Miracle-dz/UniFAR-FTUs huggingface dataset:
A Pioneer Case Study on Identification of Infant Rhinoceros Horn

Objective: To investigate the authenticity of infant Rhino horn sample from morphometric, microscopic, genetic and phylogenetic studies. Methods: A suspected rhino horn sample (11 cm × 13 cm) was sent to the laboratory for identification. Relevant morphometric data of sample were taken. Similarly, established methods for microscopic examination of rhino horn were adopted. Using standard universal primer, a part of Cytochrome b (Cyt b) and 12S rRNA was amplified from sample, sequenced and aligned using BLAST of the GenBank (NCBI) and in-house reference database available at Wildlife Institute of India, Dehradun, India for decisive confirmation of species. Results: Morphometric analysis showed the sample was oval, dome shaped with a bony part which was supported by upper skin. Presence of filamentous units is the microscopic identifying feature of genuine rhino horn. However, microscopic examination showed very unclear filamentous units because of the immature nature of sample. Mitochondrial sequence data revealed the source of suspected sample was of a one-horn Rhinoceros (Rhinoceros unicornis). Similarly, NJ method for phylogenetic analysis for both Cytb and 12S rRNA identified sequence similarity with Rhinoceros unicornis. Conclusion: Even though the morphometric and microscopic data do not reveal much about the infant rhino horn, mtDNA sequencing used in this pioneer study can be applied in the wildlife forensic for identification of such parts in future and data used as evidence against the poachers in the court of law.
Antioxidants and their role in nurture human life and industry: A review

The present paper deals with the antioxidants and their role in human life. The comprehensive review has been taken in this paper which aims to state the types of different antioxidants present in plants and herbs, the constituents present in plant and their role as antioxidant is because of their phenolic and flavonoids contents. The paper deals with the antioxidant activity of a number of fruits, vegetables, leaf and grains of different plants. The selected fruits and vegetables such as mulberries, papaya, red grapes, mango, guava, tomato, red onion, red cauliflower, carrot, beetroot etc. are used in this study. The higher levels of radical scavenging capacity are observed in beetroot, red onion, red cauliflower, red grapes and mulberries as compared to other fruits and vegetables. The results can be compared with several other local fruits.
Surface conditioning with Escherichia coli cell wall components can reduce biofilm formation by decreasing initial adhesion

Bacterial adhesion and biofilm formation on food processing surfaces pose major risks to human health. Non-efficient cleaning of equipment surfaces and piping can act as a conditioning layer that affects the development of a new biofilm post-disinfection. We have previously shown that surface conditioning with cell extracts could reduce biofilm formation. In the present work, we hypothesized that E. coli cell wall components could be implicated in this phenomena and therefore mannose, myristic acid and palmitic acid were tested as conditioning agents. To evaluate the effect of surface conditioning and flow topology on biofilm formation, assays were performed in agitated 96-well microtiter plates and in a parallel plate flow chamber (PPFC), both operated at the same average wall shear stress (0.07 Pa) as determined by computational fluid dynamics (CFD). It was observed that when the 96-well microtiter plate and the PPFC were used to form biofilms at the same shear stress, similar results were obtained. This shows that the referred hydrodynamic feature may be a good scale-up parameter from high-throughput platforms to larger scale flow cell systems as the PPFC used in this study. Mannose did not have any effect on E. coli biofilm formation, but myristic and palmitic acid inhibited biofilm development by decreasing cell adhesion (in about 50%). These results support the idea that in food processing equipment where biofilm formation is not critical below a certain threshold, bacterial lysis and adsorption of cell components to the surface may reduce biofilm buildup and extend the operational time.
Chromosomal characteristics of rDNA in a conserved karyotype of two Sternopygus macrurus (Gymnotiformes: Sternopygidae) populations from upper Paraná River basin

