Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies into the role of peptidoglycan glycolylation in mycobacterial dormancy and resuscitation

ii Acknowledgements iii List of Common Abbreviations iv List of Figures vi List of Tables ix Chapter 1: Introduction xv 1.1 General Introduction 1 1.2 Global Burden of TB 2 1.2.1 The effect of HIV on TB prevalence 4 1.3 Clinical Symptoms 6 1.4 Diagnostics 7 1.5 Tuberculosis Treatment 9 1.6 Emergence of Drug Resistance 12 1.7 Pathophysiology 14 1.8 Mycobacteria 16 1.8. 1 MTBC 17 1.8. 2 Non-Tuberculosis Mycobacteria 18 1.8. 3 Cell Wall Architecture 20 1.8. 3.1 Mycobacterial PG and NamH 22 1.9 Latent Tuberculosis Infection and Non-Replicating Persistence . 28 1.9. 1 In Vitro and In Vivo Dormancy Models 30 1.9. 2 Reactivation and Resuscitation 33 1.9. 2.1 Resuscitation Promoting Factors 34 1.9. 2.2 Muropeptides as Signalling Molecules 39 1.10 Aims and Objectives 43 Chapter 2: Materials and Methods 44 2.1 Reagents and Media 45 2.1.1 Media 45 2.2 Bacterial Stocks 46 2.2.1 Cultivation Techniques 46 2.2.2 CFU Plating and Counting 47
Evolving the Neighbors

The aim of this section is to give brief indications of the character, content, and cost of new books in the various fields of biology. More books are received by The Quarterly than can be reviewed critically. All submitted books, however, are carefully considered for originality, timeliness, and reader interest, and we make every effort to find a competent and conscientious reviewer for each book selected for review. Of those books that are selected for consideration, some are merely listed, others are given brief notice, most receive critical reviews, and a few are featured in lead reviews. Listings, without comments, are mainly to inform the reader that the books have appeared; examples are books whose titles are self-explanatory, such as dictionaries and taxonomic revisions, or that are reprints of earlier publications, or are new editions of well-established works. Unsigned brief notices, written by one of the editors, may be given to such works as anthologies or symposium volumes that are organized in a fashion that makes it possible to comment meaningfully on them. Regular reviews are more extensive evaluations and are signed by the reviewers. The longer lead reviews consider books of special significance. Each volume reviewed becomes the property of the reviewer. Most books not reviewed are donated to libraries at Stony Brook University or other appropriate recipients. The price in each case represents the publisher's suggested list price at the time the book is received for review, and is for purchase directly from the publisher. Authors and publishers of biological books should bear in mind that The Quarterly can consider for notice only those books that are sent to The Editors, The Quarterly Review of Biology, C-2615 Frank Melville, Jr. Memorial Library, Stony Brook University, Stony Brook, NY 11794-3349 USA. We welcome prepublication copies as an aid to early preparation of reviews.
Variáveis ambientais e toxicológicas de agroquímicos utilizados na Produção Integrada de Maçãs (PIM) visando modelagem matemática

Algumas das razoes do pouco uso da modelagem matematica para gestao do ambiente no meio agricola vinculado a Producao Integrada de Macas (PIM), sao a falta de softwares adequados as condicoes brasileiras, a falta destes em lingua portuguesa e a dificuldade na coleta e organizacao de dados necessarios ao uso de tais modelos. O objetivo desta publicacao e atender esta ultima demanda, fornecendo dados fisicoquimicos e toxicologicos dos agrotoxicos na PIM utilizados ate a safra de 2005/2006, num documento unico, facilitando seu acesso.
Antimicrobial Mechanism Analysis of an Oil in Water Microemulsion by DNA Microarray‐Mediated Transcriptional Profiling of Escherichia Coli

