate the status of insect pests observed in cabbage farmers’ fields; (ii) give information on the spatial and temporal distribution of key pests and (iii) assess the effect of temperature, insecticide applications, and host crop abundance on their incidence. Atotal of 116 cabbage fields were monitored for insect pests and related damage over four crop cycles, from October 2012 to May 2014, in the main vegetable producing area of Senegal (Niayes). The diamondback moth Plutella xylostella (L.) was by far the most important pest present in all the fields and with high levels of incidence (37.1% infested plants), particularly in the latter part of the dry season in the South of Niayes (50% infested plants). The cabbage webworm Hellula undalis (F.) was mainly observed in the early dry season in the south of Niayes, with an incidence of up to 12.5% infested plants. More surprising was the detection of the tomato fruit worm Helicoverpa armigera (Hübner), with damage of up to 9.4% of cabbage heads. The incidence of sucking pests such as whiteflies Bemisia tabaci (Gennadius), or aphids (including Lipaphis pseudobrassicae (Davis, 1914), Myzus persicae (Sulzer) or Brevicoryne brassicae (L.)) was generally low. The incidence of P. xylostella increased significantly with the number of insecticide applications, indicating that control deployed by growers was ineffective. The incidence of H. undalis did not depend on the number of insecticide applications, but significantly increased with host crop abundance and decreased with temperature. This study is a first step towards developing alternative pest management strategies in the framework of sustainable vegetable production systems.
Effect of Honey & Olive Oil Supplemented Bio-Yoghurt Feeding on Lipid Profile, Blood Glucose and Hematological Parameters in Rats

Background and Objective: Yoghurt, especially bio-yoghurt has long been recognized as a product with many health benefits for consumers. Also, honey and olive oil have considerable nutritional and health effects. So, the effect of administration of yoghurt made using ABT culture and fortified with honey (2 and 6%), olive oil (1 and 4%) or honey + olive oil (2+1 and 6+4% respectively) on some biological and hematological properties of rats was investigated.The body weight gain, serum lipid level, blood glucose level, serum creatinine level, Glutamic Oxaloacetic Transaminase (GOT) activity, Glutamic Pyruvic Transaminase (GPT) activity, leukocytes and lymphocytes counts of rats were evaluated.Blending of bio-yoghurt with rats' diet improved body weight gain. Concentrations of Total plasma Cholesterol (TC), High-Density Lipoprotein cholesterol (HDL), Low-Density Lipoprotein cholesterol (LDL), Very Low-Density Lipoprotein cholesterol (VLDL) and Triglycerides (TG) significantly lowered in plasma of rats fed bio-yoghurt. Levels of TC, LDL, VLDL, and TG also decreased in rat groups feed bio-yoghurt supplemented with honey and olive oil. LDL concentrations were reduced by 10.32, 18.51, 34.17, 22.48, 43.30% in plasma of rats fed classic starter yoghurt, ABT yoghurt, ABT yoghurt contained 6% honey, ABT yoghurt contained 4% olive oil and ABT yoghurt contained 6% honey + 4% olive oil respectively. The blood glucose, serum creatinine, GOT and GPT values of rats decreased while white blood cells and lymphocytes counts increased by feeding bioyoghurt contained honey and olive oil.The findings enhanced the multiple therapeutic effects of bio-yoghurt supplemented with honey and olive oil.
Lipase inhibitory activity of Carica papaya, Chrysophyllum cainito, Corcorus olitorius, Cympogon citrates and Syzygium cumini extracts

The lipase inhibitory action of Carica papaya, Chrysophyllum cainito, Corcorus olitorius, Cymbopogon citrates and Syzygium cumini were evaluated to explore for the presence of anti-obesity compounds and their potential weight-lowering activity. Enzyme inhibition results of the alcoholic extracts of the five plants showed that C. cainito has the highest percent inhibition at 74.91% while S. cumini, C. citratus, C. olitorius and C. papaya obtained less than 50% average inhibition. C. cainito was partitioned using hexane and ethyl acetate to further concentrate the bioactive compounds. The lipase inhibition assay of hexane and ethyl acetate extracts showed 92.11% inhibition and 21.9% inhibition, respectively. The greater activity in the former may imply that majority of potential antilipase constituents are found in the hexane portion.
Control of Greenhouse Environmental Conditions with IOT Based Monitoring and Analysis System

Wireless sensor networks applications and inter-machine communication (M2M), called the Internet of Things, help decision-makers to control complex systems thanks to the low data-rate and cost-effective data collection and analysis. These technologies offer new possibilities to monitor environmental management and agricultural policies, and to improve agricultural production, especially in low-income rural areas. In this study, IoT is proposed with a low cost, flexible and scalable data collection and analysis system. For this purpose, open source hardware microprocessor cards and sensors are stored in the greenhouse computer database using the IEEE 802.15. 4 Zigbee wireless communication protocol. The data can be analyzed by greenhouse computer analysis software, which is developed with the PHP programming language. It is possible to monitor the real time data from the greenhouse computer. Also alert rules definitions can be made and the system was tested in greenhouse conditions. It has been observed that it performs operations steadily such as data transfer, sensor measurements and data processing. The proposed system may be useful for monitoring indoor climate and controlling ventilation, irrigation and heating systems, especially for small enterprises due to the modular structure.
cDeepbind: A context sensitive deep learning model of RNA-protein binding

