bluuebunny/crossref_metadata_2025_split huggingface dataset:
Women’s Work-Family Histories and Cognitive Performance in Later Life
Authors: Ice Erin , Ang Shannon , Greenberg Karra , Burgard Sarah 
Published: March 2020

Abstract
Long-term exposures to the stress and stimulation of different work, parenting, and partnership combinations might influence later life cognition. We investigated the relationship between women’s work-family life histories and cognitive functioning in later life. Analyses were based on data from women born between 1930 and 1957 in 14 European countries, from the Survey of Health, Ageing and Retirement in Europe (2004–2009) (n = 11,908). Multichannel sequence analysis identified 5 distinct work-family typologies based on women’s work, partnership, and childrearing statuses between ages 12 and 50 years. Multilevel regressions were used to test the association between work-family histories and later-life cognition. Partnered mothers who mainly worked part-time had the best cognitive function in later life, scoring approximately 0.63 (95% confidence interval (CI): 0.18, 1.07) points higher than mothers who worked full-time on a 19-point scale. Partnered mothers who were mainly unpaid caregivers or who did other unpaid activities had cognitive scores that were 1.19 (95% CI: 0.49, 1.89) and 0.93 (95% CI: 0.20, 1.66) points lower than full-time working mothers. The findings are robust to adjustment for childhood advantage and educational credentials. This study provides new evidence that long-term exposures to certain social role combinations after childhood and schooling are linked to later-life cognition.
Flower orientation in Gloriosa superba (Colchicaceae) promotes cross-pollination via butterfly wings
Authors: Daniels Ryan J , Johnson Steven D , Peter Craig I 
Published: March 2020

AbstractBackground and AimsComplex modifications of angiosperm flowers often function for precise pollen placement on pollinators and to promote cross-pollination. We explore the functional significance of the unusually elaborate morphology of Gloriosa superba flowers, which are divided into one hermaphrodite meranthium and five male meranthia (functional pollination units of a single flower).MethodsWe used controlled pollination experiments, floral measurements, pollen load analyses and visitor observations in four populations of G. superba in South Africa to determine the breeding system, mechanism of pollination and role of flower in the promotion of cross-pollination.Key ResultsWe established that G. superba is self-compatible, but reliant on pollinators for seed production. Butterflies, in particular the pierid Eronia cleodora, were the primary pollinators (&gt;90 % of visitors). Butterflies brush against the anthers and stigma during nectar feeding and pollen is carried on their ventral wing surfaces. Butterfly scales were positively correlated with the number of pollen grains on stigmas. We demonstrate that the styles were orientated towards clearings in the vegetation and we confirm that the highest proportion of initial visits was to hermaphrodite meranthia pointing towards clearings.ConclusionsThe flower morphology of G. superba results in effective pollen transfer on the wings of butterfly visitors. The style-bearing hermaphrodite meranthium of the flowers orientates towards open spaces in the vegetation, thus increasing the probability that butterflies land first on the hermaphrodite meranthium. This novel aspect of flower orientation is interpreted as a mechanism that promotes cross-pollination.
VirusCircBase: a database of virus circular RNAs
Authors: Cai Zena , Fan Yunshi , Zhang Zheng , Lu Congyu , Zhu Zhaozhong , Jiang Taijiao , Shan Tongling , Peng Yousong 
Published: March 2020

AbstractCircular RNAs (circRNAs) are covalently closed long noncoding RNAs critical in diverse cellular activities and multiple human diseases. Several cancer-related viral circRNAs have been identified in double-stranded DNA viruses (dsDNA), yet no systematic study about the viral circRNAs has been reported. Herein, we have performed a systematic survey of 11 924 circRNAs from 23 viral species by computational prediction of viral circRNAs from viral-infection-related RNA sequencing data. Besides the dsDNA viruses, our study has also revealed lots of circRNAs in single-stranded RNA viruses and retro-transcribing viruses, such as the Zika virus, the Influenza A virus, the Zaire ebolavirus, and the Human immunodeficiency virus 1. Most viral circRNAs had reverse complementary sequences or repeated sequences at the flanking sequences of the back-splice sites. Most viral circRNAs only expressed in a specific cell line or tissue in a specific species. Functional enrichment analysis indicated that the viral circRNAs from dsDNA viruses were involved in KEGG pathways associated with cancer. All viral circRNAs presented in the current study were stored and organized in VirusCircBase, which is freely available at http://www.computationalbiology.cn/ViruscircBase/home.html and is the first virus circRNA database. VirusCircBase forms the fundamental atlas for the further exploration and investigation of viral circRNAs in the context of public health.
Redundancy-weighting the PDB for detailed secondary structure prediction using deep-learning models
Authors: Sidi Tomer , Keasar Chen 
Published: March 2020