The DNA microarray was employed in this study to investigate the gene expression profiles of Escherichia coli treated by oil in water (o/w) microemulsion in order to better understand the antimicrobial mechanism of the microemulsion as a promising food-grade antimicrobial system. Among 5,440 open reading frames of E. coli, a total of 634 and 501 were highly induced and repressed, respectively. According to the annotation and analysis in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, it was found that the differently expressed genes were mainly involved in the biosynthesis of cell wall components and membranes, phosphate-related metabolism and some other biosynthetic pathways, suggesting that the main antibacterial mechanisms of the o/w microemulsion were the attacks to the cell surface structure, especially the cell wall, and its influences on the metabolism of phosphate of the E. coli cells through phosphate absorption inhibition. Practical Applications In the panorama of the increasing need to search for novel strategies in order to prevent foodborne outbreaks, microemulsion systems have been of great interest to researchers for their broad antimicrobial properties. In our group, a series of food-grade or pharmaceutical microemulsion systems based on glycerol monolaurate have been established for antimicrobial applications. It was found that the prepared microemulsions possessed excellent broad-spectrum antimicrobial activities due to the disruption and dysfunction of biological membranes and cell walls, as suggested by the transmission electron microscopy observations and membrane permeability experiments. The antimicrobial mechanisms analysis of the microemulsion mediated by DNA microarray in this work will be of great importance in exploring the structure–activity relationship of the o/w microemulsion at molecular biological levels in future work, in order to provide a guideline in designing food-grade antimicrobial microemulsions.
List of Contributors

CATHERINE ANDREYEV, Lecturer in Modern European History, Christ Church College, University of Oxford, Oxford OX1 1DP, UK. Email: catherine.andreyev@chch.ox. ac.uk. RICHARD ARNOLD, Assistant Professor of Political Science, Muskingum University, 163 Stormont Street, New Concord, OH 43762, USA. Email: rarnold@muskingum.edu. JUDITH BEYER, Research Fellow, Project Group Legal Pluralism, Max Planck Institute for Social Anthropology, Advokatenweg 36, 06114 Halle/Saale, Germany. Email: beyer@ eth.mpg. de. STEPHEN J. BLANK, Professor of National Security Affairs, US Army War College, Strategic Studies Institute, 122 Forbes Avenue, Carlisle, PA 17013-5244, USA. Email: Stephen. Blank@us.army. mil. LÁSZLÓ CSABA, Professor of International Political Economy, Central European University, Nador u. 9, 1051 Budapest, Hungary. Email: csabal@ceu.hu. ZOLTÁN CSIPKE, School of History, University of Liverpool, 9 Abercromby Square, Liverpool L69 7WZ, UK. Email: zoltan@bolted.net. INDRA DEDZE, Project Manager, University of Latvia, Raina bulv. 19, Riga, LV 1586, Latvia. Email: indra@lanet.lv. SERGIU GHERGHINA, PhD Candidate, University of Leiden, Department of Political Science, Wassenaarseweg 52, Office 5A51, Leiden, Zuid Holland 2333 AK, Netherlands. Email: sergiulor@yahoo.com. ROBERT HORVATH, Charles La Trobe Research Fellow, School of Social Sciences, La Trobe University, VIC 3086, Australia. Email: r.horvath@latrobe.edu. au. GEORGE JIGLAU, Babes-Bolyai University, Department of Political Science, Zambilei Street, Cluj-Napoca, Romania. Email: george.jiglau@yahoo.com. WILLY JOU, University of California Irvine, Department of Political Science, School of Social Science, 3151 Social Science Plaza, Irvine, CA 92697-5100, USA. Email: jouw@uci.edu. PÄIVI KARHUNEN, Head of Research, Aalto University School of Economics, Centre for Markets in Transition, PO Box 21210, Aalto 00076, Finland. Email: paivi.karhunen@hse.fi. RIITTA KOSONEN, Director, Aalto University School of Economics, Centre for Markets in Transition, PO Box 21210, Aalto 00076, Finland. Email: riitta.kosonen@hse.fi. MARTIN LARYŠ, PhD Candidate, Masaryk University, Department of Political Science, Faculty of Social Studies, Jostova 10, Brno 60200, Czech Republic. Email: Larys.Martin@seznam.cz. MIROSLAV MAREŠ, Masaryk University, Department of Political Science, Faculty of Social Studies, Jostova 10, Brno 60200, Czech Republic. Email: mmares@fss.muni. cz. BRANISLAV RADELJIĆ, PhD Candidate, Department of Politics, Goldsmiths College, University of London, New Cross, London SE14 6NW, UK. Email: branislav.radeljic@gold.ac.uk. SUVI SALMENNIEMI, Postdoctoral Researcher, University of Helsinki, Helsinki Collegium for Advanced Studies, PO Box 10, Helsinki 00014, Finland. Email: suvi.salmenniemi@helsinki.fi. ANDREAS UMLAND, Catholic University of Eichstätt-Ingolstadt, Ostenstraße 27, 85072 Eichstätt, Germany. Email: andreumland@yahoo.com. JONATHAN ZARTMAN, Assistant Professor of National Security Studies, Air Command and Staff College, 2730 Windsor Avenue, Montgomery, AL 36109, USA. Email: jzartman@ securenym.net. EUROPE-ASIA STUDIES Vol. 63, No. 1, January 2011, 173
The involvement of single-stranded DNA, replication protein A, and the DNA double-strand break dose in the damage checkpoint of Saccharomyces cerevisiae

