bluuebunny/crossref_metadata_2025 huggingface dataset:
Coleoptera in the Canopy of the Cloud Forest From Tlanchinol in the State of Hidalgo, Mexico
Authors: Márquez Juan , Asiain Julieta , Martínez-Falcón Ana P , Escoto-Moreno Jaime A
Published: May 2019

We describe the biodiversity, seasonal variation, and the possible edge effect of Coleoptera found in the canopy of the cloud forest in Tlanchinol in the state of Hidalgo. The coleopterans were collected by means of three fogging events during the dry season and another three during the rainy season in three sites of the forest: the edge, an intermediate, and an internal site. In total, 3,487 coleopterans were collected, belonging to 325 morphospecies from 52 families. The family with the largest number of morphospecies and abundance was Staphylinidae, followed by Curculionidae and Chrysomelidae. Species richness and abundance were higher in the dry season than in the rainy season. The biodiversity analyses, however, suggest that the rainy season showed the highest biodiversity levels, mainly because of the pronounced dominance of some species in the dry season. Species composition was different between the dry and rainy seasons. The internal site showed the lowest biodiversity compared with the intermediate and edge sites. The main edge effect detected was that species composition in the edge site differed from the intermediate and internal sites. Species composition did not differ significantly between the two latter sites. These results suggest that the study zone had a considerable level of biodiversity of Coleoptera and that it was very likely in a well-preserved condition, which supports the findings of another study previously performed in the same site using flight intercept traps.
The novel coronary artery disease risk gene JCAD/KIAA1462 promotes endothelial dysfunction and atherosclerosis
Authors: Xu Suowen , Xu Yanni , Liu Peng , Zhang Shuya , Liu Huan , Slavin Spencer , Kumar Sandeep , Koroleva Marina , Luo Jinque , Wu Xiaoqian , Rahman Arshad , Pelisek Jaroslav , Jo Hanjoong , Si Shuyi , Miller Clint L , Jin Zheng Gen
Published: May 2019

Aims

Recent genome-wide association studies (GWAS) have identified that the JCAD locus is associated with risk of coronary artery disease (CAD) and myocardial infarction (MI). However, the mechanisms whereby candidate gene JCAD confers disease risk remain unclear. We addressed whether and how JCAD affects the development of atherosclerosis, the common cause of CAD.

Methods and results

By mining data in the Genotype-Tissue Expression (GTEx) database, we found that CAD-associated risk variants at the JCAD locus are linked to increased JCAD gene expression in human arteries, implicating JCAD as a candidate causal CAD gene. We therefore generated global and endothelial cell (EC) specific-JCAD knockout mice, and observed that JCAD deficiency attenuated high fat diet-induced atherosclerosis in ApoE-deficient mice. JCAD-deficiency in mice also improved endothelium-dependent relaxation. Genome-wide transcriptional profiling of JCAD-depleted human coronary artery ECs showed that JCAD depletion inhibited the activation of YAP/TAZ pathway, and the expression of downstream pro-atherogenic genes, including CTGF and Cyr61. As a result, JCAD-deficient ECs attracted fewer monocytes in response to lipopolysaccharide (LPS) stimulation. Moreover, JCAD expression in ECs was decreased under unidirectional laminar flow in vitro and in vivo. Proteomics studies suggest that JCAD regulates YAP/TAZ activation by interacting with actin-binding protein TRIOBP, thereby stabilizing stress fiber formation. Finally, we observed that endothelial JCAD expression was increased in mouse and human atherosclerotic plaques.

Conclusion

The present study demonstrates that the GWAS-identified CAD risk gene JCAD promotes endothelial dysfunction and atherosclerosis, thus highlighting the possibility of new therapeutic strategies for CAD by targeting JCAD.
Satisfaction with mental health treatment among patients with a non-Western migrant background: a survey in a Danish specialized outpatient mental health clinic
Authors: Lindberg Laura Glahder , Mundy Sara Skriver , Kristiansen Maria , Johansen Katrine Schepelern , Carlsson Jessica
Published: May 2019

Background

Global migration increases ethnic and cultural diversity and demands mental health services to adapt to provide all patients with equal access to good quality care. Patient satisfaction surveys can inform this service delivery, thus we explored patient satisfaction among non-Western migrants receiving treatment in a Danish specialized outpatient mental health clinic [Competence Centre for Transcultural Psychiatry (CTP)].

Methods

We used multivariate logistic regression models to estimate associations between ‘Overall treatment satisfaction’ and treatment-related items plus potential confounders from a cross-sectional patient satisfaction survey (n = 686). The satisfaction questionnaire was a self-report measurement tool developed locally at CTP. Participants were non-Western migrants above 18 years with Post-Traumatic Stress Disorder (PTSD) or depression diagnoses according to ICD-10.

Results

Most participants (n = 497; 82.6%) reported overall satisfaction with their mental health treatment, but less than half (n = 311; 48.8%) reported an improvement in health and situation after end of treatment. Participants who experienced a subjective improvement in their health and situation had significantly higher odds of being satisfied with their mental health treatment [odds ratio (OR) = 8.5, 95% confidence interval (CI): 4.0–18.1]. Perceptions of influence on the treatment course (OR = 4.7, 95% CI: 2.4–9.2), and of understanding and respect for one’s cultural background (OR = 3.4, 95% CI: 1.5–7.6) were significantly associated with treatment satisfaction. Age and sex were insignificant in the final regression model.