Abstract

Motivation
The Protein Data Bank (PDB), the ultimate source for data in structural biology, is inherently imbalanced. To alleviate biases, virtually all structural biology studies use nonredundant (NR) subsets of the PDB, which include only a fraction of the available data. An alternative approach, dubbed redundancy-weighting (RW), down-weights redundant entries rather than discarding them. This approach may be particularly helpful for machine-learning (ML) methods that use the PDB as their source for data. Methods for secondary structure prediction (SSP) have greatly improved over the years with recent studies achieving above 70% accuracy for eight-class (DSSP) prediction. As these methods typically incorporate ML techniques, training on RW datasets might improve accuracy, as well as pave the way toward larger and more informative secondary structure classes.

Results
This study compares the SSP performances of deep-learning models trained on either RW or NR datasets. We show that training on RW sets consistently results in better prediction of 3- (HCE), 8- (DSSP) and 13-class (STR2) secondary structures.

Availability and implementation
The ML models, the datasets used for their derivation and testing, and a stand-alone SSP program for DSSP and STR2 predictions, are freely available under LGPL license in http://meshi1.cs.bgu.ac.il/rw.

Supplementary information
Supplementary data are available at Bioinformatics online.
Deep brain stimulation modulates directional limbic connectivity in obsessive-compulsive disorder
Authors: Fridgeirsson Egill Axfjord , Figee Martijn , Luigjes Judy , van den Munckhof Pepijn , Schuurman P Richard , van Wingen Guido , Denys Damiaan 
Published: March 2020

Abstract
Deep brain stimulation is effective for patients with treatment-refractory obsessive-compulsive disorder. Deep brain stimulation of the ventral anterior limb of the internal capsule rapidly improves mood and anxiety with optimal stimulation parameters. To understand these rapid effects, we studied functional interactions within the affective amygdala circuit. We compared resting state functional MRI data during chronic stimulation versus 1 week of stimulation discontinuation in patients, and obtained two resting state scans from matched healthy volunteers to account for test-retest effects. Imaging data were analysed using functional connectivity analysis and dynamic causal modelling. Improvement in mood and anxiety following deep brain stimulation was associated with reduced amygdala-insula functional connectivity. Directional connectivity analysis revealed that deep brain stimulation increased the impact of the ventromedial prefrontal cortex on the amygdala, and decreased the impact of the amygdala on the insula. These results highlight the importance of the amygdala circuit in the pathophysiology of obsessive-compulsive disorder, and suggest a neural systems model through which negative mood and anxiety are modulated by stimulation of the ventral anterior limb of the internal capsule for obsessive-compulsive disorder and possibly other psychiatric disorders.
Theorizing Dependency Relations in Small Media
Authors: Semujju Brian 
Published: March 2020

AbstractThe paper questions the pervasive western intellectual universalism which disregards Global South imaginations for generalized approaches. Using field data from Uganda about Community Audio Towers (CATs), the western-generated community media theory is interrogated, accentuating its failure to account for the intricate relationship between the individual, society, and small media. To cover the gap, the Small Media System Dependency theory is herein introduced as a geocultural response to lack of theory from the South.
Straw decreased N2O emissions from flooded paddy soils via altering denitrifying bacterial community compositions and soil organic carbon fractions
Authors: Wang Ning , Luo Jia-Lin , Juhasz Albert L , Li Hong-Bo , Yu Jian-Guang 
Published: March 2020