In response to DNA damage, eukaryotic cells activate a checkpoint signalling cascade, resulting in cell cycle arrest, stabilisation of replication forks and activation of repair. While many players in these pathways have been identified, little is known about the original sensors, or of the DNA structures involved. Because it is present in all checkpoint-inducing lesions, single-stranded DNA (ssDNA) is a good candidate for a common structure recognised by the DNA damage response. The role of ssDNA in checkpoint activation in the yeast Saccharomyces cerevisiae was investigated using three different approaches. Firstly, an attempt was made to produce ssDNA independently of strand breaks by inducing replication-independent plasmid unwinding. Secondly, the effects of depleting the major ssDNA-binding complex, replication protein A (RPA) were analysed. Lastly, an assay to quantify ssDNA generated at a defined DNA double-strand break (DSB) was developed. Despite extensive efforts, the first approach proved unsuccessful, as the method used did not generate unwound plasmid. Using the second approach, it was found that depletion of RPA did not inhibit checkpoint activation during replication stress. Furthermore, replication with limiting amounts of RPA led to rapid cell death and checkpoint activation that was mediated independently of the response to stalled replication forks. Lastly, at a defined DSB it was found that less ssDNA was being generated than had previously been estimated from results based on non-quantitative methods. Additionally, an element of dose dependency was observed in the checkpoint response to DSBs, with stronger and more rapid responses being generated by higher numbers of breaks. Formation of four DSBs resulted in checkpoint activation even in G1 arrested cells. Together, these results raise the possibility of a DNA damage checkpoint pathway largely independent of long tracts of RPA-coated ssDNA and show that checkpoint activation to DSB-damage is possible in G1.
Multi One-Class Incremental SVM for Document Stream Digitization

Inside the DIGIDOC project (ANR-10-CORD-0020)-CONTenus et INTeractions (CONTINT), our approach was applied to several scenarios of classification of image streams which can cores ond to real cases in digitization projects. Most of the time, the processing of documents is considered as a well-defined task: the classes (also called concepts) are defined and known before the processing starts. But in real industrial workflows of document processes, it may frequently happen that the concepts can change during the time. In a context of document stream processing, the information and content included in the digitized pages can evolve over the time as well as the judgment of the user on what he wants to do with the resulting classification. The goal of this application is to create a module of learning, for a steam-based document images classification (especially dedicated to a digitization process with a huge volume of data), that adapts different situations for intelligent scanning tasks: adding, extending, contracting, splitting, or merging the classes in on an online mode of streaming data processing.
Prediction of Protein-Protein Interaction Sites from Three-Dimensional Structure

