Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection of aptamers targeting a hypoxia marker:Carbonic Anhydrase-IX (CA-IX)

Aptamers are selected by an in vitro combinatorial chemistry approach, named Systematic Evolution of Ligands by Exponential enrichment (SELEX), and they are able to bind with high affinity and specificity virtually any given molecule. Compared to monoclonal antibodies, they have a small size that results in their rapid tumour penetration; they are not immunogenic and could be easily modified to increase their in vivo stability. Thus, in this study we describe the selection of RNA-based aptamers directed against an hypoxic biomarker. Firstly, we performed two different cell-based SELEX protocols that allowed the specific enrichment for the target. Furthermore, we characterized and improved the two best sequences selected, named S-47s1 and S-51s1, that we are still studying to handle a final product usable for diagnostic and therapeutic purposes.
Interconnection of self-healing rings

A new architecture called the dual-homing hierarchical self-healing ring (DH-HSHR) architecture is proposed to interconnect SONET self-healing rings, and the design of DH-HSHR network is considered. A DH-HSHR survives all single network failures, including single link and single node failures. A link cost model that incorporates both the route mileage and the capacity of the fiber systems is used. Network design is obtained through a heuristic algorithm. Simulated annealing is applied to further reduce the cost of the design. Numerical results are presented on the design of a DH-HSHR network and comparison is made between the heuristic and simulated annealing algorithms for various network sizes and demand patterns.
Qualidade da carne de cordeiros Santa Inês e F1 Santa Inês X Dorper

ABSTRACT. Costa R.S. , Henriques L.S. V. , Tavares E.M. , Alves E.N. , Henry F.C. & Quirino C.R. [Meat quality of Santa Ines and F1 Santa Ines x Dorper Lambs. ] Qualidade da carne de cordeiros Santa Ines e F1 Santa Ines x Dorper. Revista Brasileira de Medicina Veterinaria, 36(3):337-343, 2014. Centro de Ciencias e Tecnologias Agropecuarias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, Parque California, Campos dos Goytacazes, RJ 28013-602, Brasil. E-mail: fabiocosta@uenf.br Fifty intact male ovines breed were randomly assembled, 25 of the Santa Ines breed and 25 F1 Santa Ines x Dorper to evaluation of dental cronology, live weight at slaughter, withers height, hip height, body length and thorax circumference. After exsanguination, were measured temperature and pH at different times (4h; 12h and 24h) of Semitendinosus and Triceps brachii muscles and shear force or tenderness (48h) of Semitendinosus muscle. In parallel was accomplished the sensorial analysis relationships to instrumental values of this muscle. The chilling room temperature varied between 12.2°C (4h) a -0.5°C (24h), and the mean temperature of carcasses was 26.80°C and -0.20°C, respectively. The mean initial pH of Semitendinosus was 6.62 and final 5.64 and of Triceps brachii was 6.50 (4h) and 5.68 (24h). Semitendinosus muscle shear force and tenderness was similar in lambs of Santa Ines breed and F1 Dorper x Santa Ines, demonstrating that the genetic group did not affect meat tenderness. The sensory panel confirmed the results obtained in instrumental analysis. The correlation of instrumental analysis (shear force) when compared different genetic groups, was found a good inversed correlation (r = -0.87). The mean of body length and thorax circumference levels don’t have significant difference between genetic groups. The mean of morphometric measurements analyzed on Santa Ines was higher than F1 Santa Ines x Dorper, but don’t have significant difference between genetic groups.
Ultrasmall superparamagnetic nanoparticles targeting E-selectin: synthesis and effects in mice in vitro and in vivo