ABSTRACT
Straw return is widely applied to increase soil fertility and soil organic carbon storage. However, its effect on N2O emissions from paddy soil and the associated microbial mechanisms are still unclear. In this study, wheat straw was amended to two paddy soils (2% w/w) from Taizhou (TZ) and Yixing (YX), China, which were flooded and incubated for 30 d. Real-time PCR and Illumina sequencing were used to characterize changes in denitrifying functional gene abundance and denitrifying bacterial communities. Compared to unamended controls, straw addition significantly decreased accumulated N2O emissions in both TZ (5071 to 96 mg kg–1) and YX (1501 to 112 mg kg–1). This was mainly due to reduced N2O production with decreased abundance of major genera of nirK and nirS-bacterial communities and reduced nirK and nirS gene abundances. Further analyses showed that nirK-, nirS- and nosZ-bacterial community composition shifted mainly along the easily oxidizable carbon (EOC) arrows following straw amendment among four different soil organic carbon fractions, suggesting that increased EOC was the main driver of alerted denitrifying bacterial community composition. This study revealed straw return suppressed N2O emission via altering denitrifying bacterial community compositions and highlighted the importance of EOC in controlling denitrifying bacterial communities.
Glyphosate-based herbicide affects the composition of microbes associated with Colorado potato beetle (Leptinotarsa decemlineata)
Authors: Gómez-Gallego Carlos , Rainio Miia J , Collado M Carmen , Mantziari Anastasia , Salminen Seppo , Saikkonen Kari , Helander Marjo 
Published: March 2020

ABSTRACT
Here, we examined whether glyphosate affects the microbiota of herbivores feeding on non-target plants. Colorado potato beetles (Leptinotarsa decemlineata) were reared on potato plants grown in pots containing untreated soil or soil treated with glyphosate-based herbicide (GBH). As per the manufacturer's safety recommendations, the GBH soil treatments were done 2 weeks prior to planting the potatoes. Later, 2-day-old larvae were introduced to the potato plants and then collected in two phases: fourth instar larvae and adults. The larvae's internal microbiota and the adults’ intestinal microbiota were examined by 16S rRNA gene sequencing. The beetles’ microbial composition was affected by the GBH treatment and the differences in microbial composition between the control and insects exposed to GBH were more pronounced in the adults. The GBH treatment increased the relative abundance of Agrobacterium in the larvae and the adults. This effect may be related to the tolerance of some Agrobacterium species to glyphosate or to glyphosate-mediated changes in potato plants. On the other hand, the relative abundances of Enterobacteriaceae, Rhodobacter, Rhizobium and Acidovorax in the adult beetles and Ochrobactrum in the larvae were reduced in GBH treatment. These results demonstrate that glyphosate can impact microbial communities associated with herbivores feeding on non-target crop plants.
Technology-Mediated Communication in Familial Relationships: Moderated-Mediation Models of Isolation and Loneliness
Authors: Burholt Vanessa , Windle Gill , Gott Merryn , Morgan Deborah Jane 
Published: March 2020

Abstract

Background and Objectives
We examined whether technology-mediated communication has functional or emotional equivalence to face-to-face (FtF) contact in familial relationships, by scrutinizing the effects of phone, text/e-mail, and video contact on isolation and loneliness.

Research Design and Methods
We tested whether FtF contact with a relative would mediate the pathway between proximity to family and (i) isolation and (ii) loneliness. We then tested hypotheses that telephone, text/e-mails, and video contact would moderate this mediated pathway. We compared models for younger (&lt;75) and older (≥75) cohorts, expecting to observe moderation effects for text/e-mail and video contact in the younger cohort only. Data were drawn from Wave 2 of CFAS Wales (United Kingdom) study (N = 2,099).

Results
Proximity to a relative had a significant indirect effect on isolation and loneliness through the mediating variable FtF contact. Phone and text/e-mail contact moderated the effect of FtF contact on isolation for all samples. None of the technologies moderated the impact of FtF contact on loneliness for the full sample. Telephone contact had a moderating influence on loneliness for the younger cohort only. Video calls had no significant moderation effect.