Conclusions

Implications for practice based on our findings are to enhance person-centred care and shared decision-making with all patients regardless of cultural background and to prioritize pre- and postgraduate training in cultural competences and cultural humility for healthcare providers.
A Pas De Deux for a Cathedral and a Hunchback: Roland Petit’s Ballet Notre-Dame De Paris
Authors: Bührle Iris Julia
Published: May 2019

In 1965, the French choreographer Roland Petit set himself the task of making a ballet out of Victor Hugo’s voluminous novel Notre-Dame de Paris. The result departed radically from earlier attempts to transpose the work into movement by choreographers who included Jules Perrot and Marius Petipa. Although the love plot (which revolves around a dancer), the wide range of emotions depicted, the stark contrasts, and alternation between crowd scenes and more intimate scenes favour its transposition into a ballet, the novel also presents numerous difficulties, such as the importance of politics, philosophy and architecture. Quasimodo, Frollo and the cathedral seem rather unsuitable protagonists for a ballet. This paper argues that Petit’s adaptation of Notre-Dame de Paris engaged with the literary source on a much deeper level than its predecessors. Petit’s innovative ballet does not merely illustrate the novel: it reveals underlying elements in the source and sheds new light on it.
Black and Chestnut Oak Seedling Response to Glaciated Soil: Implications for Northward Expansion in Response to Climate Warming
Authors: Pile Lauren S , Rebbeck Joanne , Brose Patrick H , Long Robert P
Published: May 2019

Species ranges are expected to move northward with climate warming. However, species will likely encounter soil conditions that differ from their historic ranges. Black (Quercus velutina) and chestnut (Q. montana) oaks are expected to do well in climates that are hotter and drier, but it is unknown as to how they respond to soils of different geological histories. At a glaciated and nonglaciated site in northwestern Pennsylvania, we compared the growth, biomass allocation, and mycorrhizal association for black and chestnut oak seedlings at two different levels of light. On nutrient-poor, nonglaciated soils at high light levels, both species had greater growth and biomass accumulation than on nutrient-rich, glaciated soils. However, at low light levels, these responses were greatest on glaciated soils, especially for chestnut oak. Although mycorrhizal association was beneficial on nonglaciated soil at high light levels, low light levels were associated with reduced growth when compared to glaciated soils. In low light and nutrient-poor soils, mycorrhizal association may result in a carbon sink with lower net photosynthesis, as carbon for plant growth is, instead, allocated to the mycorrhizae symbiont. Variable species response to soil types indicates reduced performance for black and chestnut oak seedlings on high-quality glaciated soils especially in high light environments.
Cellular stressors may alter islet hormone cell proportions by moderation of alternative splicing patterns
Authors: Jeffery Nicola , Richardson Sarah , Chambers David , Morgan Noel G , Harries Lorna W
Published: May 2019

Changes to islet cell identity in response to type 2 diabetes (T2D) have been reported in rodent models, but are less well characterized in humans. We assessed the effects of aspects of the diabetic microenvironment on hormone staining, total gene expression, splicing regulation and the alternative splicing patterns of key genes in EndoC-βH1 human beta cells. Genes encoding islet hormones [somatostatin (SST), insulin (INS), Glucagon (GCG)], differentiation markers [Forkhead box O1 (FOXO1), Paired box 6, SRY box 9, NK6 Homeobox 1, NK6 Homeobox 2] and cell stress markers (DNA damage inducible transcript 3, FOXO1) were dysregulated in stressed EndoC-βH1 cells, as were some serine arginine rich splicing factor splicing activator and heterogeneous ribonucleoprotein particle inhibitor genes. Whole transcriptome analysis of primary T2D islets and matched controls demonstrated dysregulated splicing for ~25% of splicing events, of which genes themselves involved in messenger ribonucleic acid processing and regulation of gene expression comprised the largest group. Approximately 5% of EndoC-βH1 cells exposed to these factors gained SST positivity in vitro. An increased area of SST staining was also observed ex vivo in pancreas sections recovered at autopsy from donors with type 1 diabetes (T1D) or T2D (9.3% for T1D and 3% for T2D, respectively compared with 1% in controls). Removal of the stressful stimulus or treatment with the AKT Serine/Threonine kinase inhibitor SH-6 restored splicing factor expression and reversed both hormone staining effects and patterns of gene expression. This suggests that reversible changes in hormone expression may occur during exposure to diabetomimetic cellular stressors, which may be mediated by changes in splicing regulation.
A cross continental scale comparison of Australian offshore recreational fisheries research and its applications to Marine Park and fisheries management
Authors: Lynch T P , Smallwood C B , Ochwada-Doyle F A , Lyle J , Williams J , Ryan K L , Devine C , Gibson B , Jordan A
Published: May 2019

