On the Number of π-Electrons Involved in Stepwise Cycloaddition Reactions.

The development of higher-order cycloadditions has mainly been restricted by the requisite usage of highly conjugated and reactive π-systems. Recent years have witnessed organocatalysis as a potent mediator for several of the challenges associated herein, rendering higher-order cycloadditions a legitimate option for achieving the selective construction of specific molecular scaffolds. These developments reinvigorate the efforts to try to understand the underlying principles for cycloadditions involving a higher number of π-electrons than the "classical" cycloadditions; how do we properly address the impact which the addition of further π-electrons have on the reactivity of a system? Herein, computational investigations of two model higher-order cycloaddition systems have been performed to try to provide insights on changes in energetic barriers induced by the presence of benzofusions in a position which is unobstructive to the reactivity. With experimental substantiation as support, these studies might open up for a discussion on whether the π-electrons of benzofused systems simply act as spectator electrons, or play a tangible role on the observed reactivity to an extent where a distinct nomenclature is meritable.

Faith-Based Organizations' Support of Veteran Congregants at Risk for Mental Health Conditions and Suicide: A Qualitative Study of Clergy Experiences in Los Angeles County.

Faith-based organizations (FBOs) are often "gatekeepers" to mental health care for congregants at risk of mental illness and suicide, especially U.S. military Veterans, but data to inform better collaboration are needed. We conducted focus groups with clergy in Los Angeles County to understand the mental health support FBOs provide and barriers to collaboration with the mental healthcare system. Clergy detailed strategies used to support the mental health of Veteran congregants. Barriers included stigma, limits in clergy training, and incomplete knowledge about community and VA mental health resources. Results suggest strategies to improve collaboration between FBOs and the mental healthcare system in Los Angeles County.

Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources.

As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture, to curation of novel data types, to incorporation of data from, and collaboration with, other knowledgebases. We are continuing to make steps toward providing the community with an S. cerevisiae pan-genome. Here, we describe software upgrades, a new nomenclature system for genes not found in the reference strain, and additions to gene pages. With these improvements, we aim to remain a leading resource for students, researchers, and the broader scientific community.

Experimental study of the influence of using polyurethane cushion to reduce vibration received by a wheelchair user.

PURPOSE: The aim of this experimental study was to compare the ability of polyurethane cushions of three arbitrary selected thicknesses to minimize vibrations transmitted from the wheelchair to its user. METHODS: Measurements were made during passive motion on five different surfaces often found in public spaces. Two tests were carried out during the measurements. In the first test, the sensor was located directly on the surface of the wheelchair seat. In the second test, a polyurethane cushion was placed on the seat, on which the measuring sensor was then placed. RESULTS: The study showed that regardless of the surface on which the wheelchair user moves, the threshold defined in the ISO standard for frequencies in the range of 4-40 Hz was exceeded. However, thanks to the use of polyurethane cushions, vibration damping was visible for frequencies ranging from 10 to 40 Hz. The impact of the user's weight on the magnitude of the perceived vibrations was also observed. CONCLUSIONS: Studies show that wheelchair users are exposed to whole body vibration that can negatively affect their health. Cushions made of polyurethane seem to be a promising solution to reduce whole body vibration in the frequency range that is burdensome and harmful to human health.

How to Use the Candida Genome Database.

The Candida Genome Database provides access to biological information about genes and proteins of several medically important Candida species. The website is organized into easily navigable pages that enable data retrieval and analysis. This chapter shows how to explore the CGD Home page and Locus Summary pages, which are the main access points to the database. It also provides a description of how to use the GO analysis tools, GO Term Finder, and GO Slim Mapper and how to browse large-scale datasets using the JBrowse genome browser. Finally, it shows how to search and retrieve data for user-defined sets of genes using the Advanced Search and Batch Download tools.

Antioxidant and Antibacterial Activity of Helichrysum italicum (Roth) G. Don. from Central Europe.