Discussion and Implications
Telephone and text/e-mail contact have functional equivalence to FtF contact in familial relationships. None of the forms of technological communication have emotional equivalence to the “gold standard” of embodied presence. The study demonstrates the importance of theorizing about the pathways to isolation and loneliness to better understand the likelihood of implementing successful interventions using technology-mediated communication within families.
Analysis of a model for the formation of fold-type oscillation marks in the continuous casting of steel
Authors: Devine K M , Vynnycky M , Mitchell S L , O’Brien S B G 
Published: March 2020

Abstract
This paper investigates the different possible behaviours of a recent asymptotic model for oscillation-mark formation in the continuous casting of steel, with particular focus on how the results obtained vary when the heat transfer coefficient ($m$), the thermal resistance ($R_{mf}$) and the dependence of the viscosity of the flux powder as a function of temperature, $\mu _{f}\left ( T\right ),$ are changed. It turns out that three different outcomes are possible: (I) the flux remains in molten state and no solid flux ever forms; (II) both molten and solid flux are present, and the profile of the oscillation mark is continuous with respect to the space variable in the casting direction; (III) both molten and solid flux are present, and the profile of the oscillation mark is discontinuous with respect to the space variable in the casting direction. Although (I) gave good agreement with experimental data, it suffered the drawback that solid flux is typically observed during actual continuous casting; this has been rectified in this work via alternative (II). On the other hand, alternative (III) can occur as a result of hysteresis-type phenomenon that is encountered in other flows that involve temperature-dependent viscosity; in the present case, this manifests itself via the possibility of multiple states for the oscillation-mark profile at the instants in time when solid flux begins to form and when it ceases to form.
Results from the Survey of Antibiotic Resistance (SOAR) 2015–18 in Tunisia, Kenya and Morocco: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints
Authors: Torumkuney D , Hammami A , Mezghani Maalej S , Ayed N Ben , Revathi G , Zerouali K , Elmdaghri N , Gachii A K , Morrissey I 
Published: March 2020

Abstract

Objectives
To determine antibiotic susceptibility of community-acquired respiratory tract infection (CA-RTI) isolates of Streptococcus pneumoniae and Haemophilus influenzae collected in 2015–18 from Tunisia, Kenya and Morocco.

Methods
MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

Results
S. pneumoniae isolates from Tunisia (n = 79), Kenya (n = 44) and Morocco (n = 19) and H. influenzae isolates (n = 74) from Tunisia only were collected and analysed. Low antibiotic susceptibility was observed in S. pneumoniae from Tunisia, with &gt;90% susceptible only to the fluoroquinolones (all breakpoints), penicillin (CLSI IV and EUCAST high-dose) and ceftriaxone (CLSI, EUCAST high-dose and PK/PD breakpoints). In addition, isolate susceptibility in Kenya was &gt;90% to amoxicillin and amoxicillin/clavulanic acid (CLSI and PK/PD breakpoints). Antibiotic activity was highest in Morocco, where ≥89.5% of pneumococci were susceptible to most antibiotics, excluding trimethoprim/sulfamethoxazole (68.4% by CLSI or PK/PD and 79%–84.2% by EUCAST), macrolides (79%–84.2% by all breakpoints) and cefaclor (0% by EUCAST and 52.6% by PK/PD). The majority (≥86.5%) of H. influenzae isolates from Tunisia were susceptible to most antibiotics by all available breakpoints, except ampicillin and amoxicillin (almost one-third were β-lactamase positive), trimethoprim/sulfamethoxazole (51.4%–56.8%), cefaclor (1.4% by PK/PD), cefuroxime (4.1% by EUCAST), macrolides (1.4%–2.7% by PK/PD) and cefdinir (66.2% by PK/PD). The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

Conclusions
Low antibiotic susceptibility was observed in S. pneumoniae from Tunisia, but susceptibility was higher in isolates from Kenya and highest in those from Morocco. H. influenzae from Tunisia were highly susceptible to most antibiotics. These factors are important in decision making for empirical therapy of CA-RTIs.
Results from the Survey of Antibiotic Resistance (SOAR) 2016–18 in Vietnam, Cambodia, Singapore and the Philippines: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints
Authors: Torumkuney D , Van P H , Thinh L Q , Koo S H , Tan S H , Lim P Q , Sivhour C , Lamleav L , Somary N , Sosorphea S , Lagamayo E , Morrissey I 
Published: March 2020

Abstract

Objectives
To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates collected from community-acquired respiratory tract infections (CA-RTIs) in 2016–18 in four Asian countries.