Recreational fishing is popular in Australia and is managed by individual states in consultation with the Commonwealth for those fisheries that they regulate and also for Australian Marine Parks (AMPs). Fishers regularly access both state and offshore Commonwealth waters but this offshore component of the recreational fishery is poorly understood. Our study tested the functionality of existing state-based surveys in Western Australia (WA) and New South Wales (NSW) to better inform Commonwealth fisheries and AMP managers about recreational fishing in their jurisdictions. Catch estimates for nine species of interest to the Commonwealth were developed and two case study AMPs [Ningaloo (WA) and The Hunter (NSW)] were also chosen to test the ability of the state survey data to be disaggregated to the park scale. As each state’s fishery survey designs were contextual to their own management needs, the application of the data to Commonwealth jurisdictions were limited by their statistical power, however aspects of each states surveys still provided useful information. Continued evolution of state-wide survey methods, including collection of precise spatial data, and regional over-sampling would be beneficial, particularly where there are multiple stakeholder and jurisdictional interests. National coordination, to temporally align state surveys, would also add value to the existing approaches.
A Randomized, Double-Blinded, Placebo-Controlled, Phase 1 Study of a Replication-Defective Herpes Simplex Virus (HSV) Type 2 Vaccine, HSV529, in Adults With or Without HSV Infection
Authors: Dropulic Lesia K , Oestreich Makinna C , Pietz Harlan L , Laing Kerry J , Hunsberger Sally , Lumbard Keith , Garabedian Doreen , Turk Siu Ping , Chen Aiying , Hornung Ronald L , Seshadri Chetan , Smith Malisa T , Hosken Nancy A , Phogat Sanjay , Chang Lee-Jah , Koelle David M , Wang Kening , Cohen Jeffrey I
Published: May 2019

Background

Herpes simplex virus 2 (HSV2) causes genital herpes in >400 million persons worldwide.

Methods

We conducted a randomized, double-blinded, placebo-controlled trial of a replication-defective HSV2 vaccine, HSV529. Twenty adults were enrolled in each of 3 serogroups of individuals: those negative for both HSV1 and HSV2 (HSV1−/HSV2−), those positive or negative for HSV1 and positive for HSV2 (HSV1±/HSV2+), and those positive for HSV1 and negative for HSV2 (HSV1+/HSV2−). Sixty participants received vaccine or placebo at 0, 1, and 6 months. The primary end point was the frequency of solicited local and systemic reactions to vaccination.

Results

Eighty-nine percent of vaccinees experienced mild-to-moderate solicited injection site reactions, compared with 47% of placebo recipients (95% confidence interval [CI], 12.9%–67.6%; P = .006). Sixty-four percent of vaccinees experienced systemic reactions, compared with 53% of placebo recipients (95% CI, −17.9% to 40.2%; P = .44). Seventy-eight percent of HSV1−/HSV2− vaccine recipients had a ≥4-fold increase in neutralizing antibody titer after 3 doses of vaccine, whereas none of the participants in the other serogroups had such responses. HSV2-specific CD4+ T-cell responses were detected in 36%, 46%, and 27% of HSV1−/HSV2−, HSV1±/HSV2+, and HSV1+/HSV2− participants, respectively, 1 month after the third dose of vaccine, and CD8+ T-cell responses were detected in 14%, 8%, and 18% of participants, respectively.

Conclusions

HSV529 vaccine was safe and elicited neutralizing antibody and modest CD4+ T-cell responses in HSV-seronegative vaccinees.

Clinical Trials Registration

NCT01915212.
A new syntopic species of Stygobromus Cope, 1872 (Amphipoda: Crangonyctidae) from groundwaters in Georgia and Florida, USA, with notes on S. floridanus Holsinger & Sawicki, 2016
Authors: Cannizzaro Andrew G , Balding Donna , Stine Michael , Sawicki Thomas R
Published: May 2019

Stygobromus doughertyensis n. sp. is described from groundwater habitats in Jackson County, Florida and Dougherty County, Georgia, USA using both morphological and molecular methods. This species occurs syntopically with the morphologically similar S. floridanus, which is newly recorded in Jackson County. The occurrence of S. floridanus in Jackson County marks a range extension for this species, which was described from two caves in Washington County, Florida. The description of S. doughertyensis n. sp. brings the number of described species in the genus Stygobromus to 142 and marks the second species of Stygobromus to be described from the Floridan aquifer.
Genetic diversity among populations of the Western Atlantic mangrove crab Ucides cordatus (Linnaeus, 1763) (Decapoda: Brachyura: Ocypodidae): evidence for panmixia and useful data for future management and conservation
Authors: Buranelli Raquel C , Felder Darryl L , Mantelatto Fernando L
Published: May 2019

The mangrove crab Ucides cordatus (Linnaeus, 1763) is a keystone species in mangroves, and recent changes in population sizes have been attributed primarily to overharvest, selective capture, and loss of habitat due to destruction of mangroves. We analyzed genetic variability and phylogeographic pattern among populations of U. cordatus along the western Atlantic coast in order to document levels of genetic differentiation, aiming to provide data to be used in future management and conservation strategies. MtDNA cytochrome oxidase I (COI) was analyzed and compared among populations. We computed a haplotype network, haplotype and nucleotide diversities, index of fixation, Mantel test, analysis of molecular variance (AMOVA), neutrality tests, and pairwise mismatch distributions under the sudden expansion model of demographic expansion; Maximum likelihood phylogenetic reconstruction was also undertaken for the haplotypes found. We found no geographic structure and no significant indication for restricted gene flow between populations from sites along a distance of 12,000 km, indicating that sampled individuals currently represent a single panmictic population. Demographic results revealed demographic expansion along the evolutionary history of U. cordatus, probably related to climatic biogeographic events. Although there is no current evidence of any substantial genetic break or of demographic reduction between the western Atlantic populations that we investigated, the genetic signal of regional population depletion warrants future monitoring in the course of resource management.
Evaluation of different kinds of disturbance on the efficiency of sampling methods employed for an endangered freshwater crayfish, Austropotamobius pallipes Lereboullet, 1858 (Decapoda: Astacidea: Astacidae), in the northern Iberian Peninsula
Authors: Olarte Nuria , García-Arberas Loreto , Antón Alvaro
Published: May 2019

