bluuebunny/crossref_metadata_2025 huggingface dataset:
NuSTAR observations of four nearby X-ray faint AGNs: low luminosity or heavy obscuration?
Authors: Annuar A , Alexander D M , Gandhi P , Lansbury G B , Asmus D , Baloković M , Ballantyne D R , Bauer F E , Boorman P G , Brandt W N , Brightman M , Chen C-T J , Del Moro A , Farrah D , Harrison F A , Koss M J , Lanz L , Marchesi S , Masini A , Nardini E , Ricci C , Stern D , Zappacosta L
Published: June 2020

We present NuSTAR (Nuclear Spectroscopic Telescope Array) observations of four active galactic nuclei (AGNs) located within 15 Mpc. These AGNs, namely ESO 121-G6, NGC 660, NGC 3486, and NGC 5195, have observed X-ray luminosities of L2–10 keV,obs ≲ 1039 erg s−1, classifying them as low-luminosity AGN (LLAGN). We perform broad-band X-ray spectral analysis for the AGN by combining our NuSTAR data with Chandra or XMM–Newton observations to directly measure their column densities (NH) and infer their intrinsic power. We complement our X-ray data with archival and new high-angular resolution mid-infrared (mid-IR) data for all objects, except NGC 5195. Based on our X-ray spectral analysis, we found that both ESO 121-G6 and NGC 660 are heavily obscured (NH > 1023 cm−2; L2–10 keV,int ∼ 1041 erg s−1), and NGC 660 may be Compton thick. We also note that the X-ray flux and spectral slope for ESO 121-G6 have significantly changed over the last decade, indicating significant changes in the obscuration and potentially accretion rate. On the other hand, NGC 3486 and NGC 5195 appear to be unobscured and just mildly obscured, respectively, with L2–10 keV,int < 1039 erg s−1, i.e. genuine LLAGN. Both of the heavily obscured AGNs have Lbol > 1041 erg s−1 and λEdd ≳ 10−3, and are detected in high-angular resolution mid-IR imaging, indicating the presence of obscuring dust on nuclear scale. NGC 3486, however, is undetected in high-resolution mid-IR imaging, and the current data do not provide stringent constraints on the presence or absence of obscuring nuclear dust in the AGN.
Optical studies of two stripped-envelope supernovae – SN 2015ap (Type Ib) and SN 2016P (Type Ic)
Authors: Gangopadhyay Anjasha , Misra Kuntal , Sahu D K , Wang Shan-Qin , Kumar Brajesh , Li Long , Anupama G C , Dastidar Raya , Elias-Rosa N , Kumar Brijesh , Singh Mridweeka , Pandey S B , Sanwal Pankaj , Singh Avinash , Srivastav S , Tartaglia L , Tomasella L
Published: June 2020

We present the photometric and spectroscopic studies of a Type Ib SN 2015ap and a Type Ic SN 2016P. SN 2015ap is one of the bright (MV = −18.04 mag) Type Ib while SN 2016P lies at an average value among the Type Ic SNe (MV = −17.53 mag). Bolometric light-curve modelling of SNe 2015ap and 2016P indicates that both the SNe are powered by 56Ni + magnetar model with 56Ni masses of 0.01 and 0.002 M⊙, ejecta masses of 3.75 and 4.66 M⊙, spin period P0 of 25.8 and 36.5 ms, and magnetic field Bp of 28.39 × 1014 and 35.3 × 1014 G, respectively. The early spectra of SN 2015ap show prominent lines of He with a ‘W’ feature due to Fe complexes while other lines of Mg ii, Na i, and Si ii are present in both SNe 2015ap and 2016P. Nebular phase [O i] profile indicates an asymmetric profile in SN 2015ap. The [O i]/[Ca ii] ratio and nebular spectral modelling of SN 2015ap hint towards a progenitor mass between 12 and 20 M⊙.
Water transport throughout the TRAPPIST-1 system: the role of planetesimals
Authors: Đošović Vladimir , Novakovć Bojan , Vukotć Branislav , Ćirković Milan M
Published: June 2020

Observational data suggest that a belt of planetesimals is expected close to the snow line in protoplanetary discs. Assuming there is such a belt in the TRAPPIST-1 system, we examine possibilities of water delivery to the planets via planetesimals from the belt. The study is accomplished by numerical simulations of dynamical evolution of a hypothetical planetesimal belt. Our results show that the inner part of the belt is dynamically unstable and planetesimals located in this region are quickly scattered away, with many of them entering the region around the planets. The main dynamical mechanism responsible for the instability are close encounters with the outermost planet Trappist-1h. A low-order mean-motion resonance 2:3 with Trappist-1h, located in the same region, also contributes to the objects transport. In our nominal model, the planets have received a non-negligible amount of water, with the smallest amount of 15 per cent of the current Earth’s water amount (EWA) being delivered to the planet 1b, while the planets Trappist-1e and Trappist-1g have received more than 60 per cent of the EWA. We have found that while the estimated efficiency of water transport to the planets is robust, the amount of water delivered to each planet may vary significantly, depending on the initial masses and orbits of the planets. The estimated dynamical ‘half-lives’ have shown that the impactors’ source region should be emptied in less then 1 Myr. Therefore, the obtained results suggest that the transport of planetesimals through the system preferably occurs during an early phase of the planetary system evolution.
A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals
Authors: Turakhia Yatish , Chen Heidi I , Marcovitz Amir , Bejerano Gill
Published: June 2020

Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (amino acid deletions and substitutions) and sister species support as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using human as reference, we discovered over 400 unique human ortholog erosion events across 58 mammals. This includes dozens of clade-specific losses of genes that result in early mouse lethality or are associated with severe human congenital diseases. Our discoveries yield intriguing potential for translational medical genetics and evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.
Anti-inflammatory functions of the glucocorticoid receptor require DNA binding
Authors: Escoter-Torres Laura , Greulich Franziska , Quagliarini Fabiana , Wierer Michael , Uhlenhaut Nina Henriette
Published: June 2020

The glucocorticoid receptor is an important immunosuppressive drug target and metabolic regulator that acts as a ligand-gated transcription factor. Generally, GR’s anti-inflammatory effects are attributed to the silencing of inflammatory genes, while its adverse effects are ascribed to the upregulation of metabolic targets. GR binding directly to DNA is proposed to activate, whereas GR tethering to pro-inflammatory transcription factors is thought to repress transcription. Using mice with a point mutation in GR’s zinc finger, that still tether via protein–protein interactions while being unable to recognize DNA, we demonstrate that DNA binding is essential for both transcriptional activation and repression. Performing ChIP-Seq, RNA-Seq and proteomics under inflammatory conditions, we show that DNA recognition is required for the assembly of a functional co-regulator complex to mediate glucocorticoid responses. Our findings may contribute to the development of safer immunomodulators with fewer side effects.
Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei
Authors: Aphasizheva Inna , Yu Tian , Suematsu Takuma , Liu Qiushi , Mesitov Mikhail V , Yu Clinton , Huang Lan , Zhang Liye , Aphasizhev Ruslan
Published: June 2020

In Trypanosoma brucei, mitochondrial pre-mRNAs undergo 3′-5′ exonucleolytic processing, 3′ adenylation and uridylation, 5′ pyrophosphate removal, and, often, U-insertion/deletion editing. The 3′ modifications are modulated by pentatricopeptide repeat (PPR) Kinetoplast Polyadenylation Factors (KPAFs). We have shown that KPAF3 binding to the 3′ region stabilizes properly trimmed transcripts and stimulates their A-tailing by KPAP1 poly(A) polymerase. Conversely, poly(A) binding KPAF4 shields the nascent A-tail from uridylation and decay thereby protecting pre-mRNA upon KPAF3 displacement by editing. While editing concludes in the 5′ region, KPAF1/2 dimer induces A/U-tailing to activate translation. Remarkably, 5′ end recognition and pyrophosphate hydrolysis by the PPsome complex also contribute to mRNA stabilization. Here, we demonstrate that KPAF4 functions as a heterodimer with KPAF5, a protein lacking discernable motifs. We show that KPAF5 stabilizes KPAF4 to enable poly(A) tail recognition, which likely leads to mRNA stabilization during the editing process and impedes spontaneous translational activation of partially-edited transcripts. Thus, KPAF4/5 represents a poly(A) binding element of the mitochondrial polyadenylation complex. We present evidence that RNA editing substrate binding complex bridges the 5′ end-bound PPsome and 3′ end-bound polyadenylation complexes. This interaction may enable mRNA circularization, an apparently critical element of mitochondrial mRNA stability and quality control.
A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics
Authors: Deprey Kirsten , Batistatou Nefeli , Kritzer Joshua A
Published: June 2020

RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo
Authors: Yang Minglei , Woolfenden Hugh C , Zhang Yueying , Fang Xiaofeng , Liu Qi , Vigh Maria L , Cheema Jitender , Yang Xiaofei , Norris Matthew , Yu Sha , Carbonell Alberto , Brodersen Peter , Wang Jiawei , Ding Yiliang
Published: June 2020

MicroRNA (miRNA)-mediated cleavage is involved in numerous essential cellular pathways. miRNAs recognize target RNAs via sequence complementarity. In addition to complementarity, in vitro and in silico studies have suggested that RNA structure may influence the accessibility of mRNAs to miRNA-induced silencing complexes (miRISCs), thereby affecting RNA silencing. However, the regulatory mechanism of mRNA structure in miRNA cleavage remains elusive. We investigated the role of in vivo RNA secondary structure in miRNA cleavage by developing the new CAP-STRUCTURE-seq method to capture the intact mRNA structurome in Arabidopsis thaliana. This approach revealed that miRNA target sites were not structurally accessible for miRISC binding prior to cleavage in vivo. Instead, we found that the unfolding of the target site structure plays a key role in miRISC activity in vivo. We found that the single-strandedness of the two nucleotides immediately downstream of the target site, named Target Adjacent nucleotide Motif, can promote miRNA cleavage but not miRNA binding, thus decoupling target site binding from cleavage. Our findings demonstrate that mRNA structure in vivo can modulate miRNA cleavage, providing evidence of mRNA structure-dependent regulation of biological processes.
Assessment of the Subarachnoid Hemorrhage International Trialists (SAHIT) Models for Dichotomized Long-Term Functional Outcome Prediction After Aneurysmal Subarachnoid Hemorrhage in a United Kingdom Multicenter Cohort Study
Authors: Hostettler Isabel C , Pavlou Menelaos , Ambler Gareth , Alg Varinder S , Bonner Stephen , Walsh Daniel C , Bulters Diederik , Kitchen Neil , Brown Martin M , Grieve Joan , Houlden Henry , Werring David J ,   on behalf of the Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study investigators
Published: June 2020

BACKGROUND

Long-term outcome after subarachnoid hemorrhage, beyond the first few months, is difficult to predict, but has critical relevance to patients, their families, and carers.

