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  1. Ismail SI, Batzer JC, Harrington TC, Crous PW, Lavrov DV, Li H, et al.
    Mycologia, 2016 Mar-Apr;108(2):292-302.
    PMID: 26740537 DOI: 10.3852/15-036
    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi.
  2. Hanna GS, Choo YM, Harbit R, Paeth H, Wilde S, Mackle J, et al.
    J Nat Prod, 2021 Nov 26;84(11):3001-3007.
    PMID: 34677966 DOI: 10.1021/acs.jnatprod.1c00625
    The pressing need for SARS-CoV-2 controls has led to a reassessment of strategies to identify and develop natural product inhibitors of zoonotic, highly virulent, and rapidly emerging viruses. This review article addresses how contemporary approaches involving computational chemistry, natural product (NP) and protein databases, and mass spectrometry (MS) derived target-ligand interaction analysis can be utilized to expedite the interrogation of NP structures while minimizing the time and expense of extraction, purification, and screening in BioSafety Laboratories (BSL)3 laboratories. The unparalleled structural diversity and complexity of NPs is an extraordinary resource for the discovery and development of broad-spectrum inhibitors of viral genera, including Betacoronavirus, which contains MERS, SARS, SARS-CoV-2, and the common cold. There are two key technological advances that have created unique opportunities for the identification of NP prototypes with greater efficiency: (1) the application of structural databases for NPs and target proteins and (2) the application of modern MS techniques to assess protein-ligand interactions directly from NP extracts. These approaches, developed over years, now allow for the identification and isolation of unique antiviral ligands without the immediate need for BSL3 facilities. Overall, the goal is to improve the success rate of NP-based screening by focusing resources on source materials with a higher likelihood of success, while simultaneously providing opportunities for the discovery of novel ligands to selectively target proteins involved in viral infection.
  3. Ord TJ, Klomp DA, Summers TC, Diesmos A, Ahmad N, Das I
    Ecol Lett, 2021 Sep;24(9):1750-1761.
    PMID: 34196091 DOI: 10.1111/ele.13773
    Convergence in communication appears rare compared with other forms of adaptation. This is puzzling, given communication is acutely dependent on the environment and expected to converge in form when animals communicate in similar habitats. We uncover deep-time convergence in territorial communication between two groups of tropical lizards separated by over 140 million years of evolution: the Southeast Asian Draco and Caribbean Anolis. These groups have repeatedly converged in multiple aspects of display along common environmental gradients. Robot playbacks to free-ranging lizards confirmed that the most prominent convergence in display is adaptive, as it improves signal detection. We then provide evidence from a sample of the literature to further show that convergent adaptation among highly divergent animal groups is almost certainly widespread in nature. Signal evolution is therefore curbed towards the same set of adaptive solutions, especially when animals are challenged with the problem of communicating effectively in noisy environments.
  4. Bastidas A, de la Serna J, El Idrissi M, Oostvogels L, Quittet P, López-Jiménez J, et al.
    JAMA, 2019 07 09;322(2):123-133.
    PMID: 31287523 DOI: 10.1001/jama.2019.9053
    Importance: Herpes zoster, a frequent complication following autologous hematopoietic stem cell transplantation (HSCT), is associated with significant morbidity. A nonlive adjuvanted recombinant zoster vaccine has been developed to prevent posttransplantation zoster.

    Objective: To assess the efficacy and adverse event profile of the recombinant zoster vaccine in immunocompromised autologous HSCT recipients.

    Design, Setting, and Participants: Phase 3, randomized, observer-blinded study conducted in 167 centers in 28 countries between July 13, 2012, and February 1, 2017, among 1846 patients aged 18 years or older who had undergone recent autologous HSCT.

    Interventions: Participants were randomized to receive 2 doses of either recombinant zoster vaccine (n = 922) or placebo (n = 924) administered into the deltoid muscle; the first dose was given 50 to 70 days after transplantation and the second dose 1 to 2 months thereafter.

