Building an Online Data Management Plan Tool

Following the 2011 announcement by the National Science Foundation (NSF) that it would begin requiring Data Management Plans with every funding application, the University of Houston Libraries explored ways to support our campus researchers in meeting this requirement. A small team of librarians built an online tool using a Drupal module. The tool includes informational content, an interactive questionnaire, and an extensive FAQ to meet diverse researcher needs. This easily accessible and locally maintained tool allows us to provide a high level of personalized service to our researchers

Interactive Regulation of Dissolved Copper Toxicity by an Estuarine Microbial Community

Cultured marine microorganisms under copper stress produce extracellular compounds having a high affinity for copper (copper-complexing ligands). These ligands are similar in binding strength to those found in natural waters, but few studies have examined the relationship between copper, copper-complexing ligand concentrations, and natural microbial populations. A series of in situ experiments in the Elizabeth River, Virginia, revealed that an intact estuarine microbial community responded to copper stress by production of extracellular, high-affinity copper-complexing ligands. The rate of ligand production was dependent on copper concentration and resulted in a reduction of the concentration of free cupric ions, Cu2+, by more than three orders of magnitude during a 2-week period in one experiment. We believe that this interactive response to copper stress represents a feedback system through which microbial communities can potentially buffer dissolved Cu2+ ion concentrations, thereby regulating copper bioavailability and toxicity

Antimicrobial Treatmdent of "Complicated" Intra-Abdominal Infections and The New IDSA Guidelines - A Commentary and an Alternative European Approach According to Clinical Definitions

Recently, an update of the IDSA guidelines for the treatment of complicated intraabdominal infections has been published. No guideline can cater for all variations in ecology, antimicrobial resistance patterns, patient characteristics and presentation, health care and reimbursement systems in many different countries. In the short time the IDSA guidelines have been available, a number of practical clinical issues have been raised by physicians regarding interpretation of the guidelines. The main debatable issues of the new IDSA guidelines are described as follows

Verrucous carcinoma of the vulva: patterns of care and treatment outcomes.

Background: Verrucous vulvar carcinoma (VC) is an uncommon and distinct histologic subtype of squamous cell carcinoma (SCC). The available literature on VC is currently limited to case reports and small single institution studies. Aims: The goals of this study were to analyze data from the National Cancer Database (NCDB) to quantitate the incidence of VC and to investigate the effects of patient demographics, tumor characteristics, and treatment regimens on overall survival (OS) in women with verrucous vulvar carcinoma. Methods and results: Patients diagnosed with vulvar SCC or VC between the years of 2004 and 2016 were identified in the NCDB. OS was assessed with Kaplan–Meier curves and the log-rank test. Construction of a Cox model compared survival after controlling for confounding variables. The reported incidence of SCC of the vulva has significantly increased since 2004 (p \u3c .0001). In contrast, the incidence of VC has remained stable (p = .344) since 2004. Compared to SCC, VC was significantly more likely to be diagnosed in older women (p \u3c .0001) and treated with surgery alone (p \u3c .0001). However, on propensity score weighted analysis there was a trend toward improved 5-year OS in women with VC compared to those with SCC (63.4% vs. 57.7%, p = .0794). Multivariable Cox survival analysis showed an improvement in OS in VC patients treated with both primary site and regional lymph node surgery compared to primary site surgery alone (adjusted hazard ratio [aHR] 0.67, 95% confidence interval [CI] 0.46–0.97, p = .0357). Conclusion: Verrucous carcinoma is more likely to present in older women. Regional lymph node surgery in addition to primary site surgery significantly improves OS in VC patients

Consumption and digestion of forages by male rusa (Cervus timorensis russa) deer – the effects of castration and season

In a split-unit design, 12 Javan rusa (Cervus tinzorensis russa) stags (6 castrated and 6 entire) were used to investigate seasonal (winter, spring and summer) effects on intake, digestibility of food constituents, volatile fatty acid profile, and nitrogen retention, which given lucerne (Medicago sativa) or rhodes grass (Chloris guyana) hays. Entire stags ate 9% more dry matter (DM) than castrates (