The knowledge of protein-protein interactions is essential for the understanding of protein functions and protein-protein interaction networks. Hence, the capability to identify protein-protein interaction sites is crucial to decipher the reaction mechanisms of protein function. In this work we develop am approach based on machine-learning method to predict protein-protein interaction sites from three-dimensional structure. We have tried a multiple of feature vectors such as amino acid composition, secondary structure, relative solvent accessible surface area, position substitution specific matrix and structural neighboring residues. Our results compare favorably with those of others for a benchmark dataset.
Compensation for Injury? Modified multi-modal courtship of wolf spiders following autotomy of signalling appendages

Male Schizocosa ocreata wolf spiders court females using displays that involve dramatic waving motions of their ornamented forelegs. In nature males are often found missing one, and sometimes both, of these legs. We here find that, when exposed to female draglines, males missing these signalling appendages perform a high intensity courtship element (‘jerky tapping’) at a greater rate than intact males. Loss of forelegs was also associated with changes in chemoexploration activity, tendency to stand stationary, and performance of a low intensity courtship element (‘tapping’). The age of the virgin female from which draglines were collected also had an important influence on male courtship behaviour; males on the draglines of old females were less likely to court and, if they did court, did so at a lower rate. These data indicate that courtship behaviour of male S. ocreata is flexible, varying both with the state of the male himself and the state of the female whose draglines he has encountered. Such individual courtship flexibility raises challenging questions of what processes and trade-offs underlie male courtship decision-making, and whether autotomy-induced changes in courtship activity represent adaptive compensation.
Determining the action spectrum of UVR-induced mitochondrial DNA damage, and related UVR-induced cellular effects in human skin

Nichols, J. A. , Lloyd, J. and Birch-Machin, M. A. (2011) 'The action spectrum of UVRinduced damage within an 11 kb segment of mitochondrial DNA in human skin cells', British Journal of Dermatology, 164(4), pp. 924-924. Latimer, J. A. , Russell, E. V. and Birch-Machin, M. A. (2012) 'The Effects of Infrared Radiation versus Ultraviolet Radiation in Human Skin Cells ', Journal Of Invesigative Dermatology, 132(2), pp. S122-S122. Russell, E. V. , Latimer, J. A. , Oyewole, A. and Birch-Machin, M. A. (2012) 'Investigating the Protective Potential of the Antioxidant Tiron in Human Skin Cells Exposed to Ultraviolet Radiation ', Journal Of Invesigative Dermatology, 132(2), pp. S121-S121. Chapter 8 References
Aphyosemion teugelsi (Cyprinodontiformes: Nothobranchiidae), a new species from a remote locality in the southern Democratic Republic of the Congo

Aphyosemion teugelsi is described from specimens collected in a small creek in the upper Wamba River basin in the southwest of the Democratic Republic of the Congo not far from the Angolan border. This is ~400 km outside the known distribution area of the genus. It is distinguished from all other members of the genus Aphyosemion by the combination of broad black margins on all fins in males, a robust lower jaw, a more convex back, a large head with large eyes, a more anterior position of the dorsal fin relative to anal fin, and absence of extensions on the upper and lower caudal fin.
Enzymatic Regulation of Opioid Antinociception and Tolerance

