bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting Antiretroviral Drug Resistance from the Latest or the Cumulative Genotype
Authors: Garcia Federico , Alvarez Marta , Fox Zoe , Garcia-Diaz Ana , Guillot Vicente , Johnson Margaret , Chueca Natalia , Phillips Andrew , Hernández-Quero José , Geretti Anna Maria 
Published: March 2011

Background This study evaluates the added benefit when estimating antiretroviral drug resistance of combining all available resistance test results in a cumulative genotype relative to using the latest genotype alone. Methods The prevalence of resistance and genotypic sensitivity scores (GSS) predicted by the latest and the cumulative genotype, together with virological outcomes after the latest genotype, were measured in treatment-experienced patients who underwent ≥2 resistance tests in 1999–2008. Results Comparing the latest with the cumulative genotype in 227 patients, 4 (1.7%) versus 0 (0.0%) showed no major resistance mutations, whereas 74 (32.6%) versus 46 (20.3%), 88 (38.8%) versus 76 (33.5%) and 61 (26.9%) versus 105 (46.3%) showed single-class, dual-class and triple-class resistance mutations, respectively. The median (IQR) number of fully or partially active drugs was 6 (5–6) versus 5 (4–6) for the nucleoside/nucleotide reverse transcriptase inhibitors, 3 (1–3) versus 1 (1–3) for the non-nucleoside reverse transcriptase inhibitors and 7 (7–7) versus 7 (7–7) for the protease inhibitors, respectively. Among 163 patients who started a new regimen after the latest genotype, both the latest and the cumulative GSS were predictive of early (≤24 weeks) virological responses. The GSS decreased by median 1 unit (IQR 0.5–1.0) in the cumulative genotype and larger differences relative to the latest genotype corresponded to smaller decreases in viral load. Conclusions The cumulative genotype offers a more comprehensive evaluation of the burden of resistance. This approach can guide small but appreciable improvements in the selection of antiretroviral regimens for treatment-experienced patients.
IFN-α Mediates the Development of Autoimmunity both by Direct Tissue Toxicity and through Immune Cell Recruitment Mechanisms
Authors: Akeno Nagako , Smith Eric P. , Stefan Mihaela , Huber Amanda K. , Zhang Weijia , Keddache Mehdi , Tomer Yaron 
Published: March 2011

Abstract
IFN-α is known to play a key role in autoimmunity, but the mechanisms are uncertain. Although the induction of autoimmunity by IFN-α is consistent with primarily immunomodulatory effects, the high frequency of nonautoimmune inflammation suggests other mechanisms. We used thyroiditis as a model to dissect these possibilities. IFN-α treatment of cultured thyrocytes increased expression of thyroid differentiation markers, thyroglobulin, thyroid-stimulating hormone receptor, thyroid peroxidase, and sodium iodide transporter. RNAseq analysis demonstrated that pathways of Ag presentation, pattern recognition receptors, and cytokines/chemokines were also stimulated. These changes were associated with markedly increased nonapoptotic thyroid cell death, suggesting direct toxicity. To corroborate these in vitro findings, we created transgenic mice with thyroid-specific overexpression of IFN-α under control of the thyroglobulin promoter. Transgenic mice developed marked inflammatory thyroid destruction associated with immune cell infiltration of thyroid and surrounding tissues leading to profound hypothyroidism, findings consistent with our in vitro results. In addition, transgenic mice thyroids showed upregulation of pathways similar to those observed in cultured thyrocytes. In particular, expression of granzyme B, CXCL10, a subset of the tripartite motif-containing family, and other genes involved in recruitment of bystander cytotoxic immune responses were increased. Pathways associated with apoptosis and autophagy were not induced. Taken together, our data demonstrate that the induction of tissue inflammation and autoimmunity by IFN-α involves direct tissue toxic effects as well as provocation of destructive bystander immune responses.
Differential Requirements for Th1 and Th17 Responses to a Systemic Self-Antigen
Authors: Katzman Shoshana D. , Gallo Eugenio , Hoyer Katrina K. , Abbas Abul K. 
Published: March 2011