    Main Outcomes and Measures: The primary end point was occurrence of confirmed herpes zoster cases.

    Results: Among 1846 autologous HSCT recipients (mean age, 55 years; 688 [37%] women) who received 1 vaccine or placebo dose, 1735 (94%) received a second dose and 1366 (74%) completed the study. During the 21-month median follow-up, at least 1 herpes zoster episode was confirmed in 49 vaccine and 135 placebo recipients (incidence, 30 and 94 per 1000 person-years, respectively), an incidence rate ratio (IRR) of 0.32 (95% CI, 0.22-0.44; P 

  5. Pan GT, Chong S, Yang TC, Huang CM
    Materials (Basel), 2017 Mar 31;10(4).
    PMID: 28772727 DOI: 10.3390/ma10040370
    Mesoporous Mn1.5Co1.5O₄ (MCO) spinel films were prepared directly on a conductive nickel (Ni) foam substrate via electrodeposition and an annealing treatment as supercapacitor electrodes. The electrodeposition time markedly influenced the surface morphological, textural, and supercapacitive properties of MCO/Ni electrodes. The (MCO/Ni)-15 min electrode (electrodeposition time: 15 min) exhibited the highest capacitance among three electrodes (electrodeposition times of 7.5, 15, and 30 min, respectively). Further, an asymmetric supercapacitor that utilizes (MCO/Ni)-15 min as a positive electrode, a plasma-treated activated carbon (PAC)/Ni electrode as a negative electrode, and carboxymethyl cellulose-lithium nitrate (LiNO₃) gel electrolyte (denoted as (PAC/Ni)//(MCO/Ni)-15 min) was fabricated. In a stable operation window of 2.0 V, the device exhibited an energy density of 27.6 Wh·kg-1 and a power density of 1.01 kW·kg-1 at 1 A·g-1. After 5000 cycles, the specific energy density retention and power density retention were 96% and 92%, respectively, demonstrating exceptional cycling stability. The good supercapacitive performance and excellent stability of the (PAC/Ni)//(MCO/Ni)-15 min device can be ascribed to the hierarchical structure and high surface area of the (MCO/Ni)-15 min electrode, which facilitate lithium ion intercalation and deintercalation at the electrode/electrolyte interface and mitigate volume change during long-term charge/discharge cycling.
  6. Grabowski MK, Gray RH, Serwadda D, Kigozi G, Gravitt PE, Nalugoda F, et al.
    Sex Transm Infect, 2014 Jun;90(4):337-43.
    PMID: 24482488 DOI: 10.1136/sextrans-2013-051230
    OBJECTIVES: High-risk human papillomavirus (HR-HPV) viral load is associated with HR-HPV transmission and HR-HPV persistence in women. It is unknown whether HR-HPV viral load is associated with persistence in HIV-negative or HIV-positive men.
    METHODS: HR-HPV viral load and persistence were evaluated among 703 HIV-negative and 233 HIV-positive heterosexual men who participated in a male circumcision trial in Rakai, Uganda. Penile swabs were tested at baseline and 6, 12 and 24 months for HR-HPV using the Roche HPV Linear Array, which provides a semiquantitative measure of HPV shedding by hybridisation band intensity (graded: 1-4). Prevalence risk ratios (PRR) were used to estimate the association between HR-HPV viral load and persistent detection of HR-HPV.
    RESULTS: HR-HPV genotypes with high viral load (grade:3-4) at baseline were more likely to persist than HR-HPV genotypes with low viral load (grade: 1-2) among HIV-negative men (month 6: adjPRR=1.83, 95% CI 1.32 to 2.52; month 12: adjPRR=2.01, 95% CI 1.42 to 3.11), and HIV-positive men (month 6: adjPRR=1.33, 95% CI 1.06 to 1.67; month 12: adjPRR=1.73, 95% CI 1.18 to 2.54). Long-term persistence of HR-HPV was more frequent among HIV-positive men compared with HIV-negative men (month 24: adjPRR=2.27, 95% CI 1.47 to 3.51). Persistence of newly detected HR-HPV at the 6-month and 12-month visits with high viral load were also more likely to persist to 24 months than HR-HPV with low viral load among HIV-negative men (adjPRR=1.67, 95% CI 0.88 to 3.16).
    CONCLUSIONS: HR-HPV genotypes with high viral load are more likely to persist among HIV-negative and HIV-positive men, though persistence was more common among HIV-positive men overall. The results may explain the association between high HR-HPV viral load and HR-HPV transmission.
  7. Phoon BL, Lai CW, Pan GT, Yang TC, Juan JC
    Nanomaterials (Basel), 2021 Aug 11;11(8).
    PMID: 34443873 DOI: 10.3390/nano11082041