Purpose: We developed a contrast agent for targeting E-selectin expression. We detected the agent using magnetic resonance imaging (MRI) in vivo in nude mice that had undergone nasopharyngeal carcinoma (NPC) metastasis. Methods: Sialyl Lewis X (sLeX) was conjugated with ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles. Hydrodynamic size, polydispersity index, and ζ-potential of USPIO–polyethylene glycol (PEG) nanoparticles and USPIO-PEG-sLeX nanoparticles were measured. Component changes in nanoparticles of USPIO, USPIO-PEG, and USPIO-PEG-sLeX were analyzed by thermogravimetric analysis and Fourier-transform infrared spectroscopy. A model of NPC metastasis to inguinal lymph nodes in nude mice was used to investigate characteristics of the USPIO-PEG-sLeX nanoparticles in vivo. We investigated the ability of the T2* value, change in T2* value (ΔT2* value), and enhancement rate (ER) to assess accumulation of USPIO-PEG-sLeX nanoparticles quantitatively in mice of a metastasis group and control group. Four MRI scans were undertaken for each mouse. The first scan (t0) was done before administration of USPIO-PEG-sLeX nanoparticles (0.1 mL) via the tail vein. The other scans were carried out at 0 (t1), 1 (t2), and 2 hours (t3) postinjection. The mean optical density was used to reflect E-selectin expression. Results: sLeX was labeled onto USPIO successfully. In vivo, there were significant interactions between the groups and time for T2* values after administration of USPIO-PEG-sLeX nanoparticles. Six parameters (T2* at t2, ΔT2* at t1, ΔT2* at t2, ER at t1, ER at t2, and ER at t3) were correlated with the mean optical density. Conclusion: USPIO-PEG-sLeX nanoparticles can be used to assess E-selectin expression quantitatively. Use of such molecular probes could enable detection of early metastasis of NPC, more accurate staging, and treatment monitoring.
Leveraging new opportunities from the use of web widgets in online Web 2.0 environments

Over the past two decades the world has experienced a phenomenal rise in popularity of new Internet technologies in the shape of innovative software, applications and services. Online social networking websites, blogging, Wikis and multimedia sharing have all become the mainstay of what we now describe as the World Wide Web, and all have the common function of allowing end-users customise and share information with others online. The old ways of understanding the Internet one where content was in the hands of the few is quickly fading into memory. People now build their personal profiles and share information with friends using freely available, easy-to-use social software on available platforms. With Internet activity rapidly evolving organisations are finding it increasingly difficult to remain successful doing business the old way. The traditional methods of reaching audiences have broken down and become critically fragmented. Business can no longer simply interrupt the dialogue occurring online with their message they must somehow become part of the discourse. Into this environment steps the web widget. Widgets are short software programs that display content in small screen format. At present they are largely seen as fun objects but with their ability to be virally syndicated across the network, and elsewhere, any message associated with the application will stealthy find its way into people’s private online space. This paper endeavours to demonstrate the advertising and marketing potential from the use of web widgets, particularly given modern web operating environments, by using an innovative methodology. The research sets out to reinforce the belief that online social networking, the main delivery vehicle for widgets, is a popular and growing mode of modern communication and, widgets are easy to use and virally distributed to a number of diverse platforms. In addition, the paper investigates how Journal of Internet Business Issue 8 – 2011 _____________________________________________________________________________________________ 3 people interact with these applications in a very practical manner, to further expand upon current understanding of the World Wide Web in these new emerging and challenging online environments.
Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and the occurrence of hybridization between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker dataset containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our dataset that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.
Cellular responses to proteostasis perturbations reveal non-optimal feedback in chaperone networks

The proteostasis network (PN) comprises a plethora of proteins that are dedicated to aid in protein folding; some with over-lapping functions. Despite this, there are multiple pathophysiological states associated with depletion of chaperones. This is counter-intuitive assuming cells have the ability to re-program transcriptional outputs in accordance with its proteostasic limitations. To this effect, we have used S. cerevisiae to understand the route a cell takes as a response when challenged with different proteostasis impairments. Using 14 single deletion strains of genes of Protein Quality Control (PQC) system, we quantify their proteostasis impairment and the transcriptional response. In most cases cellular response was incapable of restoring proteostasis. The response did not activate proteostasis components or pathways that could complement the function of the missing PQC gene. Over-expression of alternate machineries, could restore part of the proteostasis defect in deletion strains. We posit that epistasis guided synthetic biology approaches may be helpful in realizing the true potential of the cellular chaperone machinery.
Elephantid genomes reveal the molecular bases of Woolly Mammoth adaptations to the arctic