Abstract Karyotype and chromosomal characteristics of both minor and major rDNA of Sternopygus macrurus, a weakly electric South American fish, from two populations of the upper Paraná River basin, were investigated using conventional (Giemsa staining, silver staining, C-banding and base-specific fluorochromes) and molecular (fluorescent in situ hybridization (FISH) with 5S and 18S rDNA probes) cytogenetic techniques. Diploid chromosome number was invariably 2n = 46 and karyotype composed of 23 pairs of biarmed chromosomes (28m+18sm). The nucleolus organizer regions (NORs) were located in the secondary constriction of the p arm of pair No. 2; this site corresponded with CMA3 positive as well as with 18S rDNA signals, respectively. This 18S rDNA cluster was not syntenic to the 5S rDNA sites located at pairs Nos. 1, 5 and 15. The karyotypes and other chromosomal characteristics of individuals from the two populations in the upper Paraná River basin were identical. The karyotype differences among individuals identified as S. macrurus from Paraná River and the São Francisco and Amazon River basins, respectively, may indicate that these taxa might represent distinct species.
MEMS based monolithic Phased array using 3-bit Switched-line Phase Shifter

This article details the design of an electronically scanning phased array antenna with proposed fabrication process steps. Structure is based upon RF micro-electromechanical system (MEMS) technology. Capacitive type shunt switches have been implemented here to cater high frequency operation. The architecture, which is deigned at 30 GHz, consists of 3-bit (11.25o, 22.5o & 45o) integrated Switched-line phase shifter and a linearly polarized microstrip patch antenna. Detailed design tricks of the Kaband phase shifter is outlined here. The whole design is targeted for future monolithic integration. So, the substrate of choice is High Resistive Silicon (ρ > 8kΩ-cm, tan δ =0.01 and εr =11.8). The overall circuit occupies an crosssectional area of 20 × 5 mm. The simulated results show that the phase shifter can provide nearly 11.25o/22.5o/45o phase shifts and their combinations at the expense of 1dB average insertion loss at 30 GHz for eight combinations. Practical fabrication process flow using surface micromachining is proposed here. Critical dimensions of the phased array structure is governed by the deign rules of the standard CMOS/MEMS foundry. Index terms –MEMS, Phase shifter, Phased array, CPWMS transition.
Medical entomology : a textbook on public health and veterinary problems caused by arthropods

1. Introduction to Medical Entomology B.F. Eldridge, J.D. Edman. 2. Introduction to Arthropods: Structure, Function and Development W.S. Romoser. 3. Introduction to Arthropods: Systematics, Behavior and Ecology W.S. Romoser. 4. Direct Injury: Phobias, Psychoses, Annoyance, Allergies, Toxins, Venoms and Myiasis J.F. Day, et al. 5. Arthropod Transmission of Vertebrate Parasites J.D. Edman. 6. The Epidemiology of Arthropodborne Diseases B.F. Eldridge. 7. Malaria, Babesiosis, Theileriosis and Related Diseases T.R. Burkot, P.M. Graves. 8. Leishmaniasis and Trypanosomiasis P.G. Lawyer, P.V. Perkins. 9. Filariasis J.B. Lok, et al. 10. Bacterial and Rickettsial Diseases J. Piesman, K.L. Gage. 11. Arbovirus Diseases B.F. Eldridge, et al. 12. Mechanical Transmission of Disease Agents by Arthropods L.D. Foil, J.R. Gorham. 13. Surveillance for Arthropodborne Diseases B.F. Eldridge. 14. Management of Arthropodborne Diseases by Vector Control D.E. Weidhaas, D.A. Focks. 15. Prevention and Control of Arthropodborne Diseases J.F. Sutcliffe. Subject Index. Scientific Names Index.
Control of Powdery Mildew in Cut Roses using Natural Products in the Greenhouse