    A highly mesoporous graphitic carbon nitride g-C3N4 (GCN) has been produced by a template-free method and effectively photodegrade tetracycline (TC) antibiotic under solar light irradiation. The mesoporous GCN (GCN-500) greatly improves the photoactivity (0.0247 min-1) by 2.13 times, as compared to that of bulk GCN (0.0116 min-1). The efficiently strengthened photoactivity is ascribed to the high porosity (117.05 m2/g), and improves the optical absorption under visible light (Eg = 2.65 eV) and good charge carrier separation efficiency. The synthesized mesoporous GCN shows a uniform pore size (~3 nm) distribution. GCN-500 shows large pore volume (0.210 cm3/g) compared to GCN-B (0.083 cm3/g). Besides, the GCN-500 also exhibits good recyclability and photostability for TC photodegradation. In conclusion, GCN-500 is a recyclable photocatalyst for the removal of TC under visible light irradiation.
  8. Balu S, Chen YL, Juang RC, Yang TC, Juan JC
    Environ Pollut, 2020 Dec;267:115491.
    PMID: 32911336 DOI: 10.1016/j.envpol.2020.115491
    Surface functionalization and shape modifications are the key strategies being utilized to overcome the limitations of semiconductors in advanced oxidation processes (AOP). Herein, the uniform α-Fe2O3 nanocrystals (α-Fe2O3-NCs) were effectively synthesized via a simple solvothermal route. Meanwhile, the sulfonic acid functionalization (SAF) and the impregnation of α-Fe2O3-NCs on g-C3N4 (α-Fe2O3-NCs@CN-SAF) were achieved through complete solvent evaporation technique. The surface functionalization of the sulfonic acid group on g-C3N4 accelerates the faster migration of electrons to the surface owing to robust electronegativity. The incorporation of α-Fe2O3-NCs with CN-SAF significantly enhances the optoelectronic properties, ultrafast spatial charge separation, and rapid charge transportation. The α-Fe2O3-HPs@CN-SAF and α-Fe2O3-NPs@CN-SAF nanocomposites attained 97.41% and 93.64% of Cr (VI) photoreduction in 10 min, respectively. The photocatalytic efficiency of α-Fe2O3-NCs@CN-SAF nanocomposite is 2.4 and 2.1 times higher than that of pure g-C3N4 and α-Fe2O3, respectively. Besides, the XPS, PEC and recycling experiments confirm the excellent photo-induced charge separation via Z-scheme heterostructure and cyclic stability of α-Fe2O3-NCs@CN-SAF nanocomposites.
  9. Baddeley TC, de Souza MVN, Wardell JL, Jotani MM, Tiekink ERT
    Acta Crystallogr E Crystallogr Commun, 2019 Apr 01;75(Pt 4):516-523.
    PMID: 31161067 DOI: 10.1107/S2056989019003980
    The asymmetric unit of the title compound, C13H11N3O2S2, comprises two independent mol-ecules (A and B); the crystal structure was determined by employing synchrotron radiation. The mol-ecules exhibit essentially the same features with an almost planar benzo-thia-zole ring (r.m.s. deviation = 0.026 and 0.009 Å for A and B, respectively), which forms an inclined dihedral angle with the phenyl ring [28.3 (3) and 29.1 (3)°, respectively]. A difference between the mol-ecules is noted in a twist about the N-S bonds [the C-S-N-N torsion angles = -56.2 (5) and -68.8 (5)°, respectively], which leads to a minor difference in orientation of the phenyl rings. In the mol-ecular packing, A and B are linked into a supra-molecular dimer via pairwise hydrazinyl-N-H⋯N(thiazol-yl) hydrogen bonds. Hydrazinyl-N-H⋯O(sulfon-yl) hydrogen bonds between A mol-ecules assemble the dimers into chains along the a-axis direction, while links between centrosymmetrically related B mol-ecules, leading to eight-membered {⋯HNSO}2 synthons, link the mol-ecules along [001]. The result is an undulating supra-molecular layer. Layers stack along the b-axis direction with benzo-thia-zole-C-H⋯O(sulfon-yl) points of contact being evident. The analyses of the calculated Hirshfeld surfaces confirm the relevance of the above inter-molecular inter-actions, but also serve to further differentiate the weaker inter-molecular inter-actions formed by the independent mol-ecules, such as π-π inter-actions. This is also highlighted in distinctive energy frameworks calculated for the individual mol-ecules.
  10. Rosli H, Batzer JC, Harrington TC, Gleason ML
    Mycologia, 2018 09 21;110(5):822-834.
    PMID: 30240341 DOI: 10.1080/00275514.2018.1486679