OBJECTIVE

To assess the performance of the Subarachnoid Hemorrhage International Trialists (SAHIT) prediction models, which were initially designed to predict short-term (90 d) outcome, as predictors of long-term (2 yr) functional outcome after aneurysmal subarachnoid hemorrhage (aSAH).

METHODS

We included 1545 patients with angiographically-proven aSAH from the Genetic and Observational Subarachnoid Haemorrhage (GOSH) study recruited at 22 hospitals between 2011 and 2014. We collected data on age, WNFS grade on admission, history of hypertension, Fisher grade, aneurysm size and location, as well as treatment modality. Functional outcome was measured by the Glasgow Outcome Scale (GOS) with GOS 1 to 3 corresponding to unfavorable and 4 to 5 to favorable functional outcome, according to the SAHIT models. The SAHIT models were assessed for long-term outcome prediction by estimating measures of calibration (calibration slope) and discrimination (area under the receiver-operating characteristic curve [AUC]) in relation to poor clinical outcome.

RESULTS

Follow-up was standardized to 2 yr using imputation methods. All 3 SAHIT models demonstrated acceptable predictive performance for long-term functional outcome. The estimated AUC was 0.71 (95% CI: 0.65-0.76), 0.73 (95% CI: 0.68-0.77), and 0.74 (95% CI: 0.69-0.79) for the core, neuroimaging, and full models, respectively; the calibration slopes were 0.86, 0.84, and 0.89, indicating good calibration.

CONCLUSION

The SAHIT prediction models, incorporating simple factors available on hospital admission, show good predictive performance for long-term functional outcome after aSAH.
Do Politicians Discriminate against Ethnic Minority Constituents? A Field Experiment on Social Interactions between Citizens and Swedish Local Politicians
Authors: Larsson Taghizadeh Jonas , Åström Angelica , Adman Per
Published: June 2020

In ethnically diverse societies, are citizens treated equally by their political representatives? Several field experiments find that politicians discriminate in their daily communication with voters. However, these studies only focus on the USA and South Africa and may overestimate the degree of discrimination by ignoring sex and socio-economic status. We address these shortcomings by investigating ethnic discrimination in Sweden. In an email experiment, all 812 municipal commissioners were randomly contacted by voters with Arabic- or Swedish-sounding names. Our results do not show any clear signs of discrimination; thus, previous results might not be generalisable to Sweden or similar democracies.
Muon and electron g − 2 and the origin of the fermion mass hierarchy
Authors: Haba Naoyuki , Shimizu Yasuhiro , Yamada Toshifumi
Published: June 2020

We present a model that gives a natural explanation to the charged lepton mass hierarchy and study the contributions to the electron and the muon $g-2$. In the model, we introduce lepton-flavor-dependent $U(1)_F$ symmetry and three additional Higgs doublets with $U(1)_F$ charges, to realize that each generation of charged leptons couples to one of the three additional Higgs doublets. The $U(1)_F$ symmetry is softly broken by $+1$ charges, and the smallness of the soft breaking naturally gives rise to the hierarchy of the Higgs vacuum expectation values, which then accounts for the charged lepton mass hierarchy. Since electron and muon couple to different scalar particles, each scalar contributes to the electron and the muon $g-2$ differently. We survey the space of parameters of the Higgs sector and find that there are sets of parameters that explain the muon $g-2$ discrepancy. On the other hand, we cannot find parameter sets that can explain the $g-2$ discrepancy within 2 $\sigma$. Here, the $U(1)_F$ symmetry suppresses charged lepton flavor violation.
Dealing with Community Mental Health post the Fukushima disaster: lessons learnt for the COVID-19 pandemic
Authors: Momoi M , Murakami M , Horikoshi N , Maeda M
Published: June 2020