We discuss the suitability of several sampling methods in terms of effort, efficiency, accuracy, obtained data, and the degree of disturbance in the endangered crayfish Austropotamobius pallipes (Lereboullet, 1858) and its habitat. Not all sampling strategies can be undertaken in headwater streams, and it is difficult to reach and work in remote areas. We compared three different sampling methods for five years at five sites in two small headwater streams in the Basque Country (Euskadi), northern Iberian Peninsula. We used night viewing from the river bank, hand searching during one removal pass, and the removal method by hand searching (abundance estimates) to determine their accuracy, efficiency, effort, and the disruption of crayfish and their habitat. Comparison of data between both relative abundance estimates, evaluated as captures per unit effort, were not significantly different between the estimates but they both differed significantly from the abundance estimates. Night hand searching or night viewing from the river bank required a longer surveying time and even some risk due to night work. Daylight manual searching could be consequently suitable if management of the species is supported by presence/absence data. The removal method is otherwise recommended when population estimates are required, even if it implies greater disturbance and effort from surveyors.
Annual and lunar breeding rhythmicity in females of the terrestrial hermit crab Coenobita rugosus H. Milne Edwards, 1837 (Decapoda: Anomura: Coenobitidae) in Okinawa, Japan
Authors: Osaka Naoya , Takemura Akihiro
Published: May 2019

We investigated the reproductive characteristics of a terrestrial hermit crab (Coenobita rugosus H. Milne Edwards, 1837) inhabiting Okinawa-Jima. Monthly changes in the gonadosomatic index and ovarian histology revealed that this species had fully developed oocytes from May to October. Data showing that females with (ovigerous females) and without (non-ovigerous females) embryos on their pleopods appeared simultaneously on the shore from June to September 2014 demonstrates that this species undergoes larval release several times for four months. When non-ovigerous females were reared under a combination of two day lengths and two temperatures, oocyte development was induced in the high-temperature group, suggesting that temperature is a proximate factor in ovarian development. The weekly collection of females during the spawning season revealed that the proportion of fully developed oocytes in an ovary increased toward the time of the new moon and decreased around the first-quarter moon, suggesting that this species is a lunar-spawner with a new-moon preference. Some females releasing larvae around the new or full moon were recaptured at approximately 30 d intervals, suggesting at least two major groups with lunar-synchronized larval release. The ovarian development and larval release of C. rugosus are likely entrained to external factors, which change periodically in their habitats.
A first fecundity study of the female snow crab Chionoecetes opilio Fabricius, 1788 (Decapoda: Brachyura: Oregoniidae) of the newly established population in the Barents Sea
Authors: Danielsen Hanna E H , Hjelset Ann M , Bluhm Bodil A , Hvingel Carsten , Agnalt Ann-Lisbeth
Published: May 2019

The snow crab Chionoecetes opilioFabricius, 1788 is a newly established species in the Barents Sea. Since the first individuals were recorded in 1996, the population has increased and a fishery was initiated in 2012. Mature female snow crab caught in the central Barents Sea were investigated with regards to fecundity. Ovigerous females (N = 185) ranged from 48 to 100 mm carapace width (CW). Fecundity was 15,000–184,000 eggs per female with 100% clutch fullness, and was positively related to body size (fecundity = 0.233 * CW2.944) consistent with relationships described for other snow crab populations. Eight females had less than 100% clutch fullness, two of which had only 10% clutch fullness along with an old shell, indicating senescence. Dry egg weight was on average 0.065 mg and was hardly affected by CW. Females across all sizes invest similarly in individual eggs, and potential size-dependent differences in fitness are more related to the number of eggs produced than to the investment into individual eggs. We conclude that the fecundity-at-size of females is overall comparable to that of other populations, although the presence of large females results in high maximum individual fecundity estimates.
A Sequential Mixed-Methods Study of Pre-Professionals’ Understanding of the Undergraduate Music Therapy Internship
Authors: Clements-Cortes Amy
Published: May 2019

Despite the importance of the clinical music therapy internship, little research has been conducted to understand the perspectives, perceived musical, clinical, and personal skills, concerns, challenges, and anxieties of pre-professionals prior to and upon completion of the internship. This sequential mixed-methods study aimed to assess the perspectives and experiences of undergraduate students in the United States at two stages in the internship in music therapy practice. In total, 177 pre-professionals from the United States participated in this two-part study: (1) an online survey and (2) individual interviews with 25% (n = 44) of the participants. Survey results indicate statistically significant increases in clinical, musical, and personal skill development from pre- to post-internship. Six broad categories emerged from the interviews: confidence, anxiety, role clarity, professional suitability, loneliness, and boundaries/ethics. The results are encouraging, showing that the internship is a valued clinical experience that fosters improvement in the clinical, musical, and personal skills needed to work as a music therapist. This paper concludes with recommendations and suggestions for educators and supervisors on preparing and supporting pre-professionals in their skill development prior to and during internship.
Reduced inflammatory state promotes reinnervation of endometriotic-like lesions in TNFRp55 deficient mice
Authors: Ghersa F , Delsouc M B , Goyeneche A A , Vallcaneras S S , Meresman G , Telleria C M , Casais M
Published: May 2019