    Sooty blotch and flyspeck (SBFS) fungi infect the cuticle of fruit, including apple fruit, and produce pigmented colonies. A new member of this fungal complex in the genus Peltaster is described on the basis of molecular and morphological evidence. The SBFS complex is a diverse group of ectophytic fungi that reside primarily within the order Capnodiales. Sooty blotch and flyspeck isolates from apple orchards in the central United States were subjected to parsimony and Bayesian analyses based on the internal transcribed spacer regions of nuc rDNA, the partial translation elongation factor 1-α gene, and the partial mitochondrial small subunit rRNA gene. Phylogenetic analysis delineated a new species, Peltaster gemmifer, from P. cerophilus and P. fructicola. Peltaster gemmifer conidiophores bear primary conidia that produce secondary conidia either through budding or through microcyclic conidiation; these were not seen in cultures of P. cerophilus and P. fructicola. On cellulose membrane that was placed on water agar amended with apple juice, P. gemmifer produced brown to black pycnothyria in a superficial brownish mycelial mat, similar to the colonies produced on apple fruit. Findings from the present study add to the >80 named and putative SBFS species so far described worldwide.
  11. McClure-Thomas C, Lim C, Sebayang S, Fausiah F, Gouda H, Leung J
    Asia Pac J Public Health, 2022 Nov;34(8):770-777.
    PMID: 35880310 DOI: 10.1177/10105395221115220
    Tobacco use among youth in the South-East Asian region is quite prevalent. This study aims to examine if psychosocial factors (perceived loneliness, peer, and parental relationships) were associated with adolescent smoking, and whether the effects were different according to sex and age. Data came from the Global School-based Student Health Surveys collected between 2012 and 2015 in Brunei, Cambodia, Indonesia, Laos, Malaysia, Philippines, Thailand, Timor-Leste, and Vietnam. 64 578 (males = 48.5%) adolescents aged 13-18 completed the survey. Prevalence of past-month cigarette use was 10.6%. Adolescent smoking was associated with loneliness (OR = 1.75), lack of close friends (OR = 1.43), and lack of parental understanding (OR = 1.35). There was significant interactions between sex with loneliness, close friends, and parental understanding (p < .001). Interactions indicated having no close friends is associated with smoking and is stronger for females than males. Conversely, loneliness was associated with smoking more strongly in males than females. Results indicate that psychosocial factors are linked to adolescent smoking in South-East Asia, suggesting a further need for research on the relation of psychosocial factors with smoking, and their underlying factors.
  12. Ng KT, Ng KY, Khong WX, Chew KK, Singh PK, Yap JK, et al.
    PLoS One, 2013;8(12):e80884.
    PMID: 24312505 DOI: 10.1371/journal.pone.0080884
    HIV-1 subtype B and CRF01_AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and the recently characterized CRF51_01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatment-naïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 - 2629), gp120 (HXB2: 6942 - 7577) and gp41 (HXB2: 7803 - 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01_AE and one within CRF51_01B lineages) of different sizes (involving 3 - 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01_AE. Exponential increase in effective population size for both subtype B and CRF01_AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51_01B lineages were probably generated through series of recombination events involving CRF01_AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and CRF51_01B viral strains circulating among MSM in Singapore.
  13. Muthulingam D, Hassett TC, Madden LM, Bromberg DJ, Fraenkel L, Altice FL
    J Subst Use Addict Treat, 2023 Nov;154:209138.
    PMID: 37544510 DOI: 10.1016/j.josat.2023.209138
    INTRODUCTION: The opioid epidemic continues to be a public health crisis that has worsened during the COVID-19 pandemic. Medications for opioid use disorder (MOUD) are the most effective way to reduce complications from opioid use disorder (OUD), but uptake is limited by both structural and individual factors. To inform strategies addressing individual factors, we evaluated patients' preferences and trade-offs in treatment decisions using conjoint analysis.