Methods
MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

Results
In total, 260 S. pneumoniae and 258 H. influenzae isolates were tested. Pneumococci from Vietnam (n = 161) were the least susceptible, with rates of susceptibility &gt;90% for fluoroquinolones by CLSI breakpoints, ∼60% for amoxicillin, amoxicillin/clavulanic acid and ceftriaxone but &lt;14% for most other agents. Pneumococcal isolates from Cambodia (n = 48) and Singapore (n = 34) showed susceptibilities ranging from ∼30% for trimethoprim/sulfamethoxazole and oral penicillin to 100% for fluoroquinolones. Among isolates of H. influenzae from Cambodia (n = 30), the Philippines (n = 59) and Singapore (n = 80), rates of susceptibility using CLSI breakpoints were &gt;90% for amoxicillin/clavulanic acid, cephalosporins [except cefaclor in Singapore (77.5%)], macrolides and fluoroquinolones; for isolates from Vietnam (n = 89) the rates of susceptibility were &gt;85% only for amoxicillin/clavulanic acid (95.5%), ceftriaxone (100%) and macrolides (87.6%–89.9%). Susceptibility to other antibiotics ranged from 7.9% (trimethoprim/sulfamethoxazole) to 57.3%–59.6% (fluoroquinolones) and 70.8% (cefixime). The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified. A limitation of the study was the small sample sizes and only one or two sites participating per country; however, since susceptibility data are scarce in some of the participating countries any information concerning antibiotic susceptibility is of value.

Conclusions
Antibiotic susceptibility varied across countries and species, with isolates from Vietnam demonstrating the lowest susceptibility. Knowledge of resistance patterns can be helpful for clinicians when choosing empirical therapy options for CA-RTIs.
Results from the Survey of Antibiotic Resistance (SOAR) 2015–17 in Latin America (Argentina, Chile and Costa Rica): data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints
Authors: Torumkuney D , Smayevsky J , Relloso M S , Sucari A , Pennini M , Brilla E , Vilches V , De la Cruz Y , Morrissey I 
Published: March 2020

Abstract

Objectives
To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015–17 from Argentina, Chile and Costa Rica.

Methods
MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

Results
A total of 170 S. pneumoniae and 218 H. influenzae isolates were collected at five centres in Argentina, Chile and Costa Rica in 2015–17. Small S. pneumoniae isolate numbers from Costa Rica (n = 2) meant that these could only be included in the penicillin susceptibility analysis; they were excluded from further country analyses. Around one-third of pneumococcal isolates from Argentina and two-thirds from Chile were non-susceptible to penicillin by CLSI oral or EUCAST low-dose IV breakpoints, but most (≥89%) were susceptible by CLSI IV or EUCAST high-dose breakpoints. Amongst pneumococci from Argentina, about 80% or more were susceptible to most other antibiotics except cefaclor (all breakpoints), cefixime (PK/PD breakpoints), cefuroxime (EUCAST breakpoints) and trimethoprim/sulfamethoxazole (CLSI and PK/PD breakpoints). S. pneumoniae isolates from Chile showed significantly lower susceptibility (P &lt; 0.05) using CLSI breakpoints compared with those from Argentina for many of the antibiotics tested. Among isolates of H. influenzae from Latin America, more than 90% were susceptible to amoxicillin/clavulanic acid (high dose), cefixime, cefpodoxime, ceftriaxone and fluoroquinolones, irrespective of the breakpoints used. The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

Conclusions
Antibiotic susceptibility of H. influenzae isolates was generally high in the Latin American countries studied; however, susceptibility profiles varied for S. pneumoniae by country and depending on the breakpoints used, especially for cefaclor. These factors are important in decision making for empirical therapy of bacterial infections.