Endometriosis is a chronic gynecological disease, characterized by growth of endometrial tissue in ectopic sites due to alteration of peritoneal homeostasis and deregulation of apoptosis. Here we have examined whether TNFRp55 deficiency modulates the pro-inflammatory state and the reinnervation of endometriotic-like lesions in mice. Two-month-old female C57BL/6 mice, eight wild type (WT) and eight TNFRp55−/− (KO) were used in the study. Endometriotic-like lesions were induced experimentally. The right uterine horn was removed from the animal, divided longitudinally, cut in three square pieces and sutured to the intestine mesentery. After 4 weeks, the lesions and the peritoneal fluid were collected. The level of TNFα in the peritoneal fluid was evaluated by enzyme-linked immunosorbent assay (EIA). The expressions of COX2, GRα and GRβ were evaluated in the lesions by western blot and immunohistochemistry. β-III TUBULIN, BDNF and NGF protein concentrations were evaluated in the lesions by western blot. Gene expression of Pgp 9.5, SP and Th was analyzed by RT-PCR, whereas relative concentrations of TRKA, NTRp75, phosphorylated NFκB (pNFκB) and total NFκB in lesions were measured by EIA. Compared with the WT group, the KO mice showed lower TNFα levels in the peritoneal fluid and lower numbers of COX2 immunoreactive cells along with increased expression of GRα, β-III TUBULIN, Pgp 9.5, SP, Th, BDNF, NGF, NTRp75 and pNFκB in the lesions. Future histological studies will be necessary to confirm the sensory/sympathetic imbalance in the endometriotic-like lesions of the KO mice. Our results suggest that a reduced inflammatory state promotes reinnervation of endometriotic-like lesions in TNFRp55−/− mice. Chronic deregulation of TNF receptors can have serious consequences for women with advanced endometriosis.
Resting-State Functional Network Organization Is Stable Across Adolescent Development for Typical and Psychosis Spectrum Youth
Authors: Jalbrzikowski Maria , Liu Fuchen , Foran William , Roeder Kathryn , Devlin Bernie , Luna Beatriz
Published: May 2019

Background

Resting-state functional neuroimaging captures large-scale network organization; whether this organization is intact or disrupted during adolescent development across the psychosis spectrum is unresolved. We investigated the integrity of network organization in psychosis spectrum youth and those with first episode psychosis (FEP) from late childhood through adulthood.

Methods

We analyzed data from Philadelphia Neurodevelopmental Cohort (PNC; typically developing = 450, psychosis spectrum = 273, 8–22 years), a longitudinal cohort of typically developing youth (LUNA; N = 208, 1–3 visits, 10–25 years), and a sample of FEP (N = 39) and matched controls (N = 34). We extracted individual time series and calculated correlations from brain regions and averaged them for 4 age groups: late childhood, early adolescence, late adolescence, adulthood. Using multiple analytic approaches, we assessed network stability across 4 age groups, compared stability between controls and psychosis spectrum youth, and compared group-level network organization of FEP to controls. We explored whether variability in cognition or clinical symptomatology was related to network organization.

Results

Network organization was stable across the 4 age groups in the PNC and LUNA typically developing youth and PNC psychosis spectrum youth. Psychosis spectrum and typically developing youth had similar functional network organization during all age ranges. Network organization was intact in PNC youth who met full criteria for psychosis and in FEP. Variability in cognitive functioning or clinical symptomatology was not related to network organization in psychosis spectrum youth or FEP.

Discussion

These findings provide rigorous evidence supporting intact functional network organization in psychosis risk and psychosis from late childhood through adulthood.
Decent Care for Migrant Households: Policy Alternatives to Sri Lanka’s Family Background Report
Authors: Withers Matt
Published: May 2019

Domestic worker migration can profoundly reconfigure unpaid care arrangements within migrant households, often exacerbating gendered inequalities in providing and receiving care. While the International Labor Organization has led rights advocacy around migrant domestic work, there remains a dearth of attention to the relationship between feminized migration and unpaid care. In Sri Lanka, this policy space has been occupied by the Family Background Report: a series of regulations that reinforce maternal caregiving by restricting the migration of women with young children. An alternative “decent care” approach, involving investment in local care infrastructure, could yield multiple benefits while promoting a gender-inclusive decent work agenda.
Probabilistic Species Tree Distances: Implementing the Multispecies Coalescent to Compare Species Trees Within the Same Model-Based Framework Used to Estimate Them
Authors: Adams Richard H , Castoe Todd A
Published: May 2019