    METHOD: We developed a conjoint analysis survey evaluating patients' preferences for FDA-approved MOUDs. We recruited patients with OUD presenting to initiate treatment. This survey included five attributes: induction, location and route of administration, impact on mortality, side effects, and withdrawal symptoms with cessation. Participants performed 12 choice sets, each with two hypothetical profiles and a "none" option. We used Hierarchical Bayes to identify relative importance of each attribute and part-worth utility scores of levels, which we compared using chi-squared analysis. We used the STROBE checklist to guide our reporting of this cross-sectional observational study.

    RESULTS: Five-hundred and thirty participants completed the study. Location with route of administration was the most important attribute. Symptom relief during induction and withdrawal was a second priority. Mortality followed by side effects had lowest relative importance. Attribute levels with highest part-worth utilities showed patients preferred monthly pick-up from a pharmacy rather than daily supervised dosing; and oral medications more than injection/implants, despite the latter's infrequency.

    CONCLUSION: We measured treatment preferences among patients seeking to initiate OUD treatment to inform strategies to scale MOUD treatment uptake. Patients prioritize the route of administration in treatment preference-less frequent pick up, but also injections and implants were less preferred despite their convenience. Second, patients prioritize symptom relief during the induction and withdrawal procedures of medication. These transition periods influence the sustainability of treatment. Although health professionals prioritize mortality, it did not drive decision-making for patients. To our knowledge, this is the largest study on patients' preferences for MOUD among treatment-seeking people with OUD to date. Future analysis will evaluate patient preference heterogeneity to further target program planning, counseling, and decision aid development.

  14. Alishaq M, Al Ajmi JA, Shaheen M, Elgendy M, Vinoy S, Thomas AG, et al.
    PLoS One, 2023;18(10):e0291989.
    PMID: 37792687 DOI: 10.1371/journal.pone.0291989
    BACKGROUND: There is debate over whether physical attendance at school affects the spread of the SARS-CoV-2 pandemic.

    METHODS: A cohort of personnel from several schools in Qatar provided nasopharyngeal swabs (NPS) for SARS-CoV-2 RT-PCR and rapid antigen testing. Each of them was monitored for infection until February 2022.