Abstract
T cell–APC interactions are essential for the initiation of effector responses against foreign and self-antigens, but the role of these interactions in generating different populations of effector T cells in vivo remains unclear. Using a model of CD4+ T cell responses to a systemic self-antigen without adjuvants or infection, we demonstrate that activation of APCs augments Th17 responses much more than Th1 responses. Recognition of systemic Ag induces tolerance in self-reactive CD4+ T cells, but induction of CD40 signaling, even under tolerogenic conditions, results in a strong, Ag-specific IL-17 response without large numbers of IFN-γ–producing cells. Transfer of the same CD4+ T cells into lymphopenic recipients expressing the self-antigen results in uncontrolled production of IL-17, IFN-γ, and systemic inflammation. If the Ag-specific T cells lack CD40L, production of IL-17 but not IFN-γ is decreased, and the survival time of recipient mice is significantly increased. In addition, transient blockade of the initial MHC class II-dependent T cell–APC interaction results in a greater reduction of IL-17 than of IFN-γ production. These data suggest that Th17 differentiation is more sensitive to T cell interactions with APCs than is the Th1 response, and interrupting this interaction, specifically the CD40 pathway, may be key to controlling Th17-mediated autoimmunity.
Artinianness of Certain Graded Local Cohomology Modules
Authors: Mafi Amir , Saremi Hero 
Published: March 2011

AbstractWe show that ifR= ⴲn∈ℕ0Rnis a Noetherian homogeneous ring with local base ring (R0, m0), irrelevant idealR+, andMa finitely generated gradedR-module, thenis Artinian forj= 0, 1 wheret= inf﹛i∈ ℕ0:is not finitely generated﹜. Also, we prove that if cd(R+,M) = 2, then for eachi∈ ℕ0,) is Artinian if and only ifis Artinian, where cd(R+,M) is the cohomological dimension ofMwith respect toR+. This improves some results of R. Sazeedeh.
Comunicación y cambio organizacional
Authors: Arras Vota Ana María , Jáquez Balderrama José Luis , Fierro Murga Luz Ernestina 
Published: March 2011

La comunicación es un elemento esencial en la vida de las organizaciones, gracias e este proceso, a través del cual se ponen en común las experiencias y vivencias del ser humano, es posible que las personas realicen acciones conjuntas, generen acuerdos, compromisos y participen en el cambio organizacional. En esta investigación se tiene como propósito analizar -a través de las circulares abiertas en forma de cartel- la influencia que tienen las comunicaciones como estrategias de poder en el cambio organizacional.
Medicinal Inorganic Chemistry: Metallotherapeutics for Chronic Diseases
Authors: Thompson Katherine H. 
Published: March 2011

AbstractMetal‐containing therapeutic agents designed for use in chronic disorders, such as gastrointestinal dyspepsia, bipolar disease, diabetes mellitus, osteoporosis, and arthritis, present additional challenges to the medicinal chemist. Beyond the immediate toxicity issues seen with acute disease treatments, chronic use of metallotherapeutic agents may result in metal ion accumulation or in gradually developing intolerance that can require discontinuation of the drug. Metallotherapeutic agents that have passed the rigorous testing required for chronic use include bismuth subsalicylates, for a variety of gastrointestinal disorders; lithium carbonate, for bipolar disease; lanthanum carbonate, for end‐stage renal disease; strontium ranelate, for osteoporosis; and the gold‐based antiarthritic, Auranofin™, although the last has fallen out of favor. Chromium picolinate is an approved nutritional supplement, a designation that allows less stringent testing than for new chronic‐use drugs. Among those compounds not currently approved for clinical use, but showing promise, the copper – indomethacin and zinc – indomethacin complexes, for inflammation resulting from rheumatoid arthritis; vanadium compounds, for glucose‐ and lipid‐lowering in type 2 diabetes mellitus; and selenium compounds, as possible cancer preventatives, are worthy of consideration.
Drying
Authors: McCormick P. Y. 
Published: March 2011