Despite the ubiquitous use of statistical models for phylogenomic and population genomic inferences, this model-based rigor is rarely applied to post hoc comparison of trees. In a recent study, Garba et al. derived new methods for measuring the distance between two gene trees computed as the difference in their site pattern probability distributions. Unlike traditional metrics that compare trees solely in terms of geometry, these measures consider gene trees and associated parameters as probabilistic models that can be compared using standard information theoretic approaches. Consequently, probabilistic measures of phylogenetic tree distance can be far more informative than simply comparisons of topology and/or branch lengths alone. However, in their current form, these distance measures are not suitable for the comparison of species tree models in the presence of gene tree heterogeneity. Here, we demonstrate an approach for how the theory of Garba et al. (2018), which is based on gene tree distances, can be extended naturally to the comparison of species tree models. Multispecies coalescent (MSC) models parameterize the discrete probability distribution of gene trees conditioned upon a species tree with a particular topology and set of divergence times (in coalescent units), and thus provide a framework for measuring distances between species tree models in terms of their corresponding gene tree topology probabilities. We describe the computation of probabilistic species tree distances in the context of standard MSC models, which assume complete genetic isolation postspeciation, as well as recent theoretical extensions to the MSC in the form of network-based MSC models that relax this assumption and permit hybridization among taxa. We demonstrate these metrics using simulations and empirical species tree estimates and discuss both the benefits and limitations of these approaches. We make our species tree distance approach available as an R package called pSTDistanceR, for open use by the community.
Naive tinea corporis et cruris in an Immunocompetent adult caused by a geophile Nannizzia gypsea susceptible to Terbinafine–Rarity in the current scenario of Dermatophytosis in India
Authors: Vanam Hari Pankaj , Mohanram Kalyani , Reddy K. Siva Rami , Rengasamy Madhu , Rudramurthy Shivaprakash Mandya
Published: May 2019

Introduction. Dermatophytosis caused by Nannizzia gypsea formerly Microsporum gypse
um is rare in occurrence due to its geophilic adaptation and weak pathogenic potential in establishing infection in humans. The taxonomical status of N. gypsea has been controversial over the years and has now reached a concordance among mycologists. Innumerable reports of N. gypsea causing widespread infection in human immunodeficiency virus patients trails them as an important agent of consideration in an immunocompromised host. There have been sporadic reports of N. gypsea causing glabrous skin tinea and onychomycosis in healthy patients and the prevalence reports gravitate around 1–6.5  %. A variety of non-anthropophilic dermatophytes including novel species have now been implicated in causing dermatophytosis reflecting the era of crux changes in the epidemiology.

Case report. We present a case of chronic dermatophytosis in a 22-year-old healthy Indian with a history of contact with a dog and soil and other factors favouring dermatophytosis. Conventional and molecular sequencing established the isolate as N. gypsea. Antifungal susceptibility test revealed a higher MIC of griseofulvin and lower MIC to azoles and terbinafine. The patient had complete clinical resolution following administration of oral terbinafine.

Conclusion. Amidst the hyper-endemic-like scenario of tinea in India, this case report stands as a unique example of a patient infected with N. gypsea showing complete clinical resolution using terbinafine. Studies implicating N. gypsea in an immunocompetent host are rare and there is a need for more studies on geophilic dermatophytes causing tinea in the man for laying down effective preventive measures.
Captive green iguana is a reservoir of diarrheogenicEscherichia colipathotypes
Authors: Bautista-Trujillo Gerardo Uriel , Gutiérrez-Miceli Federico Antonio , Mandujano-García Leonel , Oliva-Llaven María Angela , Ibarra-Martínez Carlos , Mendoza-Nazar Paula , Ruiz-Sesma Benigno , Tejeda-Cruz Carlos , Pérez-Vázquez Liset Candelaria , Pérez-Batrez Jesús Eduardo , Vidal Jorge E. , Gutiérrez-Jiménez Javier
Published: May 2019

The green iguana appears to be a reservoir for bacteria causing gastrointestinal infections in humans. The presence of diarrheogenicE. coli(DEC) pathotypes, however, has not been studied in this reptile. The aim of the current work was to investigate the prevalence of DEC in the intestines of 240 captive green iguanas, their phylogenetic groups, and the antibiotic susceptibility profile.E. colistrains were isolated from 41.7% of the intestinal content of green iguanas. DEC strains was identified in 25.9% of the screened population and were detected in the majority (62%, p=0.009] of those reptiles carryingE. colistrains. Among DEC strains, STEC strains carrying thestx1gene were the most prevalent pathotype isolated (38.7%), followed by EAEC and ETEC (27.4% each). Genetic markers of DEC strains belonging to the EHEC pathotype were not detected. More than a half of DEC strains were classified into the Clade I-II phylogroup (64.5%), followed by the phylogroup A (14.5%). The antibiotic susceptibility method demonstrated that a high proportion of DEC strains were resistance, or non-susceptible, to carbenicillin, amikacin, and ampicillin (85, 74, and 66%, respectively). We conclude that the green iguana kept in captivity is a reservoir of DEC strains bearing resistance to first-line antibiotics, including penicillins. Given the increase presence of the green iguana in Latin American households, these reptiles represent a potential source of transmission to susceptible humans and therefore a potential source of gastrointestinal disease.