Under the COVID-19 pandemic, mitigation of psychological distress is required. At present, the demand for remote intervention for the numerous affected people is increasing, and telephonic support can be useful. Since the Fukushima nuclear disaster in 2011, we have been developing a large-scale telephonic support system and implementing brief interventions for the Fukushima people identified at risk of psychological problems such as depression and post-traumatic stress disorder. In this article, we report the lessons from the Fukushima disaster that can be applied to the COVID-19 pandemic and describe how the telephonic intervention facilitates easier access to psychological help for people with a broad range of psychological distress who are not able to visit treatment or care resources. In our telephonic intervention, we first sent a mental health and lifestyle survey to the people affected by the Fukushima disaster. The counselor team then provided telephonic intervention to high-risk persons as identified on the basis of the survey results. The individuals had expected to receive from the telephonic system help mainly in the form of stress-coping methods, social resource information such as schools, public offices or medical facilities, and lifestyle advice. Since we also experienced that psychological care for telephone counselors was necessary to mitigate the substantial emotional burden, we used the following three approaches: (i) regular supervision of the telephone counseling methods, (ii) seminars for improvement of counseling skills and (iii) individual psychological support. The positive loops between counselors and consulters will help advance a society affected by a disaster.
Highly sensitive serum cardiac troponin T and cardiovascular events in patients with systemic lupus erythematosus (TROPOPLUS study)
Authors: Chezel Julie , Costedoat-Chalumeau Nathalie , Laouénan Cedric , Rouzaud Diane , Chenevier-Gobeaux Camille , Le Guern Véronique , Mathian Alexis , Belhadi Drifa , de Almeida Chaves Sébastien , Duhaut Pierre , Fain Olivier , Galicier Lionel , Ghillani-Dalbin Pascale , Kahn Jean Emmanuel , Morel Nathalie , Perard Laurent , Pha Micheline , Saidoune Fanny , Sarrot-Reynauld Francoise , Aumaitre Olivier , Chasset François , Limal Nicolas , Desmurs-Clavel Helene , Ackermann Felix , Amoura Zahir , Papo Thomas , Sacre Karim
Published: June 2020

Objective

Identification of biological markers able to better stratify cardiovascular risks in SLE patients is needed. We aimed to determine whether serum cardiac troponin T (cTnT) levels measured with a highly sensitive assay [high sensitivity cTnT (HS-cTnT)] may predict cardiovascular events (CVEs) in SLE.

Method

All SLE patients included between 2007 and 2010 in the randomized, double-blind, placebo-controlled, multicentre PLUS trial were screened. Patients with no past history of CVE at inclusion and a follow-up period of >20 months were analysed. HS-cTnT concentration was measured using the electrochemiluminescence method on serum collected at PLUS inclusion. The primary outcome was the incident CVE. Factors associated with the primary outcome were identified and multivariate analysis was performed.

Results

Overall, 442 SLE patients (of the 573 included in the PLUS study) were analysed for the primary outcome with a median follow up of 110 (interquartile range: 99–120) months. Among them, 29 (6.6%) experienced at least one CVE that occurred at a median of 67 (interquartile range: 31–91) months after inclusion. Six out of 29 patients had more than one CVE. In the multivariate analysis, dyslipidaemia, age and HS-cTnT were associated with the occurrence of CVE. Kaplan–Meier analysis showed that a concentration of HS-cTnT > 4.27 ng/l at inclusion increased by 2.7 [hazard ratio 2.7 (95% CI: 1.3, 5.6), P =0.0083] the risk of CVE in SLE.

Conclusion

HS-cTnT measured in serum is the first identified biomarker independently associated with incident CVE in SLE patients.
RF-EMF EXPOSURE LEVELS IN SENSITIVE LAND USE IN GREECE: EDUCATIONAL UNITS CENSUS IN THE MUNICIPALITY OF KORYDALLOS
Authors: Alexias Aris , Kiouvrekis Yiannis , Softa Vasiliki , Kappas Constantin , Tyrakis Charilaos , Theodorou Kiki
Published: June 2020

Background

The growing popularity of mobile phones and the expansion of network infrastructure in Greece have raised concerns about the possible negative health effects on sensitive groups, such as children, from exposure to long-term radiofrequency electromagnetic fields (RF-EMFs).

Aims

The objective of this study is to estimate mean RF-EMF exposure levels of primary and secondary education schools located in the municipality of Korydallos, Athens, Greece.

Methods

We performed measurements to all the schools units ($n=62$) in the region in order to calculate the mean value for RF-EMF exposure in the range of 27 MHz–3 GHz, which covers the whole spectrum of RF-EMF sources.

Results

At the $97.5\%$ of schools found in Korydallos region, the exposure level is at least 2200 times below the Greek exposure limits.

Conclusion

The exposure levels in the locations tested are both below $60\%$ of the highest limit set by the International Commission on Non-Ionizing Radiation Protection regarding school exposures.
Gender Regimes in the Middle East and North Africa: The Power of Feminist Movements
Authors: Moghadam Valentine M
Published: June 2020

Applying Walby’s model of gender regime, with some modifications, to the Middle East and North Africa, I highlight the importance of the family as an institutional domain, replace the ideal types of social-democratic and neoliberal public gender regimes with neopatriarchal and conservative-corporatist, and elucidate feminist organizing and mobilizing as a key driver in the transition from one public gender regime to another in Algeria, Morocco, and Tunisia. The article contributes to theory-building on (varieties of) gender regimes by underscoring (sub)regional specificities across the capitalist world-system’s economic zones and emphasizing the role of feminist activism.
Relationship between genetic knowledge and familial communication of CRC risk and intent to communicate CRCP genetic information: insights from FamilyTalk eMERGE III
Authors: Makhnoon Sukh , Bowen Deborah J , Shirts Brian H , Fullerton Stephanie M , Meischke Hendrika W , Larson Eric B , Ralston James D , Leppig Kathleen , Crosslin David R , Veenstra David , Jarvik Gail P
Published: June 2020