Abstract
Polymer drying is an important industrial operation employed to isolate the saleable product from the reaction process. Before melting and reextrusion for molding or spinning, many polymers have to be dried again because they are slightly hygroscopic and susceptible to degradation if melted in the presence of moisture. Terminology, psychrometry, drying mechanisms, drying operations, and other topics are covered. Examples of specific commercial polymers are presented.
Chemical Analysis
Authors: Rubinson Kenneth A. 
Published: March 2011

Abstract

This chapter outlines the tools of chemical analysis that are used to determine the identities and amounts of elements and molecules that comprise material—the usual solids, liquids, and gases but also including flames and interstellar matter and so forth. The choice of the method or instrument to be used depends on what fraction of the material to be measured is present in a material and the size of the sample. Current capabilities of analysis range from essentially unity (100%) to about one part in 10
12
. In addition, the complexity of samples encountered often dictates using a method that can isolate the responses from one or many species to be measured from those of the rest of the sample—a consideration that becomes more important when the fraction of the measured species the lower. Each method, tool, or instrument has its own characteristic abilities, and the choice of the best one can be quite involved.
Photoacoustic Spectroscopy
Authors: Harren Frans J. M. , Persijn Stefan , Cristescu Simona M. 
Published: March 2011

Abstract
After a short introduction and description of particular features of the equipment used, attention is centered on applications. Solids, surfaces, and solutions have been studied by photoacoustic (PA) spectroscopy; recent work is quoted. Gas‐phase investigations are discussed with emphasis on trace gas detection. Especially, applications in biology and human health are considered.
Metrology of Time and Frequency
Authors: Arias Felicitas , Bauch Andreas 
Published: March 2011

AbstractThis chapter provides a concise overview of the current status of time and frequency metrology. The definition of the time unit and of time scales is given, and the standards and procedures to realize them are described. The measures by which their properties are characterized are explained. The comparison of remote standards is discussed to the extent that it is a prerequisite for the realization of a world reference time scale by the Bureau International des Poids et Mesures (BIPM). Only a brief account is given on the various means of disseminating time and the wide applications thereof. The reader is invited to use the literature in theFurther Readingsection as well as the numerous references to get a deeper insight into the field.
Metrology in Medicine
Authors: Macdonald Rainer , Mieke Stephan 
Published: March 2011

AbstractPhysical, chemical, and biological measurements are important essentials in medical diagnosis for the prevention and treatment of disease as well as for risk assessment and monitoring of patients. Hence, measurement results that are relevant to medical diagnosis must be accurate, reliable, and comparable between different places and over time to ensure optimum patient care as well as the most efficient use of available health care funds. To ensure that medical measurement results are of known quality and to improve their accuracy and reliability, standards, reference methods, certified reference materials, and calibrations are needed. In this article, the peculiarities of medical measurements are discussed and problems encountered in fulfilling the above‐mentioned requirements are pointed out.
Viroids
Authors: Flores Ricardo , Daròs José‐Antonio , Hernández Carmen , Di Serio Francesco 
Published: March 2011

AbstractViroids are infectious, nonprotein‐coding, highly structured small circularribonucleic acids(RNAs) able to replicate autonomously and induce diseases in higher plants. Viroids and viruses differ in structure, function and evolutionary origin (with the former regarded as relics of a primitive RNA world). Viroids are classified into the familiesPospiviroidaeandAvsunviroidae, the members of which replicate in the nucleus and chloroplast, respectively, through an RNA‐based rolling circle mechanism with three steps catalysed by: (i) hostdeoxyribonucleic acid (DNA)‐dependent RNA polymerasesredirected to accept RNA templates, (ii) processing enzymes or, in the familyAvsunviroidae, hammerhead ribozymes and (iii)RNA ligases. When infecting a cell, the viroid RNA must travel to its replication organelle, with the resulting progeny moving cell‐to‐cell through plasmodesmata and reaching distal parts through the phloem. Pathogenesis could be triggered by the replicating viroid itself, or via RNA silencing. Viroids are detected by nucleic acid‐based approaches, some can be eliminated from infected plants by meristem tip culturing, and biotechnological approaches are being developed for their control.Key Concepts:Viroids are small nonprotein‐coding RNAs that infect, replicate and induce disease in higher plants.Viroids differ from viruses in fundamental aspects that include structure, function and evolutionary origin.Viroids are classified into the familiesPospiviroidae(nuclear viroids) andAvsunviroidae(chloroplastic viroids).Viroid RNAs adopt compact secondary structures additionally stabilised by elements of tertiary structure.Viroids replicate through a rolling circle mechanism with only RNA intermediates and enzyme or ribozyme processing.Different viroids have distinct host ranges and closely related viroids display cross‐protection effects when co‐infecting a common host.Viroids move intracellularly, cell‐to‐cell through plasmodesmata, and long distance through the phloem.Viroids may infect their host plants latently or induce different pathogenic alterations including death.Viroids propagate in their hosts as a population of closely related variants (quasispecies).Viroids are considered molecular fossils of the RNA world postulated to have preceded our present world dominated by DNA and proteins.
Seeds
Authors: Black Michael 
Published: March 2011