Motivation Determining RNA binding protein(RBP) binding specificity is crucial for understanding many cellular processes and genetic disorders. RBP binding is known to be affected by both the sequence and structure of RNAs. Deep learning can be used to learn generalizable representations of raw data and has improved state of the art in several fields such as image classification, speech recognition and even genomics. Previous work on RBP binding has either used shallow models that combine sequence and structure or deep models that use only the sequence. Here we combine both abilities by augmenting and refining the original Deepbind architecture to capture structural information and obtain significantly better performance. Results We propose two deep architectures, one a lightweight convolutional network for transcriptome wide inference and another a Long Short-Term Memory(LSTM) network that is suitable for small batches of data. We incorporate computationally predicted secondary structure features as input to our models and show its effectiveness in boosting prediction performance. Our models achieved significantly higher correlations on held out in-vitro test data compared to previous approaches, and generalise well to in-vivo CLIP-SEQ data achieving higher median AUCs than other approaches. We analysed the output from our model for VTS1 and CPO and provided intuition into its working. Our models confirmed known secondary structure preferences for some proteins as well as found new ones where secondary structure might play a role. We also demonstrated the strengths of our model compared to other approaches such as the ability to combine information from long distances along the input. Availability Software and models are available at https://github.com/shreshthgandhi/cDeepbind Contact ljlee@psi.toronto. edu, frey@psi.toronto. edu
ANALYSIS OF BENEFITS AND DRAWBACKS OF TRADITIONAL ERP VERSUS CLOUD BASED ERP SYSTEMS

: Traditional ERP systems provide various kinds of benefits such as mature system functionality and abilities of greater customization and integration. But purchasing and implementing traditional ERP system (on-premise) is always costly and difficult job for any organization and involves a great risk and consume more time. Implementing traditional ERP means deploying new infrastructure, purchasing servers, hardware and software thus it is always a costly affair for any organization. Cloud based ERP system architecture provides solutions to all the difficulties encountered by conventional ERP systems. It provides flexibility and improves overall efficiency. ERP software brings users economic benefits during a company’s operational management. The economic benefits of ERP users are better than the non-users. All the data and information resources are managed by ERP systems in the business organizations. This information is stored in centralized and shared data stores. These days information is priceless tool for organizations and through this perspective it is important to reach all the data of a company IT system in real time. We can use cloud computing infrastructure & SaaS for low cost working. In this paper, we identify and classify the benefits and drawbacks of traditional ERP versus cloud-based ERP systems.
VALIDATION OF THE POTENTIAL OF EULOPHIA OCHREATA L. TUBERS FOR ITS ANTI-INFLAMMATORY AND ANTIOXIDANT ACTIVITY

Summary The anti-inflammatory activity of Eulophia ochreata L. tubers extract was studied in carrageenan induced rat paw model of acute inflammation. Subplantar injection of 0.1 ml of 1 % carrageenan induced a progressive swelling of the rat paw at all the time points, that reached to a maximal volume in control between 1 and 2 h. We could demonstrate in present study that pre treatment of animals with methanolic extract of E. ochreata tubers prevented progresson of oedema up to 48 % at dose of 0.5 gm/kg b.w. and 53 % at dose of 1 gm/kg b.w. , where as diclofenac showed 61 % inhibition. The tuber extract also showed significant antioxidant activity as indicated by DPPH radical scavenging capacity, antilipid peroxidation activity, reducing power capacity and nitric oxide radical inhibition asssay.
TASEP modelling provides a parsimonious explanation for the ability of a single uORF to upregulate downstream ORF translation during the Integrated Stress Response

Translation initiation is the rate limiting step of protein synthesis that is downregulated during Integrated Stress Response (ISR). In our previous work (Andreev, O’Connor et al 2015), we demonstrated that most human mRNAs resistant to this inhibition possess translated uORFs and in some cases a single uORF is sufficient for the resistance. Here we developed a computational model of Initiation Complexes Interference with Elongating Ribosomes (ICIER) to gain insight into the mechanism. We explored the relationship between the flux of scanning ribosomes upstream and downstream of a single uORF depending on uORF features. Paradoxically our analysis predicts that reducing ribosome flux upstream of certain uORFs increases initiation downstream. The model reveals derepression of downstream translation as general mechanism of uORF-mediated stress resistance. It predicts that stress resistance can be achieved with long or slowly translated uORFs that do not favor high levels of translation re-initiation and start with non-leaky initiators.
Greatly underestimated: the role of vocational curriculum tracks in US high schools

Decades of research on the outcomes of curriculum tracking in the United States have produced inconsistent results, mainly due to insufficient attention to selection bias. Data from the [National Longitudinal Survey of Youth 1997] NLSY97 were used to conduct a re-assessment of high school tracking effects on educational attainment, with a particular focus on addressing bias from non-random selection into curriculum tracks. Career-technical education and college-preparatory tracks produced favorable outcomes at distinct attainment levels when compared to general tracks. Results indicate a need to qualify blanket assumptions about the advantages of college-preparatory tracks for all students. Moreover, results support a growing body of literature that considers career-technical education an effective option to increase high school completion rates as an important precursor to postsecondary educational attainment.