ENZYMATIC REGULATION OF OPIOID ANTINOCICEPTION AND TOLERANCE By Lynn C. Hull, Ph.D. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2009 Director: William L. Dewey, Ph.D. Department of Pharmacology and Toxicology The involvement of kinases in opioid actions has long been established. The acute actions of opioids, through the Gi/Go G-proteins, cause the inhibition of adenylyl cyclase and therefore a decrease in protein kinase A (PKA) activation. Additionally, acute opioid administration may cause the G-protein to activate the phospholipase C (PLC)-mediated cascade leading to the activation of protein kinase C (PKC). The phosphorylation of the MOR which can lead to both desensitization by uncoupling of the G-protein coupled receptors (GPCRs) from the G-proteins and to internalization by recruitment of β-arrestins has long been identified as a key process in tolerance. Phosphorylation by PKA and PKC leads primarily to uncoupling of the receptor from the G-proteins. Phosphorylation of the receptor by G-protein coupled receptor kinase (GRK) leads to the recruitment of β-arrestins and internalization of the receptor. Many in vitro studies have come to the conclusion that GRK induced internalization plays a more
CHOLESTEROL-LOWERING PROPERTY OF BACILLUS CEREUS STRAIN KAVK4 ISOLATED FROM BUTTER

ABSTRACT Objectives: The aim of the present study was to check the cholesterol-lowering property of Bacillus cereus strain KAVK4 at different concentration of cholesterol, different pH, different temperature, and different incubation time. Methods: B. cereus strain KAVK4 was isolated from butter by spread plate method. The cholesterol-lowering property was studied by adding different concentration of cholesterol in nutrient agar medium. Further, the cholesterol-lowering ability was optimized at various parameters such as different concentration of cholesterol, different pH, different temperature, and different incubation time. Results: B. cereus strain KAVK4 was utilized cholesterol and grown well in nutrient medium containing cholesterol at 1 mg/ml concentration. The cholesterol utilization was optimized at 1 mg/ml concentration, the optimal pH was at 8, the temperature at 30°C, and the incubation period was at 24 hrs. Conclusion: B. cereus strain KAVK4 was able to utilize cholesterol from the culture medium. Hence, B. cereus strain KAVK4 has been reported as cholesterol lowering agent. Keywords: Cholesterol lowering, Bacillus cereus, pH, Temperature, Time.
Fertility measures in Polish Black-and-White cattle.2. Genetic parameters of interval measures

Genetic parameters of service period, calving interval, days open, days to first service and days of pregnancy were estimated. Data were records of 42,283 cows. Heritabilities of all traits in first parity were low and ranged from 0.044 for calving interval to 0.092 for service period. Heritabilities of all intervals decreased in consecutive parities, and in the third parity were close to zero for days open and days to first service. The highest genetic correlation was found between calving interval and days open (0.99), days to first service and days open (0.74), and days to first service and calving interval (0.72). Service period was highly correlated genetically with age at first service (0.72), age at conception (0.90) and age at calving (0.90). The genetic correlation between days open and age at first insemination was 0.44. Genetic correlations of fertility traits between parities were highest when estimated for first and second parity, and ranged from 0.92 to 0.99.
Empowerment of “Street Children” Using CIPP Model to Develop Life Skills in Urban Areas of East Java Indonesia

This study aims to find an empowerment model of street children through effective and applicable life skills education. The empowerment was developed according to the will and potentials of the street children. CIPP (Content Input Process and Product) Model was used to develop the life skills of street children. The study was designed with a quasi-experimental using pre-test and post-test (before and after the training action). The goal is to develop life skills of street children in accordance with the will and potential skills they possessed. The research locations were in urban areas in East Java. The subjects were street children of junior high school and senior high school drop outs. The data collection was done by pre-test and post-test. Data analysis used tables of percentage and gain score. The results showed that street children should be given skills training according to their talents and their willingness. The types of skills to be trained were automotive, furniture, fashion, and culinary. The implementation training using CIPP system showed positive and significant results. This was indicated by the evaluation scores of the pre-test and post-test evaluation that continues to increase and the average results of gain score analysis which increased significantly. Research on the training of street children using CIPP approach has never been done by previous researchers. Training was conducted with 30% theory and 70% practice. The training schedule was tailored to the condition and character of the street children. Training was conducted in stages (the modular system) of as many as 16 sessions. Training evaluation pattern uses ongoing process system. Keywords : street children, empowerment, potential skills, and life skills training