Abstract

In the seed‐bearing plants (angiosperms and gymnosperms), the embryo‐containing seed develops from the fertilised ovule. Other tissues might also be present in the mature seed such as the endosperm (angiosperms) and the megagametophytic tissue in gymnosperms. During its formation, storage reserves are deposited in various parts of the seed. The structural and physiological features that develop during transition of the ovule into a seed confer upon it properties that account for its greatly successful role in the life cycle of the dominant plants on earth. These include the reserves, the various dispersal mechanisms and in the majority of species, the ability to withstand desiccation, which is connected with the longevity of seeds in the ‘dry’ state. Seed dormancy, where present, serves later to determine the place and time of germination. Regulation of seed processes is achieved by control of gene expression, including by the hormones abscisic acid and gibberellin. Seeds were critically important in plant domestication and are currently important in plant biotechnology.

Key Concepts:

A seed develops from a fertilised ovule and consists of an embryo and other tissues of different developmental origins.

The seed occupies a key position in the life cycle of higher plants and accounts for the great success of angiosperms and gymnosperms.

During its development, the seed lays down relatively high proportions of storage reserves for the later support of early seedling growth.

In most species, seeds tolerate the desiccation that terminates their development and thereafter remain alive for long durations in a quiescent state.

Seeds develop various structural features that later aid their dispersal.

During development, seeds of many species become dormant, a condition that later blocks germination until after certain environmental signals have been experienced.

Regulation of gene expression by hormones and other factors is central to the various processes that occur in seeds.

Various features of seeds had a key role in plant domestication and the development of crop species.

Seeds are central to plant biotechnology and the design of new crop types.
Cotranslational Translocation of Proteins Into Microsomes: Methods
Authors: Pool Martin , Dobberstein Bernhard 
Published: March 2011

Abstract

Translocation of secretory and membrane proteins through the membrane of the endoplasmic reticulum involves a signal sequence on the nascent protein, a cytosolic receptor system and a translocation channel (translocon). The process can be reconstituted using a protein‐synthesising system and rough microsomes derived from the endoplasmic reticulum (ER) of eukaryotic cells. Applications of this system have realised substantial insights into the mechanisms of protein targeting to the ER membrane and the insertion of a nascent polypeptide into the membrane. The arrest of polypeptides at distinct stages of the targeting or insertion process yielded snapshots from the movement of a polypeptide across the membrane. This has allowed identification of components of the translocation machinery and the characterisation of their sequential involvement in targeting and translocation.

Key Concepts:

Many membrane transport processes can be studied with fragmented membranes.

Mechanical shearing of cellular membranes always results in closed vesicles.

Cellular membranes are self‐organising structures without corners and breaks.

Reconstitution of cellular subfunctions is a very efficient way to characterise cellular processes at the molecular level.

When a system is too complex, then study first its parts.

