High abundances of crustose coralline algae inside cryptic coral habitats linked to coral reef functioning.

Cryptic habitats on coral reefs consist of crevices, tunnels, and holes that are estimated to comprise 30%-75% of the total reef surface area. These large habitats are vastly understudied because they are often difficult to access. Crustose coralline algae (CCA) are thought to perform important ecological functions, including calcium accretion, both inside cryptic habitats and on the exposed (top) reef.

Diel gene expression improves software prediction of cyanobacterial operons.

Cyanobacteria are important participants in global biogeochemical process, but their metabolic processes and genomic functions are incompletely understood. In particular, operon structure, which can provide valuable metabolic and genomic insight, is difficult to determine experimentally, and algorithmic operon predictions probably underestimate actual operon extent. A software method is presented for enhancing current operon predictions by incorporating information from whole-genome time-series expression studies, using a Machine Learning classifier.

A novel approach to teaching Hidden Markov Models to a diverse undergraduate population.

Hidden Markov Models (HMMs) are an essential tool for Bioinformatic analysis, with extensive success at finding patterns (e.g. CRISPR arrays or genes of interest) in DNA or protein sequences.

A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator.

The Cytochrome C Oxidase subunit I gene ("COI") is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies.

Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria.

Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed 'diazotrophs') are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier.

ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank.

Motivation: Studies of the biochemical functions and activities of uncultivated microorganisms in the environment require analysis of DNA sequences for phylogenetic characterization and for the development of sequence-based assays for the detection of microorganisms. The numbers of sequences for genes that are indicators of environmentally important functions such as nitrogen (N2) fixation have been rapidly growing over the past few decades. Obtaining these sequences from the National Center for Biotechnology Information's GenBank database is problematic because of annotation errors, nomenclature variation and paralogues; moreover, GenBank's structure and tools are not conducive to searching solely by function.

Whole genome comparison of six Crocosphaera watsonii strains with differing phenotypes.

Crocosphaera watsonii, a unicellular nitrogen-fixing cyanobacterium found in oligotrophic oceans, is important in marine carbon and nitrogen cycles. Isolates of C. watsonii can be separated into at least two phenotypes with environmentally important differences, indicating possibly distinct ecological roles and niches.

Dose ratio is important in maximizing naloxone enhancement of nalbuphine analgesia in humans.

The analgesic effect of kappa partial agonist opioids (i.e. nalbuphine, pentazocine and butorphanol) is significantly greater in women.

Sexual dimorphism in very low dose nalbuphine postoperative analgesia.

In recent studies we demonstrated that the analgesic effect of the kappa-like opioids is significantly greater in women, that low dose nalbuphine (5 mg) produces profound anti-analgesia (i.e. enhances pain) in men, and that addition of a low dose of the non-selective opioid receptor antagonist naloxone (0.

Interactions between fluoxetine and opiate analgesia for postoperative dental pain.

In a double-blind placebo-controlled study we investigated the analgesic efficacy of combinations of the serotonergic tricyclic antidepressant fluoxetine with either the mu-opiate morphine or the kappa-opiate pentazocine. Administration of oral fluoxetine (10 mg p.o.

Temporal factors in the enhancement of morphine analgesia by desipramine.

Administration of desipramine, the tricyclic noradrenergic agent, for 7 days pre-operatively, had been found to potentiate postoperative morphine analgesia. In this study we investigated the necessary timing of administration of desipramine in its action to potentiate morphine analgesia. We report that the administration of desipramine for only 3 days, starting 7 days before surgery, also potentiated postoperative morphine analgesia and that the analgesia observed was not different from that in patients receiving a full 7 days of desipramine pre-operatively.

Enhancement of pentazocine analgesia by clonidine.

Opiate-adrenergic interactions were investigated by studying the effect of the selective alpha 2-adrenergic agonist, clonidine, on the analgesia produced by intravenous placebo and by the predominantly kappa-opiate agonist, pentazocine, in patients with dental postoperative pain. Clonidine did not affect the pain level when administered with intravenous placebo. When administered with pentazocine, clonidine caused a statistically significant increase in pentazocine analgesia.

Lack of effect of ephedrine on opiate analgesia.

Opiate-adrenomimetic interaction was investigated by studying the effect of the adrenomimetic agent, ephedrine, on the analgesia produced by intravenous placebo and that produced by the predominantly kappa opiate agonist, pentazocine, in patients with dental postoperative pain. Ephedrine did not significantly affect the analgesia of intravenous placebo or of pentazocine. These results contrast with earlier studies demonstrating enhancement of opiate analgesia by other adrenomimetics.

A possible indicator of functional pain: poor pain scale correlation.

We studied correlations of pain measures in patients with either inflammatory bowel disease (IBD), a disease with a clear organic cause, or irritable bowel syndrome (IBS), a functional pain syndrome in which there is little demonstrable pathology. Correlations were determined between measures on the visual analogue scale (VAS) and on the McGill Pain Questionnaire (MPQ). The VAS score and present pain intensity scale (PPI) of the MPQ correlated well in the organic IBD but correlated poorly in the functional IBS.

Altered autonomic function in patients with arthritis or with chronic myofascial pain.

Dynamic autonomic function tests (pupillary light reflex, Valsalva maneuver, and mental arithmetic) were used to evaluate autonomic function (pupil size, heart rate, and skin conductance) in patients with inflammatory arthritis or with chronic myofascial pain. Physiological responses in both groups of patients suggest concurrent increases in tonic pupillary autonomic activity (sympathetic and parasympathetic), with a relative sympathetic dominance, and a decrease in tonic parasympathetic cardiovascular activity. Furthermore, in the arthritis group, the data suggest decreased cardiovascular parasympathetic reaction and enhanced sudomotor reaction.

Differing correlations between pain measures in syndromes with or without explicable organic pathology.

We investigated the use of pain measures in chronic pain syndromes with and without explicable organic cause by correlating scores obtained from the Visual Analog Scale and from subscales of the McGill Pain Questionnaire in patients with either inflammatory arthritis or primary fibrositis. We confirmed the finding that patients with fibrositis, despite having significantly less demonstrable pathology, report more pain on a significant number of measures. In patients with arthritis, we observed large positive correlations between scores on different pain measures, supporting the hypothesis that these scores validly measure pain secondary to tissue injury.

Cardiovascular autonomic response during preoperative stress and postoperative pain.

Heart rate response to physiologic maneuvers was used to evaluate autonomic nervous system (ANS) function in normal control subjects and during the stress and pain experienced by patients before and after surgery. In preoperative patients (stressed without pain) and postoperative patients (stressed with pain), maneuvers which routinely increase activity in the parasympathetic or sympathetic divisions of the ANS produced only 50% of the response seen in control subjects. The heart rate response was not further reduced in patients with pain compared to patients with stress alone.

Altered electrodermal responsivity associated with clinical pain.

We used certain physiologic maneuvers to perturb the autonomic nervous system (ANS) in an attempt to detect a link between the ANS and pain. In the unperturbed state, we found no difference in the electrodermal response among normal controls, preoperative patients (increased stress without pain) and postoperative patients (increased stress and pain). The electrodermal response elicited by autonomic maneuvers was significantly attenuated in postoperative patients but not in preoperative patients or in normal control subjects.