Structure of the ovaries of the Nimba otter shrew, Micropotamogale lamottei, and the Madagascar hedgehog tenrec, Echinops telfairi

The otter shrews are members of the subfamily Potamogalinae within the family Tenrecidae. No description of the ovaries of any member of this subfamily has been published previously. The lesser hedgehog tenrec, Echinops telfairi, is a member of the subfamily Tenrecinae of the same family and, although its ovaries have not been described, other members of this subfamily have been shown to have ovaries with non-antral follicles. Examination of these two species illustrated that non-antral follicles were characteristic of the ovaries of both species, as was clefting and lobulation of the ovaries. Juvenile otter shrews range from those with only small follicles in the cortex to those with 300- to 400-mu m follicles similar to those seen in non-pregnant and pregnant adults. As in other species, most of the growth of the oocyte occurred when follicles had one to two layers of granulosa cells. When larger follicles became atretic in the Nimba otter shrew, hypertrophy of the theca interna produced nodules of glandular interstitial tissue. In the tenrec, the hypertrophying theca interna cells in most large follicles appeared to undergo degeneration. Both species had some follicular fluid in the intercellular spaces between the more peripheral granulosa cells. It is suggested that this fluid could aid in separation of the cumulus from the remaining granulosa at ovulation. The protruding follicles in lobules and absence of a tunica albuginea might also facilitate ovulation of non-antral follicles. Ovaries with a thin-absent tunica albuginea and follicles with small-absent antra are widespread within both the Eulipotyphla and in the Afrosoricida, suggesting that such features may represent a primitive condition in ovarian development. Lobulated and deeply crypted ovaries are found in both groups but are not as common in the Eulipotyphla making inclusion of this feature as primitive more speculative. Copyright (C) 2005 S. Karger AG, Basel

Second-order Democratic Aggregation

Aggregated second-order features extracted from deep convolutional networks have been shown to be effective for texture generation, fine-grained recognition, material classification, and scene understanding. In this paper, we study a class of orderless aggregation functions designed to minimize interference or equalize contributions in the context of second-order features and we show that they can be computed just as efficiently as their first-order counterparts and they have favorable properties over aggregation by summation. Another line of work has shown that matrix power normalization after aggregation can significantly improve the generalization of second-order representations. We show that matrix power normalization implicitly equalizes contributions during aggregation thus establishing a connection between matrix normalization techniques and prior work on minimizing interference. Based on the analysis we present {\gamma}-democratic aggregators that interpolate between sum ({\gamma}=1) and democratic pooling ({\gamma}=0) outperforming both on several classification tasks. Moreover, unlike power normalization, the {\gamma}-democratic aggregations can be computed in a low dimensional space by sketching that allows the use of very high-dimensional second-order features. This results in a state-of-the-art performance on several datasets

How much of protein sequence space has been explored by life on Earth?

We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency

Crater lake cichlids individually specialize along the benthic-limnetic axis

A common pattern of adaptive diversification in freshwater fishes is the repeated evolution of elongated open water (limnetic) species and high-bodied shore (benthic) species from generalist ancestors. Studies on phenotype-diet correlations have suggested that population-wide individual specialization occurs at an early evolutionary and ecological stage of divergence and niche partitioning. This variable restricted niche use across individuals can provide the raw material for earliest stages of sympatric divergence. We investigated variation in morphology and diet as well as their correlations along the benthic-limnetic axis in an extremely young Midas cichlid species, Amphilophus tolteca, endemic to the Nicaraguan crater lake Asososca Managua. We found that A. tolteca varied continuously in ecologically relevant traits such as body shape and lower pharyngeal jaw morphology. The correlation of these phenotypes with niche suggested that individuals are specialized along the benthic-limnetic axis. No genetic differentiation within the crater lake was detected based on genotypes from 13 microsatellite loci. Overall, we found that individual specialization in this young crater lake species encompasses the limnetic- as well as the benthic macro-habitat. Yet there is no evidence for any diversification within the species, making this a candidate system for studying what might be the early stages preceding sympatric divergence