Successful translation of genetic information into patient-centered care and improved outcomes depends, at least in part, on patients’ genetic knowledge. Although genetic knowledge is believed to be an important facilitator of familial communication of genetic risk information, empirical evidence of this association is lacking. We examined whether genetic knowledge was related to frequency of current familial communication about colorectal cancer and polyp (CRCP) risk, and future intention to share CRCP-related genomic test results with family members in a clinical sample of patients. We recruited 189 patients eligible for clinical CRCP sequencing to the eMERGE III FamilyTalk randomized controlled trial and surveyed them about genetic knowledge and familial communication at baseline. Participants were primarily Caucasian, 47% male, average age of 68 years, mostly well educated, and with high-income levels. Genetic knowledge was positively associated with future-intended familial communication of genetic information (odds ratio = 1.11, 95% confidence interval: 1.02–1.23), but not associated with current communication of CRC risk (β = 0.01, p = .58). Greater current communication of CRC risk was associated with better family functioning (β = 0.04, p = 8.2e-5). Participants’ genetic knowledge in this study was minimally associated with their intended familial communication of genetic information. Although participants have good intentions of communication, family-level factors may hinder actual follow through of these intentions. Continued focus on improving proband’s genetic knowledge coupled with interventions to overcome family-level barriers to communication may be needed to improve familial communication rates.
Screening Andean Diversity Panel Dry Bean Lines for Resistance to Bacterial Brown Spot Disease Under Field Conditions in South Africa
Authors: Salegua Venâncio , Melis Rob , Fourie Deidré , Sibiya Julia , Musvosvi Cousin
Published: June 2020

Bacterial brown spot (BBS) disease caused by Pseudomonas syringae pv. syringae is an important disease of dry bean (Phaseolus vulgaris L.), with grain yield losses of 55% reported in South Africa. This study aimed to identify BBS disease-resistant genotypes from 415 Andean Diversity Panel (ADP) dry bean lines and 5 check cultivars under field conditions across three sites in South Africa: Warden and Middelburg under natural infestation and Potchefstroom under artificial inoculation. Plants at Potchefstroom were inoculated with P. syringae pv. syringae using three isolates at 21, 28, and 36 days after planting, and disease scoring was done at 7, 14, and 21 days after inoculation following a modified 1 to 9 International Centre for Tropical Agriculture (CIAT) scale. The BBS severity percentage and the area under the disease progress curve (AUDPC) were applied to quantify the reaction of bean genotypes to BBS disease. The study identified 17.2% of evaluated germplasm as resistant and 45.3% as moderately resistant. Genotypes ADP-0592, ADP-0790, ADP-0120, and ADP-0008 were selected for both resistance and high seed yield across the three environments. Genotypes ADP-0546, ADP-0630, ADP-0120, and ADP-0279 were selected for both high yield and resistance at Warden, whereas ADP-0038, ADP-0721, and ADP-0790 were selected for both traits at Middelburg, and lastly, ADP-0120 and ADP-0079 were selected for both traits at Potchefstroom. The best genotypes selected for both high yield and BBS resistance had grain yield >1.45 t ha−1 across sites and >1.85 t ha−1 at individual sites, and they out yielded the best-performing check cultivar (1.13 t ha−1) and the grand mean yield (0.87 t ha−1) across sites. The AUDPC had a strong negative correlation (r = −0.55, P < 0.001) with grain yield at Potchefstroom. Medium-seeded genotypes showed a lower AUDPC than the large-seeded genotypes, and indeterminate genotypes showed a lower AUDPC than determinate genotypes. The genotypes selected for resistance and yield can be utilized in future dry bean improvement efforts for the South African bean market.
Selecting Instruments for Measuring the Clinical Learning Environment of Medical Education: A 4-Domain Framework
Authors: Irby David M. , O’Brien Bridget C. , Stenfors Terese , Palmgren Per J.
Published: June 2020

Learning environments shape the experiences of learners and practitioners, making them an important component of program evaluation. However, educators find it challenging to decide whether to measure clinical learning environments with existing instruments or to design their own new instrument and, if using an existing instrument, which to choose. To assist educators with these decisions, the authors compared clinical learning environment instruments based on their characteristics, underlying constructs, and degree to which items reflect 4 domains (personal, social, organizational, material) from a recently developed model for conceptualizing learning environments in the health professions. Building on 3 prior literature reviews as well as a literature search, the authors identified 6 clinically oriented learning environment instruments designed for medical education. They collected key information about each instrument (e.g., number of items and subscales, conceptual frameworks, operational definitions of the learning environment) and coded items from each instrument according to the 4 domains. The 6 instruments varied in number of items, underlying constructs, subscales, definitions of clinical learning environment, and domain coverage. Most instruments focused heavily on the organizational and social domains and less on the personal and material domains (half omitted the material domain entirely). The variations in these instruments suggest that educators might consider several guiding questions. How will they define the learning environment and which theoretical lens is most applicable (e.g., personal vitality, sociocultural learning theory)? What aspects or domains of the learning environment do they most wish to capture (e.g., personal support, social interactions, organizational culture, access to resources)? How comprehensive do they want the instrument to be (and correspondingly how much time do they expect people to devote to completing the instrument and how frequently)? Whose perspective do they wish to evaluate (e.g., student, resident, fellow, attending, team, patient)? Each of these considerations is addressed.
UC Davis Train-the-Trainer Primary Care Pain Management Fellowship: Addressing the Pain Management Education Gap
Authors: Fishman Scott M. , Copenhaver David , Lorenzen Kathryn , Schlingmann Ellery , Chung Christy
Published: June 2020

Problem

Primary care providers are responsible for the majority of pain care and opioid prescribing, but they are often inadequately trained. Training current providers to address the crisis of excessive opioid prescribing and inadequate pain management is a substantial workforce problem that requires urgent action. This educational need is vast and requires a staged solution to amplify its effect.

