De-escalation and Discontinuation of Disease-Modifying Therapies in Multiple Sclerosis.

Purpose Of Review: Long-term use of multiple sclerosis (MS) disease-modifying therapies (DMTs) is standard practice to prevent accumulation of disability. Immunosenescence and other age-related changes lead to an altered risk-benefit ratio for older patients on DMTs. This article reviews recent research on the topic of de-escalation and discontinuation of MS DMTs.

Processing speed and memory test performance are associated with different brain region volumes in Veterans and others with progressive multiple sclerosis.

Background: Cognitive dysfunction and brain atrophy are both common in progressive multiple sclerosis (MS) but are seldom examined comprehensively in clinical trials. Antioxidant treatment may affect the neurodegeneration characteristic of progressive MS and slow its symptomatic and radiographic correlates.

Objectives: This study aims to evaluate cross-sectional associations between cognitive battery components of the Brief International Cognitive Assessment for Multiple Sclerosis with whole and segmented brain volumes and to determine if associations differ between secondary progressive (SPMS) and primary progressive (PPMS) MS subtypes.

0.1% RGN-259 (Thymosin ß4) Ophthalmic Solution Promotes Healing and Improves Comfort in Neurotrophic Keratopathy Patients in a Randomized, Placebo-Controlled, Double-Masked Phase III Clinical Trial.

We determined the efficacy and safety of 0.1% RGN-259 ophthalmic solution (containing the regenerative protein thymosin ß4) in promoting the healing of persistent epithelial defects in patients with Stages 2 and 3 neurotrophic keratopathy. Complete healing occurred after 4 weeks in 6 of the 10 RGN-259-treated subjects and in 1 of the 8 placebo-treated subjects ( = 0.

Monitoring, Switching, and Stopping Multiple Sclerosis Disease-Modifying Therapies.

Purpose Of Review: This article reviews appropriate monitoring of the various multiple sclerosis (MS) disease-modifying therapies, summarizes the reasons patients switch or stop treatment, and provides a framework for making these management decisions.

Recent Findings: With the increasing number of highly effective immunotherapies available for MS, the possibility of better control of the disease has increased, but with it, the potential for side effects has rendered treatment decisions more complicated. Starting treatment early with more effective and better-tolerated disease-modifying therapies reduces the likelihood of switching because of breakthrough disease or lack of compliance.

Alemtuzumab in multiple sclerosis: an update.

Since the introduction of IFN-β, disease-modifying treatments, acting through various immune mechanisms, have been shown to reduce disease activity and severity in relapsing multiple sclerosis. Nevertheless, there remain patients for whom these treatments are incompletely effective, poorly tolerated or contraindicated. Alemtuzumab is a humanized monoclonal antibody that works by selectively depleting circulating lymphocytes.

Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes.

Many organisms survive fluctuating and extreme environmental conditions by manifesting multiple distinct phenotypes during adulthood by means of developmental processes that enable phenotypic plasticity. We report on the discovery of putative plasticity-enabling genes that are involved in transforming the gill of the euryhaline teleost fish, Fundulus heteroclitus, from its freshwater to its seawater gill-type, a process that alters both morphology and function. Gene expression that normally enables osmotic plasticity is inhibited by arsenic.

Computational discovery of transcriptional regulatory modules in fungal ribosome biogenesis genes reveals novel sequence and function patterns.

Genes involved in ribosome biogenesis and assembly (RBA) are responsible for ribosome formation. In Saccharomyces cerevisiae, their transcription is regulated by two dissimilar DNA motifs. We were interested in analyzing conservation and divergence of RBA transcription regulation machinery throughout fungal evolution.

Dis3- and exosome subunit-responsive 3' mRNA instability elements.

Eukaryotic RNA turnover is regulated in part by the exosome, a nuclear and cytoplasmic complex of ribonucleases (RNases) and RNA-binding proteins. The major RNase of the complex is thought to be Dis3, a multi-functional 3'-5' exoribonuclease and endoribonuclease. Although it is known that Dis3 and core exosome subunits are recruited to transcriptionally active genes and to messenger RNA (mRNA) substrates, this recruitment is thought to occur indirectly.

Using SCOPE to identify potential regulatory motifs in coregulated genes.

SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data.

Identifying functional relationships within sets of co-expressed genes by combining upstream regulatory motif analysis and gene expression information.