Importance

Latin-American countries present a high burden of diarrheal disease. In this part of the world, besides common pathogens, diarrheal diseases are also caused by pathogenic types ofE. colireferred as “diarrheagenicE. coli” (DEC). While inhabitants of Latin American countries suffer of self-limiting diarrhea when infected with DEC, a main target of these strains are tourists from developed countries who are not exposed to DEC strains. Efforts are in place to decrease the burden of DEC-associated diarrheal disease. As such, this study investigated a potential reservoir of DEC strains that had been underestimated, the green iguana. These reptiles are very common in Latin American households and are found virtually everywhere in Mexico, Central and South America. We found that 25% of green iguanas carried DEC strains in their intestines. We also demonstrated a high prevalence of antibiotic resistance in these strains, posing a potential risk to humans.
Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans
Authors: Ziyatdinov Andrey , Parker Margaret M. , Vaysse Amaury , Beaty Terri H. , Kraft Peter , Cho Michael H. , Aschard Hugues
Published: May 2019

Admixture mapping has led to the discovery of many genes associated with differential disease risk by ancestry, highlighting the importance of ancestry-based approaches to association studies. However, the potential of admixture mapping in deciphering the interplay between genes and environment exposures has been seldom explored. Here, we performed a genome-wide screening of local ancestry-smoking interactions for five spirometric lung function phenotypes in 3,300 African Americans from the COPDGene study. To account for population structure and outcome heterogeneity across exposure groups, we developed a multi-component linear mixed model for mapping gene-environment interactions, and empirically showed its robustness and increased power. When applied to the COPDGene study, our approach identified two 11p15.2-3 and 2q37 loci, exhibiting local ancestry-smoking interactions at genome-wide significant level, that would have been missed by standard singlenucleotide polymorphism analyses. These two loci harbor the PARVA and RAB17 genes previously recognized to be involved in smoking behavior. Overall, our study provides the first evidence for potential synergistic effects between African ancestry and smoking on pulmonary function and underlines the importance of ethnic diversity in genetic studies.
Repurposing the aldose reductase inhibitor and diabetic neuropathy drug epalrestat for the congenital disorder of glycosylation PMM2-CDG
Authors: Iyer Sangeetha , Sam Feba S. , DiPrimio Nina , Preston Graeme , Verhejein Jan , Murthy Kausalya , Parton Zachary , Tsang Hillary , Lao Jessica , Morava Eva , Perlstein Ethan O.
Published: May 2019

Phosphomannomutase 2 deficiency, or PMM2-CDG, is the most common congenital disorder of glycosylation affecting over 1,000 patients globally. There are no approved drugs that treat the symptoms or root cause of PMM2-CDG. In order to identify clinically actionable compounds that boost human PMM2 enzyme function, we performed a multi-species drug repurposing screen using a first-ever worm model of PMM2-CDG followed by PMM2 enzyme functional studies in PMM2-CDG patient fibroblasts. Drug repurposing candidates from this study, and drug repurposing candidates from a previously published study using yeast models of PMM2-CDG, were tested for their effect on human PMM2 enzyme activity in PMM2-CDG fibroblasts. Of the 20 repurposing candidates discovered in the worm-based phenotypic screen, 12 are plant-based polyphenols. Insights from structure-activity relationships revealed epalrestat, the only antidiabetic aldose reductase inhibitor approved for use in humans, as a first-in-class PMM2 enzyme activator. Epalrestat increased PMM2 enzymatic activity in four PMM2-CDG patient fibroblast lines with genotypes R141H/F119L, R141H/E139K, R141H/N216I and R141H/F183S. PMM2 enzyme activity gains range from 30% to 400% over baseline depending on genotype. Pharmacological inhibition of aldose reductase by epalrestat may shunt glucose from the polyol pathway to glucose-1,6-bisphosphate, which is an endogenous stabilizer and coactivator of PMM2 homodimerization. Epalrestat is a safe, oral and brain penetrant drug that was approved 27 years ago in Japan to treat diabetic neuropathy in geriatric populations. We demonstrate that epalrestat is the first small molecule activator of PMM2 enzyme activity with the potential to treat peripheral neuropathy and correct the underlying enzyme deficiency in a majority of pediatric and adult PMM2-CDG patients.
Soil and vegetation conditions changes following the different sand dune restoration measures on the Zoige Plateau
Authors: Luo Jiufu , Deng Dongzhou , Zhang Li , Zhu Xinwei , Chen Dechao , Zhou Jinxing
Published: May 2019

Restoration of alpine sand dunes has been increasingly attracting the attention of ecologists due to their difficulty and importance among the mountain-river-forest-farmland-lake-grass system (referred as meta-ecosystem) restoration. Alpine sand dunes are suffered from unstable soil and lack of plants. Efficient restoration measures are vital to guide the sand dune restoration. Whether the engineering materials co-applied with seeding could achieve considerable restoration in such areas? Here, sandbag and wicker as environmental friendly materials combined with Elymus nutans seeding were implemented on the Zoige Plateau sand dune, comparing with the ‘control’ treatment that only seeding. We assessed the topsoil conditions by sampled the surface soil and measured the water capacity and nutrients. We also utilized interspecific relationship and population niche to analyse the plant community structure variances among different restoration measures. Results showed that the soil conditions got clearly improved in sandbag area than that in wicker area when compared with that in control area. The community in control area was the least structured, while the species showed the closest related in sandbag area. In addition, average population niche overlap showed a control (0.26) < wicker (0.32) < sandbag (0.39) ranking. Thus, we suggested that sandbag or wicker co-applied with indigenous grass seeding is a practical and quick restoration approach in alpine sand dunes, and the sandbag may surpasses the wicker. Moreover, soil amending measures including nutrient improvement, and microbial fertilizer addition may further accelerate sand dune restoration.
Plasmid detection and assembly in genomic and metagenomic data sets
Authors: Antipov Dmitry , Raiko Mikhail , Lapidus Alla , Pevzner Pavel A.
Published: May 2019

Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.
Crystal structures of the synthetic intermediate 3-[(6-chloro-7H-purin-7-yl)methyl]cyclobutan-1-one, and of two oxetanocin derivatives: 3-[(6-chloro-8,9-dihydro-7H-purin-7-yl)methyl]cyclobutan-1-ol and 3-[(6-chloro-9H-purin-9-yl)methyl]cyclobutan-1-ol
Authors: Yaseen Ayat , Hassan Muhammad Murtaza , Lee-Ruff Edward , Audette Gerald F.
Published: May 2019

The crystal structures of an intermediate, C10H9ClN4O, 3-[(6-chloro-7H-purin-7-yl)methyl]cyclobutan-1-one (I), and two N-7 and N-9 regioisomeric oxetanocin nucleoside analogs, C10H13ClN4O, 3-[(6-chloro-8,9-dihydro-7H-purin-7-yl)methyl]cyclobutan-1-ol (II) and C10H11ClN4O, 3-[(6-chloro-9H-purin-9-yl)methyl]cyclobutan-1-ol (IV), are reported. The crystal structures of the nucleoside analogs confirmed the reduction of the N-7- and N-9-substituted cyclobutanones with LiAl(OtBu)3 to occur with facial selectivity, yielding cis-nucleosides analogs similar to those found in nature. Reduction of the purine ring of the N-7 cyclobutanone to a dihydropurine was observed for compound (II) but not for the purine ring of the N-9 cyclobutanone on formation of compound (IV). In the crystal of (I), molecules are linked by a weak Cl...O interaction, forming a 21 helix along [010]. The helices are linked by offset π–π interactions [intercentroid distance = 3.498 (1) Å], forming layers parallel to (101). In the crystal of (II), molecules are linked by pairs of O—H...N hydrogen bonds, forming inversion dimers with an R
2
2(8) ring motif. The dimers are linked by O—H...N hydrogen bonds, forming chains along [001], which in turn are linked by C—H...π and offset π–π interactions [intercentroid distance = 3.509 (1) Å], forming slabs parallel to the ac plane. In the crystal of (IV), molecules are linked by O—H...N hydrogen bonds, forming chains along [101]. The chains are linked by C—H...N and C—H...O hydrogen bonds and C—H...π and offset π–π interactions [intercentroid distance = 3.364 (1) Å], forming a supramolecular framework.
Partial charge transfer in the salt co-crystal of L-ascorbic acid and 4,4′-bipyridine
Authors: Sylvester Eric , McGovern Mitchell , Young Lee An , Nguyen Phanxico , Park Jungeun , Benedict Jason B.
Published: May 2019

In the title 1:2 co-crystal, C10H9N2
+·(C6H7.75O6·C6H7.25O6)−, L-ascorbic acid (LAA) and 4,4′-bipyridine (BPy) co-crystallize in the chiral space group P21 with two molecules of LAA, and one molecule of bpy in the asymmetric unit. The structure was modeled in two parts due to possible proton transfer from LAA to the corresponding side of the bpy molecule having an occupancy of approximately 0.25 and part 2 with an occupancy of approximately 0.75. In this structure, LAA forms hydrogen bonds with neighboring LAA molecules, forming extended sheets of LAA molecules which are bridged by bpy molecules. A comparison to a related and previously published co-crystal of LAA and 3-bromo-4-pyridone is presented.
Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 3-{(2Z)-2-[(2,4-dichlorophenyl)methylidene]-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-4-yl}propanenitrile
Authors: Sebbar Nada Kheira , Hni Brahim , Hökelek Tuncer , Jaouhar Abdelhakim , Labd Taha Mohamed , Mague Joel T. , Essassi El Mokhtar
Published: May 2019

The title compound, C18H12Cl2N2OS, consists of a dihydrobenzothiazine unit linked by a –CH group to a 2,4-dichlorophenyl substituent, and to a propanenitrile unit is folded along the S...N axis and adopts a flattened-boat conformation. The propanenitrile moiety is nearly perpendicular to the mean plane of the dihydrobenzothiazine unit. In the crystal, C—HBnz...NPrpnit and C—HPrpnit...OThz (Bnz = benzene, Prpnit = propanenitrile and Thz = thiazine) hydrogen bonds link the molecules into inversion dimers, enclosing R
2
2(16) and R
2
2(12) ring motifs, which are linked into stepped ribbons extending along [110]. The ribbons are linked in pairs by complementary C=O...Cl interactions. π–π contacts between the benzene and phenyl rings, [centroid–centroid distance = 3.974 (1) Å] may further stabilize the structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (23.4%), H...Cl/Cl...H (19.5%), H...C/C...H (13.5%), H...N/N...H (13.3%), C...C (10.4%) and H...O/O...H (5.1%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry calculations indicate that the two independent C—HBnz...NPrpnit and C—HPrpnit...OThz hydrogen bonds in the crystal impart about the same energy (ca 43 kJ mol−1). Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.