Generating reaction intermediates blocked at defined steps allows complex processes to be broken down into simpler and more tractable subreactions.
Santalales (Including Mistletoes)
Authors: Nickrent Daniel L 
Published: March 2011

Abstract

Mistletoes are flowering plants in the sandalwood order (Santalales) that parasitise tree branches. They evolved five separate times in the order and are today represented by 88 genera and nearly 1600 species. Loranthaceae (
c
. 1000 species) and Viscaceae (550 species) have the highest species diversity. In South America

Misodendrum

(a parasite of

Nothofagus

) is the first to have evolved the mistletoe habit ca. 80 million years ago. The family Amphorogynaceae is of interest because some of its members are transitional between root and stem parasites. Many mistletoes have developed mutualistic relationships with birds that act as both pollinators and seed dispersers. Although some mistletoes are serious pathogens of forest and commercial trees (e.g.

Arceuthobium

), the vast majority are benign and in some cases beneficial to humans (e.g.

Viscum album

for anticancer drugs). Mistletoes play important roles in many forest ecosystems and their loss results in decreases in faunal diversity, thus making them keystone species.

Key Concepts:

A mistletoe is a branch parasite in the sandalwood order (Santalales).

Mistletoes have evolved from root parasitic ancestors five times independently in five different families: Misodendraceae, Loranthaceae, Santalaceae, Amphorogynaceae and Viscaceae.

The first lineage to evolve the mistletoe habit is
Misodendrum
, a South American parasite on southern hemisphere beech (
Nothofagus
).

Most mistletoe species are found in the families Loranthaceae (
c
. 1000 species) and Viscaceae (550 species).

Loranthaceae evolved on the Gondwanan supercontinent and subsequently spread from Antarctica to South America, Australia, New Zealand, Asia and Africa.

Many mistletoes have developed mutualistic relationships with birds that serve as both pollinators and seed dispersers.

Some mistletoes such as
Arceuthobium
are important pathogens of forest trees, whereas most are beneficial and even keystone species in forest ecosystems.
Chromosomes and Chromatin
Authors: Paulson James R , Vagnarelli Paola 
Published: March 2011

AbstractChromosomes are structures within the nuclei of eukaryotic cells that containdeoxyribonucleic acid(DNA) combined with proteins. Chromatin refers to the material of the chromosomes – DNA plus proteins. Before DNA replication, each chromosome contains a single, very long DNA molecule that basically runs from one end of the chromosome to the other. Core histone proteins package segments of this DNA molecule into nucleosomes, and linker histones further compact the resulting ‘string of beads’ into a 30‐nm chromatin fibre. In mitotic chromosomes, scaffold proteins fold the chromatin fibre into loops along its length. Chromosomes are very dynamic structures and take several forms, but the basic organisation is always related to the structure of mitotic chromosomes. The location of chromosomes in the nucleus, the nature of the loops and modifications to the chromatin fibre are thought to be important in determining which DNA sequences are made available for transcription and other processes.Key Concepts:In eukaryotic cells, genes are located in chromosomes in the cell nucleus.Before the DNA has been replicated, a chromosome consists of a single very long DNA double helix that is highly coiled and folded by proteins.Five major types of histone proteins, all of them highly basic, neutralise much of the DNA's negative charge and package the DNA into nucleosomes and 30‐nm fibres.TheN‐terminal tails of core histones are intrinsically disordered, allowing them to interact with many other proteins and undergo various posttranslational modifications.Transcriptional activation of genes, or readiness for transcriptional activation, is associated with histone acetylation, and inactivation is generally associated with histone methylation.In mitotic chromosomes, the chromatin fibre is folded into loops by attachment to a scaffold of nonhistone proteins.Mitotic chromosome condensation appears to involve two components: compaction of the chromatin at the onset of mitosis, which involves phosphorylation of chromosomal proteins, and establishment of a robust architecture that can withstand spindle forces, which involves condensin.The various chromosome forms that are seen throughout the cell cycle or the life cycle of the organism have closely related structures.A chromosome during interphase retains some aspects of the structure it had during mitosis and is confined to a distinct ‘territory’ within the interphase nucleus.Chromosome banding and chromosome painting are medically important for detecting chromosome abnormalities such as breaks, fusions, translocations and aneuploidy and can be used to track chromosomal rearrangements that have occurred during evolution.