Background: Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to generate functionally coherent and biologically meaningful subclusters of genes. Specifically, the approach clusters co-expressed genes on the basis of similar content and distributions of predicted statistically significant sequence motifs in their upstream regions.

Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora.

White collar-1 (WC-1) and white collar-2 (WC-2) are essential for light-mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome-wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive.

Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation.

Dendritic cells provide a critical link between innate and adaptive immunity and are essential to prime a naive T-cell response. The transition from immature dendritic cells to mature dendritic cells involves numerous changes in gene expression; however, the role of post-transcriptional changes in this process has been largely ignored. Tristetraprolin is an AU-rich element mRNA-binding protein that has been shown to regulate the stability of a number of cytokines and chemokines of mRNAs.

A novel ensemble learning method for de novo computational identification of DNA binding sites.

Background: Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorithms and the need for user-specified input parameters that describe the motif being sought.

Results: We present a novel ensemble learning method, SCOPE, that is based on the assumption that transcription factor binding sites belong to one of three broad classes of motifs: non-degenerate, degenerate and gapped motifs. SCOPE employs a unified scoring metric to combine the results from three motif finding algorithms each aimed at the discovery of one of these classes of motifs.

SCOPE: a web server for practical de novo motif discovery.

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms.

SPACER: identification of cis-regulatory elements with non-contiguous critical residues.

Motivation: Many transcription factors bind to sites that are long and loosely related to each other. De novo identification of such motifs is computationally challenging. In this article, we propose a novel semi-greedy algorithm over the space of all IUPAC degenerate strings to identify the most over-represented highly degenerate motifs.

Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA.

Biofilm formation is commonly described as a developmental process regulated by environmental cues. In the current study we present a mechanistic model to explain regulation of Pseudomonas fluorescens biofilm formation by the environmentally relevant signal inorganic phosphate (P(i)). We show that activation of the Pho regulon, the major pathway for adaptation to phosphate limitation, results in conditional expression of a c-di-GMP phosphodiesterase referred to as RapA.

BEAM: a beam search algorithm for the identification of cis-regulatory elements in groups of genes.

The identification of potential protein binding sites (cis-regulatory elements) in the upstream regions of genes is key to understanding the mechanisms that regulate gene expression. To this end, we present a simple, efficient algorithm, BEAM (beam-search enumerative algorithm for motif finding), aimed at the discovery of cis-regulatory elements in the DNA sequences upstream of a related group of genes. This algorithm dramatically limits the search space of expanded sequences, converting the problem from one that is exponential in the length of motifs sought to one that is linear.

Bounded search for de novo identification of degenerate cis-regulatory elements.

Background: The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach.

The impact of topical cyclosporine A emulsion 0.05% on the outcomes of patients with keratoconjunctivitis sicca.

Objective: To assess patients' experiences with topical cyclosporine A (tCSA) 0.05% ophthalmic emulsion (Restasis) to treat keratoconjunctivitis sicca (KCS) in a real-world setting.

Methods: A total of 4504 ophthalmologists, optometrists and primary care physicians from throughout the United States participated in the study.

Single-cell analysis reveals cell-specific patterns of expression of a family of putative voltage-gated sodium channel genes in the leech.

To understand the molecular basis of nervous system function in the leech, Hirudo medicinalis, we have isolated four novel cDNAs encoding putative voltage-gated sodium (Na) channel alpha subunits, and have analyzed the expression of these genes in individual neurons of known function. To begin, degenerate oligonucleotide primers were used in combination with pre-existing cDNA libraries and reverse transcriptase-coupled polymerase chain reactions (RT-PCR). The putative leech Na channel cDNAs (LeNas) exhibit a higher degree of sequence homology to Na channel genes in other species than to voltage-gated calcium or potassium channel genes, including those expressed in leech.

Developmentally-related candidate retinoic acid target genes regulated early during neuronal differentiation of human embryonal carcinoma.

Embryonal carcinoma is a model of embryonic development as well as tumor cell differentiation. In response to all-trans retinoic acid (RA), the human embryonal carcinoma (EC) cell line, NT2/D1, differentiates toward a neuronal lineage with associated loss of cell growth and tumorigenicity. Through the use of cDNA-based microarrays we sought to identify the early downstream targets of RA during differentiation commitment of NT2/D1 cells.