Approach

The University of California, Davis Train-the-Trainer (T3) Primary Care Pain Management Fellowship targets the most pressing topics related to pain management, including prescription drug abuse, responsible opioid prescribing, and substance abuse, as well as broad coverage of comprehensive pain management. It offers an innovative, scalable solution to address the education gap in pain management that, in part, fuels the opioid epidemic in the United States. The T3 Fellowship incorporates a competency-based curriculum and a hybrid educational model of in-person and distance-based learning and direct faculty–fellow mentoring to comprehensively train primary care providers in pain care and prepare them to train others. Since it was established in 2017, 2 cohorts (of 17 and 26 fellows) have completed the 10-month fellowship and a third cohort of 38 fellows started the program in September 2019.

Outcomes

Pre- and postprogram surveys for the first 2 cohorts, and a 6-month postprogram survey for the first cohort, demonstrated fellows’ improvement and sustained performance in pain competencies as well as increased recognition and understanding of pain and related topics.

Next Steps

If adopted by other institutions and expanded across the country, the T3 Fellowship holds potential for developing an ever-growing legion of trained professionals who will locally fill the need for effective pain management, including appropriate opioid prescribing. Advancing this model will require further economic and feasibility studies to assess costs, resources, and other variables, as well as a robust comprehensive outcomes program.
Resident Leadership in the Era of COVID-19: Harnessing Emotional Intelligence
Authors: Ward Heather Burrell
Published: June 2020

The COVID-19 pandemic is a public health emergency that demands leadership throughout the health care system. Leadership is the ability to guide a team or organization toward a stated goal or objective. In addition to hospital-wide leadership, there is need for leadership at the level of medical teams. Resident leadership is essential to ensure team function and patient care, yet residents are often overlooked as valuable leaders. This Perspective argues that residents can demonstrate leadership during a public health crisis by creating a culture of emotional intelligence in their medical teams. Emotional intelligence has been identified as a critical aspect of leadership and consists of self-awareness, self-management, social awareness, and relationship management. In psychiatry, patient interactions depend upon psychiatrists demonstrating a high level of attention to their own thoughts, feelings, and behaviors as well as those of the patient to communicate in a way that demonstrates both understanding and empathy. In this Perspective, a psychiatry resident uses expertise in emotional intelligence to recommend residents (1) be mindful, (2) ask and listen, (3) establish safety, and (4) unite around a common goal. These practical recommendations can be immediately implemented to increase emotional intelligence on medical teams to improve team function and patient care. Emotional intelligence is valuable at all levels of leadership, so hospital leadership and program directors should also heed these suggestions. While these recommendations are not unique to COVID-19, they are of paramount importance during the pandemic.
COVID-19 as a Frying Pan: The Promise and Perils of Pandemic-driven Reform
Authors: del Pozo Brandon , Beletsky Leo , Rich Josiah D.
Published: June 2020

The imposition of new regulations can send industries scrambling to comply, fostering innovation in doing so. How we police and treat people with opioid use disorder (OUD), with recent widespread social unrest in reaction to police violence and systemic racism bringing the need for lasting structural changes to our justice system and social services into especially acute relief. Arbitrary laws and counterproductive policies previously subject to only incremental reform have given way to sweeping changes: people convicted of nonviolent drug crimes have been released from jails and prisons, the enforcement of drug laws has been cast aside as a priority, and the regulations surrounding addiction treatment medications and treating patients with OUD have been greatly loosened. These are changes many practitioners and advocates have sought for years if not decades, but they come with the reality that the old systems are culturally entrenched and likely to be resilient. It is critical that researchers evaluate these changes and synthesize the results with existing evidence in ways that empower efforts to make the most effective responses permanent. The COVID-19 pandemic makes for a challenging research environment, but its OUD-related interventions have created new regulatory systems that lend themselves to valuable opportunities for evaluation as natural experiments by the burgeoning field of legal epidemiology.
Global analysis of differentially expressed genes between two Japonica rice varieties induced by low temperature during the booting stage by RNA-Seq
Authors: Guo Zhenhua , Cai Lijun , Liu Chuanxue , Huang Cuihong , Chen Zhiqiang , Pan Guojun , Guo Tao
Published: June 2020