Helichrysum italicum (Roth) G. Don. is one of the most important cosmetic and medicinal plants originating from the Mediterranean region of Europe. The aim of this study was to assess the chemical profile as well as antioxidant and antibacterial potential of the species cultivated in the temperate climate of Central Europe. The analyses were carried out using herbs and inflorescences. The content of essential oil ranged from 0.25 g × 100 g-1 in the herb to 0.31 g × 100 g-1 in the inflorescences. Neryl acetate, accompanied by α-pinene in the herb (10.42%), and nerol in inflorescences (15.73%) were the dominants here. Rutoside, as well as rosmarinic, chlorogenic, neochlorogenic, isochlorogenic b and cichoric acids, were detected in both raw materials using HPLC-DAD. Within this group, cichoric acid was the dominant (2647.90 mg × 100 g-1 in the herb, 1381.06 mg × 100 g-1 in the inflorescences). The herb appeared to be more abundant in phenolics in comparison with the inflorescences. When given antioxidant activity (determined using DPPH and ABTS assays), both methanolic extract and essential oil obtained from the herb indicated higher potential than those originating from the inflorescences (74.72, 61.38 and 63.81, 58.59% in the case of DPPH, respectively). In turn, regarding antimicrobial activity, the essential oil from inflorescences was distinguished by stronger bacteriostatic power than the herb essential oil. Gram-positive bacteria were more sensitive to both essential oils in comparison with Gram-negative ones, with S. aureus ATCC 25923 as the most susceptible (MIC 1; MBC 16 mg × mL-1) among tested strains.

New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources.

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.

Using the Fourier Methods for Cycle Counting of Bimodal Stress Histories with Variable in Time Amplitudes of Components.

The application of the Fourier methods to perform cycle identification and description for different cases of bimodal stress histories are presented and discussed in the paper. The direct spectral method and the modified direct spectral method, previously co-proposed by the author, together with the aspects of the use of Fourier methods discussed in this article, offer a unique alternative to the methods known in the literature for identifying and counting various types of bimodal stress variations in time (with constant or variable amplitudes; completely reversed, reversal, or pulsed type). The application of the Fast Fourier Transform (FFT) and the Short-Time Fourier Transform (STFT) is discussed. The method is useful, especially in cases when it is known that due to the form of work of the mechanical system the two existing components of vibrations with various frequencies can be identified, of which the one with higher frequency has a vibration amplitude lower than a component with a lower frequency and, above all, a variable in time.

Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae).

The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.

Genetic History of the Remnant Population of the Rare Orchid Cypripedium calceolus Based on Plastid and Nuclear rDNA.

The lady's slipper orchid (Cypripedium calceolus), which inhabits shady deciduous and mixed forests and meadows, is now threatened with extinction in many European countries, and its natural populations have been dramatically declining in recent years. Knowledge of its evolutionary history, genetic variability, and processes in small populations are therefore crucial for the species' protection. Nowadays, in south-west Poland, it is only distributed in seven small remnant and isolated populations, which we examined. One nuclear (ITS rDNA) and two plastid (accD-psa1, trnL-F) markers were analyzed and compared globally in this study. Based on the nuclear marker, the most common ancestor of C. calceolus and Cypripedium shanxiense existed about 2 million years ago (95% HPD: 5.33-0.44) in Asia. The division of the C. calceolus population into the European and Asian lineages indicated by C/T polymorphism started about 0.5 million years ago (95% HPD: 1.8-0.01). The observed variation of plastid DNA, which arose during the Pleistocene glacial-interglacial cycles, is still diffuse in Poland. Its distribution is explained by the result of fragmentation or habitat loss due to human impact on the environment.

Using the Effect of Compression Stress in Fatigue Analysis of the Roller Bearing for Bimodal Stress Histories.

A new approach based on the direct spectral method for fatigue analysis of elements subjected to bimodal stress histories, including high compression effects, is proposed. A correction factor, taking into account the influence of the mean compressive stresses, is used in the proposed method. Equivalent amplitude is estimated, based on criteria proposed by Smith, Watson, and Tooper, and by Bergmann and Seeger. The method is presented with example of a thrust roller bearing. Two cases in which the rollers were subjected to constant force 206 N (where constant amplitude stresses occurred in the rollers) and cyclic force (where bimodal stresses with variable amplitudes occurred in the rollers) are studied. It is observed that multiaxial fatigue criteria (Crossland, Papadopoulos) do not include the influence of bimodal stresses and should not be used for such loading conditions. The proposed method includes both kinds of stress waveforms in the fatigue analysis and can be applied for the accurate identification of stress components and the determination of fatigue life. The damage rate calculated by the proposed approach for rollers subjected to a cyclic force (equivalent load equal to 151 N) was 0.86, which is in good agreement with the recommendations provided in the literature. The obtained accuracy of the proposed method is above 95%.