    RESULTS: In total, 3,241 employees gave samples for analysis. Prior to the start of the 2020-2021 academic year (Group I), 3.49% of samples tested positive for SARS-CoV-2. Most of the positive PCR results were from male, senior, non-teaching staff members. Only 110 (3.39%) employees who had enrolled in face-to-face instruction before the B.1.1.7 variant's emergence (Group II), 238 (7.34%) after the B.1.1.7 variant's emergence (Group III), and 410 (12.65%) after the introduction of the Omicron variant (Group IV) had reported infection by PCR test. Most people who tested positive by PCR after enrolling in school were young, female teachers. In the Cox Proportional-Hazards Model, exposure to a confirmed case, the presence of symptoms in the two weeks prior to exposure in all groups-young age in Groups II and III, male gender in Groups I and IV, shared housing in Group III, and the presence of comorbidities in Groups II and III independently predicted SARS-CoV-2 infection in school staff.

    CONCLUSION: Critical information about the risk of SARS-CoV-2 infection in school workers during the whole pandemic is provided by our study. School operations in Qatar were made safer through initial and ongoing screenings, as well as widespread vaccination of school personnel.

  15. Liu J, Lončar I, Collée JM, Bolla MK, Dennis J, Michailidou K, et al.
    Sci Rep, 2016 Nov 15;6:36874.
    PMID: 27845421 DOI: 10.1038/srep36874
    NBS1, also known as NBN, plays an important role in maintaining genomic stability. Interestingly, rs2735383 G > C, located in a microRNA binding site in the 3'-untranslated region (UTR) of NBS1, was shown to be associated with increased susceptibility to lung and colorectal cancer. However, the relation between rs2735383 and susceptibility to breast cancer is not yet clear. Therefore, we genotyped rs2735383 in 1,170 familial non-BRCA1/2 breast cancer cases and 1,077 controls using PCR-based restriction fragment length polymorphism (RFLP-PCR) analysis, but found no association between rs2735383CC and breast cancer risk (OR = 1.214, 95% CI = 0.936-1.574, P = 0.144). Because we could not exclude a small effect size due to a limited sample size, we further analyzed imputed rs2735383 genotypes (r2 > 0.999) of 47,640 breast cancer cases and 46,656 controls from the Breast Cancer Association Consortium (BCAC). However, rs2735383CC was not associated with overall breast cancer risk in European (OR = 1.014, 95% CI = 0.969-1.060, P = 0.556) nor in Asian women (OR = 0.998, 95% CI = 0.905-1.100, P = 0.961). Subgroup analyses by age, age at menarche, age at menopause, menopausal status, number of pregnancies, breast feeding, family history and receptor status also did not reveal a significant association. This study therefore does not support the involvement of the genotype at NBS1 rs2735383 in breast cancer susceptibility.
  16. Nations JA, Giarla TC, Morni MA, William Dee J, Swanson MT, Hiller AE, et al.
    Zookeys, 2022;1137:17-31.
    PMID: 36760481 DOI: 10.3897/zookeys.1137.94217
    Although Borneo has received more attention from biologists than most other islands in the Malay Archipelago, many questions regarding the systematic relationships of Bornean mammals remain. Using next-generation sequencing technology, we obtained mitochondrial DNA sequences from the holotype of Suncusater, the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype of S.ater. Phylogenetic analyses of mitochondrial sequences indicate that the S.ater holotype and new Sarawak specimens do not belong to the genus Suncus, but instead are most closely related to Palawanosorexmuscorum. Until now Palawanosorex has been known only from the neighboring Philippine island of Palawan. Additional sequences from nuclear ultra-conserved elements from the new Sarawak specimens strongly support a sister relationship to P.muscorum. We therefore transfer ater to Palawanosorex. The new specimens demonstrate that P.ater is more widespread in northern Borneo than previously recorded. Continued sampling of Bornean mammal diversity and reexamination of type material are critical in understanding the evolutionary history of the biologically rich Malay Archipelago.
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