Woolly mammoths and the living elephants are characterized by major phenotypic differences that allowed them to live in very different environments. To identify the genetic changes that underlie the suite of adaptations in woolly mammoths to life in extreme cold, we sequenced the nuclear genome from three Asian elephants and two woolly mammoths, identified and functionally annotated genetic changes unique to the woolly mammoth lineage. We find that genes with mammoth specific amino acid changes are enriched in functions related to circadian biology, skin and hair development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. Finally we resurrect and functionally test the mammoth and ancestral elephant TRPV3 gene, which encodes a temperature sensitive transient receptor potential (thermoTRP) channel involved in thermal sensation and hair growth, and show that a single mammoth-specific amino acid substitution in an otherwise highly conserved region of the TRPV3 channel strongly affected its temperature sensitivity. Our results have identified a set of genetic changes that likely played important roles in the adaptation of woolly mammoths to life in the high artic.
Beyond the Experiment: The Extendable Legal Link Extractor

In this paper we describe a software framework for detecting and resolving references to (national and EU) legislation, case law, parliamentary documents and official gazettes. Meant to function in a large-scale production environment, performance, flexibility and maintainability are essential requirements. This led us to some noteworthy choices: within the pipeline architecture of Apache Cocoon we use the trie data structure for named entity recognition and a parsing expression grammar for pattern recognition, the latter having significant advantages over the use of regular expressions. Additional attention is paid to some substantive maintainability issues.
RNA Secondary Structure of 3’UTR Regulates Translation Control

ii Acknowledgements . iii List of Figures . iv Introduction . 2 Materials and Methods . 7 Apple Juice Plate Production . 7 Embryo Collection . 8 Ovary Dissection . 8 Immunohistochemistry . 9 Western Blot . 11 qRT-PCR.13 Results . 14 Stem Loop 6 Analysis: Oogenesis . 14 Stem Loop 1 Analysis: Embryogenesis and Oogenesis . 18 Stem Loop 10 Analysis: Embryogenesis and Oogenesis . 23 Protein YT521B Depletion . 24 EMSA Staining . 27 Discussion . 28 Deletion of stem loop 6 is not significant during oogenesis . 29 Deletion of stem loop 6 is not significant during embryogenesis . 30 Deletion of stem loop 1 causes 3-fold upregulation of pgc gene in oogenesis . 30 Deletion of stem loop 1 causes 3-fold upregulation of pgc gene in embryogenesis . 31 Deletion of stem loop 10 causes 5-fold upregulation of pgc gene in embryogenesis . 32 Depletion of protein YT521B causes no change in regulation in oogenesis . 33 Depletion of protein YT521B causes significant upregulation in embryogenesis . 34 Protein YT521B and stem loop 10 interact in embryogenesis . 34 Conclusions & Future Directions.35 References . 36
INO80 Chromatin Remodelling Coordinates Metabolic Homeostasis with Cell Division

Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the Yeast Metabolic Cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here we demonstrate that the INO80 chromatin-remodelling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin in order to restrict proliferation to metabolically optimal states.
Addressing Wormhole Attacks on the Internet

This paper proposes a new kind of attack, the wormhole attack, on the Internet. To launch a wormhole attack, an adversary connects two distinct malicious routers in the network using a communication link called a wormhole or a tunnel. The wormhole attack is a severe challenge especially for anomaly detection. Many existing solutions for anomaly detection try to identify the fake messages caused by malicious attack. Since the wormhole is a real path to forward packets, it is difficult to be detected via the existing routing protocols or security mechanisms. Once the wormhole is formed, the adversary can launch active or passive attacks. In this paper, we first survey related literatures about security mechanisms on the Internet, and then show their deficiencies in defending against wormhole attacks. Finally, we recommend some countermeasures that can be used to deal with the wormhole attacks in the Internet.
Protein-ligand interfaces are polarized: Discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key. Abbreviations 3D three-dimensional CATH Class Architecture Topology Homologous superfamily H-bonds hydrogen bonds MMFF94 Merck Molecular Force Field PDB Protein Data Bank PRI Protein Recognition Index
Novel Role of Histone Deacetylase 11 (HDAC11) in Regulating Normal and Malignant Hematopoiesis