Examining faith-based collaboration in U.S. States' suicide prevention guidelines.

Faith-based communities (FBCs) are recognized by most states as key players within systematic suicide prevention efforts. The aim of the present study was to conduct a thematic analysis of documents that detail the suicide prevention efforts of individual states with respect to the role(s) delegated to FBCs. Thematic analysis is recognized as a useful methodology for identifying implications for policy and practice. Documents were procured from all states, with the exception of New Mexico (n = 49). The findings suggest six areas relevant to collaboration with FBCs: suicide prevention training for the FBC, suicide prevention training for individual faith leaders, community engagement, faith leaders as gatekeepers, culturally sensitive suicide prevention, and postvention support. These state guideline documents consistently affirm the importance of engaging FBCs in suicide prevention efforts and cover a range of recommendations, though generally lack specifics with respect to how FBCs can optimally engage.

Notch signaling regulates nuclear androgen receptor AR and membrane androgen receptor ZIP9 in mouse Sertoli cells.

BACKGROUND: Notch signaling pathway is involved in contact-dependent communication between the cells of seminiferous epithelium, and its proper activity is important for undisturbed spermatogenesis. OBJECTIVES: The aim was to assess the effect of Notch pathway inhibition on the expression of nuclear (AR) and membrane (ZIP9) androgen receptors and androgen-regulated genes, claudin-5 and claudin-11, in TM4 mouse Sertoli cell line. MATERIALS AND METHODS: DAPT (γ-secretase inhibitor) treatment and recombination signal binding protein silencing were employed to reduce Notch signaling, whereas immobilized ligands were used to activate Notch pathway in TM4 cells. To reveal specific effect of each androgen receptor, AR or ZIP9 silencing was performed. RESULTS: Notch pathway inhibition increased the expression of AR and ZIP9 mRNA and proteins (p < 0.01; p < 0.05) in TM4 cells, whereas incubation with Notch ligands, rDLL1 or rJAG1, reduced AR (p < 0.01; p < 0.001) and ZIP9 (p < 0.05; p < 0.01) expressions, respectively. Testosterone enhanced the expression of both receptors (p < 0.05; p < 0.01). Androgen-regulated claudin-5 and claudin-11 (p < 0.01; p < 0.001) and cAMP (p < 0.001) were elevated in Notch-inhibited cells, while activation of Notch signaling by DLL1 or JAG1 reduced claudin-11 or claudin-5 level (p < 0.01; p < 0.001), respectively. DISCUSSION: Our findings indicate opposite effect of Notch and androgen signaling on the expression of androgen receptors in TM4 cells. We demonstrated that AR expression is regulated by DLL1-mediated Notch signaling, whereas JAG1 is involved in the regulation of ZIP9. The expression of both claudins and cAMP production is under inhibitory influence of Notch pathway. The effects of Notch signaling on claudin-5 and claudin-11 expression are mediated by ZIP9 and AR, respectively. CONCLUSION: Notch signaling may be considered as an important pathway controlling Sertoli cell physiology, and its alterations may contribute to disturbed response of Sertoli cells to androgens.

Transcriptome visualization and data availability at the Saccharomyces Genome Database.

The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.

Development of an international external quality assurance program for HIV-1 incidence using the Limiting Antigen Avidity assay.

