bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural discrimination analysis for constraint selection in protein modeling
Authors: Bottino Guilherme F , Ferrari Allan J R , Gozzo Fabio C , Martínez Leandro 
Published: June 2021

Abstract

Motivation
Protein structure modeling can be improved by the use of distance constraints between amino acid residues, provided such data reflects—at least partially—the native tertiary structure of the target system. In fact, only a small subset of the native contact map is necessary to successfully drive the model conformational search, so one important goal is to obtain the set of constraints with the highest true-positive rate, lowest redundancy and greatest amount of information. In this work, we introduce a constraint evaluation and selection method based on the point-biserial correlation coefficient, which utilizes structural information from an ensemble of models to indirectly measure the power of each constraint in biasing the conformational search toward consensus structures.

Results
Residue contact maps obtained by direct coupling analysis are systematically improved by means of discriminant analysis, reaching in some cases accuracies often seen only in modern deep-learning-based approaches. When combined with an iterative modeling workflow, the proposed constraint classification optimizes the selection of the constraint set and maximizes the probability of obtaining successful models. The use of discriminant analysis for the valorization of the information of constraint datasets is a general concept with possible applications to other constraint types and modeling problems.

Availability and implementation
MSA for the targets in this work is available on https://github.com/m3g/2021_Bottino_Biserial. Modeling data supporting the findings of this study was generated at the Center for Computing in Engineering and Sciences, and is available from the corresponding author LM on request.

Supplementary information
Supplementary data are available at Bioinformatics online.
Muslim Social Workers and Imams’ Recommendations in Marital and Child Custody Cases of Persons with Intellectual or Mental Disability
Authors: Leena Badran , Arie Rimmerman 
Published: June 2021

Abstract
Arab society in Israel is undergoing modernisation and secularisation. However, its approach to disability and mental illness is still dominated by religious and traditional stereotypes, as well as folk remedies and community practices. The present study examines differences in Muslim social workers and Imams’ recommendations in marriage/divorce and child custody cases of persons with intellectual disabilities (IDs) or mental illness. The study has two goals: (1) To examine differences in recommendations between Imams and Muslim social workers and (2) to explore variables related to their differential recommendations as observed in their responses to vignettes. Quantitative study using vignettes resembling existing Muslim religious (Sharia) court cases. Muslim social workers (138) and Imams (forty-eight) completed a background questionnaire, a religiosity questionnaire and a questionnaire that included twenty-five vignettes constructed by the researcher based on court rulings, adapted for the study. Muslim social workers tended to consider the religious recommendation when the family of person with ID or mental illness was portrayed in the vignette as religious. The same applied to Imams, albeit to a greater extent. The findings call for raising awareness amongst social workers and academics regarding the importance of religion and tradition in formulating professional recommendations.
Dual inhibition of cMET and EGFR by microRNA-338-5p suppresses metastasis of esophageal squamous cell carcinoma
Authors: Cui Di , Zhu Yun , Yan Dongdong , Lee Nikki P Y , Han Liang , Law Simon , Tsao George S W , Cheung Annie L M 
Published: June 2021

Abstract
MicroRNAs, as a group of post-transcriptional regulators, regulate multiple pathological processes including metastasis during tumor development. Here, we demonstrated the metastasis-suppressive function of microRNA (miR)-338-5p in esophageal squamous cell carcinoma (ESCC). Overexpression of miR-338-5p had inhibitory effect on invasive ability of ESCC cells and extracellular matrix degradation, whereas silencing miR-338-5p had opposite effects. Mechanistically, miR-338-5p directly targeted the 3′ untranslated regions of hepatocellular growth factor receptor cMet (cMET) and epidermal growth factor receptor (EGFR). As a result, miR-338-5p inhibited the downstream signaling cascades of cMET and EGFR and repressed cMET- and EGFR-mediated ESCC cell invasion. Re-expression of cMET or EGFR in miR-338-5p overexpressing ESCC cells was sufficient to derepress ESCC cell invasion both in vitro and in vivo. We further showed that such manipulation downregulated the expression and secretion of matrix metalloproteinases 2 and 9, which resulted in impaired extracellular matrix degradation and cell invasion. Most importantly, systemic delivery of miR-338-5p mimic significantly inhibited metastasis of ESCC cells in nude mice. Taken together, our results uncovered a previously unknown mechanism through which miR-338-5p suppresses ESCC invasion and metastasis by regulating cMET/EGFR-matrix metalloproteinase 2/9 axis and highlighted the potential significance of miR-338-5p-based therapy in treating patients with metastatic ESCC.
Assessment of Olfactory Function in Children and Adolescents: An Overview
Authors: Gellrich Janine , Zickmüller Claudia , Schriever Valentin A 
Published: June 2021

Abstract
Valid and reliable tools for assessing olfactory function are necessary for the diagnosis of olfactory dysfunction. Olfactory testing can be challenging in a pediatric population due to shorter attention span, linguistic development, and lower olfactory experience in this age group. The aim of this article is to present an overview about olfactory tests that are suitable for a pediatric population. Publications were included when reporting new developed methods of psychophysical olfactory testing in children or adaptation and applications of existing olfactory tests for a pediatric population. Olfactory tests for all 3 major aspects of olfactory function—olfactory threshold, odor discrimination, and odor identification—were included. Olfactory tests were evaluated regarding test validity, test reliability, normative data, and test availability. The current literature shows that several tests are available to assess olfactory function in children. Especially odor identification abilities in a pediatric population are well examined and understood. Tests for olfactory threshold and odor discrimination are less frequently used. In terms of the abovementioned evaluation criteria, only a few tests met all or 3 of these 4 criteria. Based on the current literature the following tests can be recommended for valid and reliable olfactory testing in children: “U-Sniff” odor identification test, the “Sniffin’ Sticks” olfactory threshold test, pBOT-6 olfactory threshold and odor identification test, NIH-Toolbox, and Smell Wheel. Age has to be considered when evaluating olfactory function in children.
Identification and Virulence of Cordyceps javanica Strain wf GA17 Isolated From a Natural Fungal Population in Sweetpotato Whiteflies (Hemiptera: Aleyrodidae)
Authors: Wu Shaohui , Toews Michael D , Castrillo Louela A , Barman Apurba K , Cottrell Ted E , Shapiro-Ilan David I 
Published: June 2021