vii Chapter 1: Background . 1 1.1 Cancer . 1 1.1.1 Cancer and host immune cyctem. 2 1.1.2 Hematopoiesis and abnormal myelopoiesis . 4 1.1.3 Current approaches for cancer immunotherapy . 6 1.2 Tumor microenvironment . 7 1.2.1 Tumor infiltrated T lymphocytes . 8 1.2.2 Tumor-derived suppressor cells . 9 1.2.2.1 The origin of MDSCs . 10 1.2.2. 2 MDSCs expansion . 11 1.2.2.3 Subsets of MDSCs . 11 1.2.2.4 Mechanisms regulating MDSCs biology . 12 1.2.2.5 Clinical evaluation of MDSCs . 15 1.2.2.6 Targeting MDSCs in Cancer . 16 1.2.3 Tumor associated macrophages . 17 1.2.4 Other cellular and non-cellular components in the tumor microenvironment . 18 1.2.5 Strategies of targeting the tumor microenvironment . 19 1.3 Histone deacetylases . 22
Graphical models for robust speech recognition in adverse environments

Robust speech recognition in acoustic environments that contain multiple speech sources and/or complex non-stationary noise is a difficult problem, but one of great practical interest. The formalism of probabilistic graphical models constitutes a relatively new and very powerful tool for better understanding and extending existing models, learning, and inference algorithms; and a bedrock for the creative, quasi-systematic development of new ones. In this thesis a collection of new graphical models and inference algorithms for robust speech recognition are presented. The problem of speech separation using multiple microphones is first treated. A family of variational algorithms for tractably combining multiple acoustic models of speech with observed sensor likelihoods is presented. The algorithms recover high quality estimates of the speech sources even when there are more sources than microphones, and have improved upon the state-of-the-art in terms of SNR gain by over 10 dB. Next the problem of background compensation in non-stationary acoustic environments is treated. A new dynamic noise adaptation (DNA) algorithm for robust noise compensation is presented, and shown to outperform several existing state-of-the-art front-end denoising systems on the new DNA + Aurora II and Aurora II-M extensions of the Aurora II task. Finally, the problem of speech recognition in speech using a single microphone is treated. The Iroquois system for multi-talker speech separation and recognition is presented. The system won the 2006 Pascal International Speech Separation Challenge, and amazingly, achieved super-human recognition performance on a majority of test cases in the task. The result marks a significant first in automatic speech recognition, and a milestone in computing.
Effect of dietary concentrate to forage ratio on growth performance, rumen fermentation and bacterial diversity of Tibetan sheep under barn feeding on the Qinghai-Tibetan plateau

This study aimed to research the effects of different dietary concentrate to forage (C:F) ratio on growth performance, rumen fermentation and bacteria diversity of barn feeding Tibetan sheep. The experiment contains fiver treatments (HS1, HS2 HS3, HS4 and HS5; n = 8, respectively) based on dietary C:F ratios 0:100, 15:85, 30:70, 45:55, and 60:40, respectively. The ruminal bacterial community structure was investigated through high-throughput sequencing of 16S rRNA genes in V4 hypervariable region. The results showed that increasing dietary concentrate feed level from 0% to 60% exerted a positive effect on DMI, BW gain, gain rate and feed conversation ratio (FCR) in Tibetan sheep. The increases dietary concentrate feed level elevatedNH3-N, propionate and valerate concentrations, whereas, reduced molar ratio of acetate to propionate (A/P ratio) (P < 0.05). For rumen bacterial diversity, increases in dietary concentrate content contributed to lower alpha diversity indexes including Shannon wiener, Chao1 and observed species, meanwhile, significantly increased the abundances of the phylum Bacteroidetes and the genus Prevotella_1 (P < 0.05). In conclusion, increases dietary concentrate content improved the growth performance and Tibetan sheep fed diets of 45% concentrate obtained a better performance; the inclusion of concentrate in feed changed rumen fermentation from acetate fermentation to propionate fermentation, and improved the energy utilization efficiency of Tibetan sheep; the increased in concentrate content significantly reduced rumen bacteria diversity and changed the abundance of some core bacteria.