As one of the abiotic stresses, low temperature severely threatens rice production during its entire growth period, especially during the booting stage. In the present study, transcriptome analysis was performed comparing Longjing (LJ) 25 (chilling-tolerant) and LJ 11 (chilling-sensitive) rice varieties to identify genes associated with chilling tolerance in rice spikelets. A total of 23 845 expressed genes and 13 205 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) enrichment analyses revealed ‘response to cold’ (containing 180 DEGs) as the only category enriched in both varieties during the entire cold treatment period. Through M
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M
an
analysis, we identified nine and six DEGs related to the Calvin cycle and antioxidant enzymes, respectively, including
OsRBCS3
,
OsRBCS2
,
OsRBCS4
,
OsAPX2
and
OsCATC
, that under chilling stress were markedly downregulated in LJ11 compared with LJ25. Furthermore, we predicted their protein–protein interaction (PPI) network and identified nine hub genes (the threshold of co-expressed gene number ≥ 11) in Cytoscape, including three RuBisCO-related genes with 14 co-expressed genes. Under chilling stress, antioxidant enzyme activities (peroxidase (POD) and catalase (CAT)) were downregulated in LJ11 compared with LJ25. However, the content of malondialdehyde (MDA) was higher in LJ11 compared with LJ25. Collectively, our findings identify low temperature responsive genes that can be effectively used as candidate genes for molecular breeding programmes to increase the chilling tolerance of rice.
Development of bacterial cellulose–ZnO–MWCNT hybrid membranes: a study of structural and mechanical properties
Authors: El Mrabate Bilal , Udayakumar Mahitha , Csiszár Emília , Kristály Ferenc , Leskó Máté , Somlyai Sipos László , Schabikowski Mateusz , Németh Zoltán
Published: June 2020

Self-supported and flexible bacterial cellulose (BC) based hybrid membranes were synthesized and decorated with zinc oxide/multi-walled carbon nanotube (ZnO–MWCNT) composite additives in order to modify and tune their surface and bulk properties. Two types of ZnO–MWCNT additives with different morphologies were used in a wide concentration range from 0 to 90% for BC-based hybrids produced by filtration. The interaction between BC and ZnO–MWCNT and the effect of concentration and morphology of additives on the properties like zeta potential, hydrophilicity, electrical conductivity, etc. would be an important factor in various applications. Furthermore, the as-prepared hybrid membranes were characterized with the use of scanning electron microscopy (SEM), focused ion beam scanning electron microscopy (FIB-SEM), energy dispersive X-ray spectroscopy (EDS), X-ray powder diffraction (XRD) and surface area measurement (BET). Applying the presented synthesis routes, the surface properties of BC-based membranes can be tailored easily. Results reveal that the as-prepared BC–ZnO–MWCNT hybrid membranes can be ideal candidates for different kinds of applications, such as water filtration or catalysts.
Weekly COVID-19 testing with household quarantine and contact tracing is feasible and would probably end the epidemic
Authors: Peto Julian , Carpenter James , Smith George Davey , Duffy Stephen , Houlston Richard , Hunter David J. , McPherson Klim , Pearce Neil , Romer Paul , Sasieni Peter , Turnbull Clare
Published: June 2020

The COVID-19 epidemic can probably be ended and normal life restored, perhaps quite quickly, by weekly SARS-CoV-2 RNA testing together with household quarantine and systematic contact tracing. Isolated outbreaks could then be contained by contact tracing, supplemented if necessary by temporary local reintroduction of population testing or lockdown. Leading public health experts have recommended that this should be tried in a demonstration project in which a medium-sized city introduces weekly testing and lifts lockdown completely. The idea was not considered by the groups whose predictions have guided UK policy, so we have examined the statistical case for such a study. The combination of regular testing with strict household quarantine, which was not analysed in their models, has remarkable power to reduce transmission to the community from other household members as well as providing earlier diagnosis and facilitating rapid contact tracing.
Patterns of annual and seasonal immune investment in a temporal reproductive opportunist
Authors: Schultz Elizabeth M. , Gunning Christian E. , Cornelius Jamie M. , Reichard Dustin G. , Klasing Kirk C. , Hahn Thomas P.
Published: June 2020

Historically, investigations of how organismal investments in immunity fluctuate in response to environmental and physiological changes have focused on seasonally breeding organisms that confine reproduction to seasons with relatively unchallenging environmental conditions and abundant resources. The red crossbill,Loxia curvirostra, is a songbird that can breed opportunistically if conifer seeds are abundant, on both short, cold, and long, warm days, providing an ideal system to investigate environmental and reproductive effects on immunity. In this study, we measured inter- and intra-annual variation in complement, natural antibodies, PIT54 and leucocytes in crossbills across four summers (2010–2013) and multiple seasons within 1 year (summer 2011–spring 2012). Overall, we observed substantial changes in crossbill immune investment among summers, with interannual variation driven largely by food resources, while variation across multiple seasons within a single cone year was less pronounced and lacked a dominant predictor of immune investment. However, we found weak evidence that physiological processes (e.g. reproductive condition, moult) or abiotic factors (e.g. temperature, precipitation) affect immune investment. Collectively, this study suggests that a reproductively flexible organism may be able to invest in both reproduction and survival-related processes, potentially by exploiting rich patches with abundant resources. More broadly, these results emphasize the need for more longitudinal studies of trade-offs associated with immune investment.
Quantitative proteomics reveals rapid divergence in the postmating response of female reproductive tracts among sibling species
Authors: McCullough Erin L. , McDonough Caitlin E. , Pitnick Scott , Dorus Steve
Published: June 2020