Roses grown under greenhouse cultivation are commonly affected by diseases and regular fungicide applications are commonly used. The aim of this research was to identify natural products that can substitute and reduce the health and environmental impacts of typical chemical treatments in the control of powdery mildew [(Podosphaera pannosa (Wallr. Fr.) de Bary] and grey mould (Botrytis cinerea Pers.). Treatments were applied in the greenhouse on the cut rose cultivars Sunluck (Gold Strike ® ) and Nirpbredy (New Fashion ® ) growing in a soilless system. Oregano and clove essential oil at 0.5 ml/l (an emulsifier was added) and sodium bicarbonate (NaHCO3) at 4 g/l were sprayed on rose plants to runoff. The controls were untreated roses and a standard chemical control (the fungicides Dinocap, Triadimenol, Dimethomorph+Sulphur, Bupirimate, Dithianon, Iprodione and Thiram) was applied in rotation. Sprays were applied every 7-10 days after the first symptoms of disease appeared. Disease incidence was checked on 100 leaflets and symptoms were evaluated using a scale from 0 (no disease) to 7 (76-100% infection). At three different times (June and November 2005 and January 2006) biometric data (stem height, stem diameter, stem flexibility, flower diameter, number of petals/flower and thorniness) and colorimetric analysis of the leaves were evaluated in order to determine the effect of treatments on cut rose quality. Treatment with essential oils and NaHCO3 was able to control the incidence and the severity of powdery mildew on roses. Ambient infection of grey mould was low and comparisons between treatments were not possible. Significant differences among the chemical and natural product treatments were found for all traits examined. Although NaHCO3 treatment controlled powdery mildew to a greater extent than essential oils, it resulted in slight phytotoxicity. These results indicate the potential use of natural products to control powdery mildew of roses and could be a good alternative to chemical fungicides. However, differences in response to powdery mildew depend on the cultivar susceptibility, period of treatments and level of control needed.
Centrality Values of Yeast Proteins in a PPI Network Are Related to Their Essentiality and Functions

It has long been investigated and understood that centrality of proteins in the context of protein-protein interaction (PPI) networks are related to their essentiality. In the present work, we validate the relations between essentiality of yeast proteins and their centrality measures in a PPI network by following a different approach using the concept of the receiver operating characteristic (ROC) curve. We found that all centrality measures are related to essentiality. However, the degree centrality performed better in case of the data we used. By deeply examining different centrality values of yeast proteins we find that they are not highly correlated, which has leaded us to hypothesize that centralities might have some relations with gene/protein functions. Indeed, we found that many of the clusters generated based on the pattern of centrality values are rich with similar function proteins. Different types of centrality values imply different types of importance of a node in a network and the functions of genes are of various types. In the present work, we hypothesized that important genes of different functions may tend to show different patterns of centralities and here we show some preliminary links between groups of similar function genes and profiles of centrality values. The concepts of network biology discussed in this paper are applicable to other networks including networks of chemical compounds.
Control molecular de la apoptosis durante la morfogénesis de la extremidad

The developing limb bud is an excellent model to analyze the molecular mechanisms that regulate the programmed cell death or apoptosis. During the formation of the limb appear four apoptotic zones that control the morphogenesis of the limb. The most extensively studied of the apoptotic zones is the interdigital zone. Here the molecular signals that control this process belongs to the family of proteins morphogenetic of smad the bone (BMP), these molecules bind to their receptors and transduce the signal through proteins. The pro-apoptotic activity of BMP signaling requires the interaction with other signaling molecules such as fibroblast growth factors (FGF), Wingless int-related protein (WNT) and retinoic acid. The FGF, WNT and retinoic acid modulate as well the capacity of BMPs to induce the apoptosis in the interdigits.
The effectiveness of DNA‐based delimitation in Synchonnus net‐winged beetles (Coleoptera: Lycidae) assessed, and description of 11 new species

Synchonnus Waterhouse, 1879 from Australia is revised. Achras Waterhouse, 1879 and Enylus Waterhouse, 1879 are found to be junior synonyms of Synchonnus due to the absence of diagnostic characters and result in the new combinations of Synchonnus amplus (Kleine, 1930), S. limbatum (Waterhouse, 1877), and S. segregatus (Waterhouse, 1879). Synchonnus is reported from the Australian mesic and monsoon zones, and 11 new species are described: S. flavonotatum sp. nov., S. maseki sp. nov., S. ailaketoae sp. nov., S. dubenovae sp. nov., S. chilvertonensis sp. nov., S. slipinskii sp. nov., S. monteithi sp. nov., S. eungellensis sp. nov., S. crypticum sp. nov., S. variabilis sp. nov. and S. campestris sp. nov. The morphology‐based species limits are compared with delimitation inferred from the shape of the phylogenetic tree and genetic distance. DNA‐based species limits agree with morphological delimitation in two clades, but a deep conflict was identified in another clade of Synchonnus consisting of three species with allopatric distributions and diversified genitalia, but strong similarities in cox1 mtDNA sequences. The failure of molecular species delimitation in some Synchonnus points to our inability to predict the performance of a barcoding approach even in closely related lineages and calls for an integrative taxonomical approach whenever possible. The Synchonnus fauna of Australia is presented as highly diverse and fragmentation of habitat in the last ~15 million years is hypothesised as the principal factor leading to the observed alpha‐taxonomic diversity.
Caracterización selvícola de los hayedos cantábricos: influencia de las condiciones de estación y los usos antrópicos