Laboratory assays for identifying recent HIV-1 infections are widely used for estimating incidence in cross-sectional population-level surveys in global HIV-1surveillance. Adequate assay and laboratory performance are required to ensure accurate incidence estimates. The NIAID-supported External Quality Assurance Program Oversight Laboratory (EQAPOL) established a proficiency testing program for the most widely-used incidence assay, the HIV-1 Limiting Antigen Avidity EIA (LAg), with US Centers for Disease Control and Prevention (CDC)-approved kits manufactured by Sedia Biosciences Corporation and Maxim Biomedical. The objective of this program is to monitor the performance of participating laboratories. Four rounds of blinded external proficiency (EP) panels were distributed to up to twenty testing sites (7 North American, 5 African, 4 Asian, 2 South American and 2 European). These panels consisted of ten plasma samples: three blinded well-characterized HIV-1-seropositive samples that were included as replicates and an HIV-negative control. The seropositive samples spanned the dynamic range of the assay and are categorized as either recent or long-term infection. Participating sites performed the assay according to manufacturers' instructions and completed an online survey to gather information on kit manufacturer, lot of kit used, laboratory procedures and the experience of technicians. On average, fifteen sites participated in each round of testing, with an average of four sites testing with only the Maxim assay, seven testing with only the Sedia assay and five sites utilizing both assays. Overall, the Sedia and Maxim assays yielded similar infection status categorization across the laboratories; however, for most of the nine HIV+ samples tested, there were significant differences in the optical density readouts, ODn (N = 8) and OD (N = 7), between LAg kit manufacturers (p < 0.05 based on mixed effects models. The EQAPOL LAg program is important for monitoring laboratory performance as well as detecting variations between manufacturers of HIV-1incidence assays.

Integration of macromolecular complex data into the Saccharomyces Genome Database.

Proteins seldom function individually. Instead, they interact with other proteins or nucleic acids to form stable macromolecular complexes that play key roles in important cellular processes and pathways. One of the goals of Saccharomyces Genome Database (SGD; www.yeastgenome.org) is to provide a complete picture of budding yeast biological processes. To this end, we have collaborated with the Molecular Interactions team that provides the Complex Portal database at EMBL-EBI to manually curate the complete yeast complexome. These data, from a total of 589 complexes, were previously available only in SGD's YeastMine data warehouse (yeastmine.yeastgenome.org) and the Complex Portal (www.ebi.ac.uk/complexportal). We have now incorporated these macromolecular complex data into the SGD core database and designed complex-specific reports to make these data easily available to researchers. These web pages contain referenced summaries focused on the composition and function of individual complexes. In addition, detailed information about how subunits interact within the complex, their stoichiometry and the physical structure are displayed when such information is available. Finally, we generate network diagrams displaying subunits and Gene Ontology annotations that are shared between complexes. Information on macromolecular complexes will continue to be updated in collaboration with the Complex Portal team and curated as more data become available.

Faith-Based Groups as a Bridge to the Community for Military Veterans: Preliminary Findings and Lessons Learned in Online Surveying.

This report examines responses to a brief online survey, comparing how faith-based (n = 27) and non-faith-based (n = 61) organizations engage with Veteran populations as well as the supportive services they provide. Data were analyzed using two-sample z-tests and Chi-squared tests. No significant differences were noted between respondents for self-reported confidence in responding to health care issues/concerns or engagement with Veteran populations. Faith-based respondents were found to provide significantly less mental health, suicide prevention, education/outreach, and other services, while providing significantly more spiritual care. There appears to be ample opportunity for expanding the supportive services provided by faith-based organizations.

A Preliminary Study Examining the Prevalence and Perceived Intensity of Morally Injurious Events in a Veterans Affairs Chaplaincy Spiritual Injury Support Group.

The aim of this descriptive study was to examine the prevalence and perceived intensity of potentially morally injurious events (PMIEs) in a group of VA chaplaincy service users. A secondary aim was to examine the relationship between PMIEs, spiritual injury, and religiosity. A convenience sample of veterans (n = 84), participants in a spiritual injury support group, completed the Moral Injury Events Scale (MIES). Most individuals also completed the Duke University Religion Index (as a measure of religiosity) and Spiritual Injury Scale. Results suggest a high prevalence of PMIEs among participants. These PMIEs were also higher in perceived intensity compared to other military and veteran samples. No significant correlations were identified between MIES scores and either religiosity or spiritual injury. These findings draw attention to the engagement of chaplains in supporting veterans affected by PMIEs. Implications for future research are discussed.