Fertility depends, in part, on interactions between male and female reproductive proteins inside the female reproductive tract (FRT) that mediate postmating changes in female behaviour, morphology, and physiology. Coevolution between interacting proteins within species may drive reproductive incompatibilities between species, yet the mechanisms underlying postmating–prezygotic (PMPZ) isolating barriers remain poorly resolved. Here, we used quantitative proteomics in siblingDrosophilaspecies to investigate the molecular composition of the FRT environment and its role in mediating species-specific postmating responses. We found that (i) FRT proteomes inD. simulansandD. mauritianavirgin females express unique combinations of secreted proteins and are enriched for distinct functional categories, (ii) mating induces substantial changes to the FRT proteome inD. mauritianabut not inD. simulans, and (iii) theD. simulansFRT proteome exhibits limited postmating changes irrespective of whether females mate with conspecific or heterospecific males, suggesting an active female role in mediating reproductive interactions. Comparisons with similar data in the closely related outgroup speciesD. melanogastersuggest that divergence is concentrated on theD. simulanslineage. Our study suggests that divergence in the FRT extracellular environment and postmating response contribute to previously described patterns of PMPZ isolation and the maintenance of species boundaries.
Polaribacter septentrionalilitoris sp. nov., isolated from the biofilm of a stone from the North Sea
Authors: Choo Simeon , Borchert Erik , Wiese Jutta , Saha Mahasweta , Künzel Sven , Weinberger Florian , Hentschel Ute
Published: June 2020

A new member of the family

Flavobacteriaceae

was isolated from the biofilm of a stone at Nordstrand, a peninsula at the German North Sea shore. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain ANORD1T was most closely related to the validly described type strains

Polaribacter porphyrae

LNM-20T (97.0 %) and

Polaribacter reichenbachii

KMM 6386T (96.9 % 16S rRNA gene sequence similarity) and clustered with

Polaribacter gangjinensis

K17-16T (96.0 %). Strain ANORD1T was determined to be mesophilic, Gram-negative, non-motile and strictly aerobic. Optimal growth was observed at 20–30 °C, within a salinity range of 2–7 % sea salt and from pH 7–10. Like other type strains of the genus

Polaribacter

, ANORD1T was tested negative for flexirubin-type pigments, while carotenoid-type pigments were detected. The DNA G+C content of strain ANORD1T was 30.6 mol%. The sole respiratory quinone detected was menaquinone 6 (MK-6). The major fatty acids identified were C15 : 0, iso-C15 : 0, C15 : 1 ω6c and iso-C15 : 0 3-OH. Based on the polyphasic approach, strain ANORD1T represents a novel species in the genus

Polaribacter

, with the name Polaribacter septentrionalilitoris sp. nov. being proposed. The type strain is ANORD1T (=DSM 110039T=NCIMB 15081T=MTCC 12685T).
Insights into SARS-CoV-2, the Coronavirus Underlying COVID-19: Recent Genomic Data and the Development of Reverse Genetics Systems
Authors: Silva Severino Jefferson Ribeiro da , Germano Mendes Renata Pessôa , Alves da Silva Caroline Targino , Lorusso Alessio , Kohl Alain , Pena Lindomar
Published: June 2020

The emergence and rapid worldwide spread of a novel pandemic of acute respiratory disease – eventually named coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO) – across the human population has raised great concerns. It prompted a mobilization around the globe to study the underlying pathogen, a close relative of severe acute respiratory syndrome coronavirus (SARS-CoV) called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Numerous genome sequences of SARS-CoV-2 are now available and in-depth analyses are advancing. These will allow detailed characterization of sequence and protein functions, including comparative studies. Care should be taken when inferring function from sequence information alone, and reverse genetics systems can be used to unequivocally identify key features. For example, the molecular markers of virulence, host range and transmissibility of SARS-CoV-2 can be compared to those of related viruses in order to shed light on the biology of this emerging pathogen. Here, we summarize some recent insights from genomic studies and strategies for reverse genetics systems to generate recombinant viruses, which will be useful to investigate viral genome properties and evolution.
Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia
Authors: Tania Tryna , Sudarmono Pratiwi , Kusumawati R. Lia , Rukmana Andriansjah , Pratama Wahyu Agung , Regmi Sanjib Mani , Kaewprasert Orawee , Chaiprasert Angkana , Chongsuvivatwong Virasakdi , Faksri Kiatichai
Published: June 2020

Introduction. Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia.

Aim. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant

Mycobacterium tuberculosis

in Java, Indonesia.

Methodology. Thirty suspected MDR-TB isolates were subjected to MGIT 960 system (MGIT)-based DST and to WGS. Phylogenetic analysis was done using the WGS data. Results obtained using MGIT-based DST and WGS-based DST were compared.

Results. Agreement between WGS and MGIT was 93.33 % for rifampicin, 83.33 % for isoniazid and 76.67 % for streptomycin but only 63.33 % for ethambutol. Moderate WGS–MGIT agreement was found for second-line drugs including amikacin, kanamycin and fluoroquinolone (73.33–76.67 %). MDR-TB was more common in isolates of the East Asian Lineage (63.3%). No evidence of clonal transmission of DR-TB was found among members of the tested population.

Conclusion. Our study demonstrated the applicability of WGS for DST and molecular epidemiology of DR-TB in Java, Indonesia. We found no transmission of DR-TB in Indonesia.