El presente trabajo tiene como objetivo la descripcion de las diferentes estructuras forestales que se presentan actualmente en los hayedos cantabricos y su relacion con las estaciones forestales y el uso humano influenciado por estas ultimas. Se realizo inicialmente una tipologia de masas de haya para posteriormente analizar su relacion con diferentes clasificaciones ecologicas elaboradas de manera previa: regiones de procedencia, clases territoriales y areas potenciales. La base de partida para la caracterizacion de los hayedos ha sido la informacion dasometrica del Tercer Inventario Forestal Nacional del que se escogieron aquellas parcelas de la Cordillera Cantabrica en las que el haya fuera especie dominante. Los datos de estas parcelas seleccionadas fueron sometidos a un analisis estadistico multivariante permitiendo definir siete grupos estructurales. La diferencia entre estos grupos reside principalmente en la densidad, la distribucion diametrica y la diversidad especifica de la masa. Por ultimo se compararon los tipos de masas obtenidos con las distintas clasificaciones ecologicas y administrativas disponibles encontrandose una mayor representacion de latizales puros en la vertiente sur de la Cordillera Cantabrica frente a una mayor presencia de fustales puros y mixtos en la vertiente norte. Los resultados obtenidos ponen de manifiesto que la heterogeneidad estructural de los hayedos estudiados esta determinada por la union de factores ecologicos y humanos.
Absence of Indirect Recognition Devoid of APCs Is Acutely Rejected in the Embryonic Thymic Epithelium Naturally

Transplants of tissues depleted of passenger leukocytes are upon in vitro culture usually accepted in allogeneic recipients. Ac-cordingly, fully allogeneic embryonic thymic epithelium was suggested to be poorly immunogenic. However, this tissue is capable of inducing donor-speciﬁc tolerance to peripheral tissues, when restoring T cell development in nude mice, through the production of regulatory cells. In the present work, adult immunocompetent allogeneic recipients were grafted with embryonic tissues isolated at stages before hemopoietic colonization or even before the establishment of circulation. Allogeneic thymic epithelium of day 10 embryos and heart primordium of day 8 embryonic donors were always rejected. Acute rejection of the thymic anlagen takes place in less than 12 days, with maximal CD4 (cid:1) and CD8 (cid:1) T cell inﬁltrates at 10 days post-transplant. In addition, a signiﬁcant inﬁltrate of NK1.1 (cid:1) cells is observed, although without any essential role in this process. Furthermore, recipients lacking the indirect pathway of Ag presentation to CD4 (cid:1) T cells do not reveal any signiﬁcant delay in rejection, even when CD8 (cid:1) T cells are also eliminated. Thus, our experimental approach reveals acute allograft rejection in the absence of all known pathways of naive T cell activation and therefore unveils a novel graft rejection mechanism that should be mediated by direct recognition of parenchymal cells. Given the importance of dendritic cells in naive T cell activation, it is likely that cross-reactive memory T cells may also drive rejection. The Journal of Immunology, 2001, 167: 5034–5041.
Atividade antioxidante do óleo essencial de Myrcia sylvatica (G. Mey.) DC. por diferentes métodos de análises antioxidantes (ABTS, DPPH, FRAP, β-caroteno/ácido linoleico)

Entre as varias especies que possuem ampla diversidade para atividades biologicas, estao as da familia Myrtaceae, que apresentam alto teor de oleo essencial. Em virtude da carencia de estudos com atividade antioxidante do genero Myrcia (Myrtaceae), o objetivo deste trabalho foi avaliar a capacidade antioxidante do oleo essencial de folhas frescas de Myrcia sylvatica (OEMS) por meio dos metodos de captura de radical livre (DPPH e ABTS) e pela auto-oxidacao do FRAP e do sistema β -caroteno/acido linoleico, comparando a padroes trolox e BHA como referencias. A capacidade antioxidante pelo metodo DPPH apresentou IC 50 de 1,94 ± 0,12 mg/mL em 60 minutos de reacao. Pelo metodo ABTS, apresentou atividade antioxidante correspondente a 32,85 ± 0,86 µM de trolox/g de OEMS. Pelo metodo FRAP apresentou Z de 193,47 ± 2,63 de µM de sulfato ferroso/g de OEMS, em 45 minutos de reacao. No teste de β -caroteno/acido linoleico, o OEMS (4 mg/mL) inibiu 26,1% da oxidacao do β -caroteno em 120 min de reacao. O oleo essencial de M. sylvatica apresentou baixa atividade antioxidante, sendo pouco eficaz comparativamente as referencias, mesmo que testado por mais de um mecanismo.
Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation

A comprehensive account of both basic and advanced material in phylogeny estimation, focusing on computational and statistical issues. No background in biology or computer science is assumed, and there is minimal use of mathematical formulas, meaning that students from many disciplines, including biology, computer science, statistics, and applied mathematics, will find the text accessible. The mathematical and statistical foundations of phylogeny estimation are presented rigorously, following which more advanced material is covered. This includes substantial chapters on multi-locus phylogeny estimation, supertree methods, Markov models of sequence evolution, multiple sequence alignment techniques, and designing methods for large-scale phylogeny estimation. The author provides key analytical techniques to prove theoretical properties about methods, as well as addressing performance in practice for methods for estimating trees. Research problems requiring novel computational methods are also presented, so that graduate students and researchers from varying disciplines will be able to enter the broad and exciting field of computational phylogenetics.
Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer

Motivation Rapid advancement in high throughput genome and transcriptome sequencing (HTS) and mass spectrometry (MS) technologies has enabled the acquisition of the genomic, transcriptomic and proteomic data from the same tissue sample. In this paper we introduce a novel computational framework which can integratively analyze all three types of omics data to obtain a complete molecular profile of a tissue sample, in normal and disease conditions. Our framework includes MiStrVar, an algorithmic method we developed to identify micro structural variants (microSVs) on genomic HTS data. Coupled with deFuse, a popular gene fusion detection method we developed earlier, MiStrVar can provide an accurate profile of structurally aberrant transcripts in cancer samples. Given the breakpoints obtained by MiStrVar and deFuse, our framework can then identify all relevant peptides that span the breakpoint junctions and match them with unique proteomic signatures in the respective proteomics data sets. Our framework's ability to observe structural aberrations at three levels of omics data provides means of validating their presence. Results We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq data sets, spanning all four major subtypes, for which proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC) have been released. A recent study on this dataset focusing on SNVs has reported many that lead to novel peptides [1]. Complementing and significantly broadening this study, we detected 244 novel peptides from 432 candidate genomic or transcriptomic sequence aberrations. Many of the fusions and microSVs we discovered have not been reported in the literature. Interestingly, the vast majority of these translated aberrations (in particular, fusions) were private, demonstrating the extensive inter-genomic heterogeneity present in breast cancer. Many of these aberrations also have matching out-of-frame downstream peptides, potentially indicating novel protein sequence and structure. Moreover, the most significantly enriched genes involved in translated fusions are cancer-related. Furthermore a number of the somatic, translated microSVs are observed in tumor suppressor genes. Contact cenksahi@indiana.edu
Optimizing DG Parameters for Voltage Profile and Real Power Loss Improvement using Elephant Herd Optimization

The purpose of distributed generation in improving voltage profile, abating losses, slashing fuel cost and boosting efficiency is becoming important in modern power system operation. This paper summarizes an unconventional optimization technique based on the elephant herd optimization for distributed generation integration in the power system which is inspired by the herding behavior of elephant group. This article elaborates a multi objective optimization problem considering two objectives to reduce the total real power losses of the system and to minimize the overall voltage deviation by placing the distributed generation at suitable location. The objectives are collaborated into a scalar objective optimization problem by using weighted sum method. The proposed elephant herd optimization based methodology is compared with the particle swarm optimization approach for IEEE 14 bus system. The comparative results relating to voltage profile, real power losses and convergence characteristics indicate the superiority of elephant herd optimization over the particle swarm optimization.