Abstract
A new strain of the entomopathogenic fungus, identified as Cordyceps javanica (Frieder. & Bally) Kepler, B. Shrestha & Spatafora (Hypocreales: Cordycipitaceae) wf GA17, was found naturally infecting the sweetpotato whitefly, Bemisia tabaci (Gennadius) MEAM1 in southern Georgia, US, in September 2017. The fungus was tested for pathogenicity and virulence in comparison with commercially available entomopathogenic fungal strains against several insect species in the laboratory. In specific, it was compared with Cordyceps fumosorosea (Wize) Kepler, B. Shrestha & Spatafora (Hypocreales: Cordycipitaceae) Apopka 97, Beauveria bassiana (Bals.-Criv.) Vuill. (Hypocreales: Cordycipitaceae) strain GHA, and Metarhizium brunneum Petch (Hypocreales: Clavicipitaceae) strain F52 for virulence against B. tabaci (4th instars) and cotton aphid, Aphis gossypii Glover (Hemiptera: Aphididae) (4th instars with or without wingbuds), on leaf-discs, and against last instars of pecan weevil Curculio caryae (Horn) (Coleoptera: Curculionidae) and citrus root weevil Diaprepes abbreviatus (L.) (Coleoptera: Curculionidae) in soil cups. Against B. tabaci, C. javanica exhibited higher mortality and mycosis development at 5 d post inoculation than other fungi. In assays against A. gossypii with and without wingbuds, C. javanica and C. fumosorosea had the highest mortality and mycosis levels and B. bassiana had the lowest; nymphs with wingbuds were more susceptible to some fungal infection than those without. Against C. caryae, B. bassiana was more effective than other fungi. For D. abbreviatus, B. bassiana also caused the highest mortality while M. brunneum had the lowest, with Cordyceps spp. being intermediate. Overall, the findings suggest high potential of the new strain, C. javanica wf GA17, for managing whiteflies and aphids, while it was not as effective as B. bassiana against the curculionids.
The presence and characteristics of ‘spin’ among randomized controlled trial abstracts in orthodontics
Authors: Guo Feiyang , Fang Xiaolin , Li Chang , Qin Danchen , Hua Fang , He Hong 
Published: June 2021

SummaryObjectivesTo identify the presence and characteristics of spin (using reporting strategies to distort study results and mislead readers) within randomized controlled trial (RCT) abstracts published in orthodontic journals, and to explore the association between spin and potentially related factors.MethodsA manual search was conducted to identify abstracts of RCTs with statistically non-significant primary outcomes published in five leading orthodontic journals between 2015 and 2020. Spin in the Results and Conclusions sections of each included abstract was evaluated and categorized according to pre-determined spin strategies. Logistic regression analyses were employed to explore the association between spin and relevant factors.ResultsA total of 111 RCT abstracts were included, of which 69 (62.2 per cent) were identified with spin. In the Results section, 47 (42.3 per cent) abstracts had spin, and ‘focusing on significant within-group comparison for primary outcomes’ was the most frequent spin strategy. In the Conclusions section, 57 (51.4 per cent) abstracts presented spin, with the most common strategy being ‘claiming equivalence or non-inferiority for statistically nonsignificant results’. According to multivariable logistic regression analysis, a significantly lower presence of spin was found in studies with international collaboration (odds ratio [OR]: 0.331, 95 per cent confidence interval [CI]: 0.120–0.912, P = 0.033) and trial registration (OR: 0.336, 95 per cent CI: 0.117–0.962, P = 0.042).ConclusionThe prevalence of spin is high among RCT abstracts in orthodontics. Clinicians need to be aware of the definition and presence of spin. Concerted efforts are needed from researchers and other stakeholders to address this issue.
Phonetic symbols vs keywords in perceptual training: the learners’ views
Authors: Fouz-González Jonás , Mompean Jose A 
Published: June 2021

Abstract
The potential of high-variability phonetic training (HVPT) to help FL learners improve their pronunciation is well documented. However, research exploring learners’ perceptions of the approach adopted after having experienced training is scarce. Likewise, the choice of labels adopted for training is not self-evident and has not been studied empirically. This study investigates EFL learners’ perceptions towards HVPT and the use of phonetic symbols vs keywords as labels for perceptual training. Seventy-one EFL learners followed four HVPT sessions using two types of labels (symbols and keywords). The results of Likert-type items and open questions in a questionnaire completed after training suggest that learners considered HVPT useful and that they would be willing to adopt it as part of their routine. The participants’ perceptions were positive towards both labels, although the group trained with symbols generally showed more positive attitudes towards training and were willing to continue using it more often.
Acute mental stress drives vascular inflammation and promotes plaque destabilization in mouse atherosclerosis
Authors: Hinterdobler Julia , Schott , Simin , Jin Hong , Meesmann Almut , Steinsiek Anna-Lena , Zimmermann Anna-Sophia , Wobst Jana , Müller Philipp , Mauersberger Carina , Vilne Baiba , Baecklund Alexandra , Chen Chien-Sin , Moggio Aldo , Braster Quinte , Molitor Michael , Krane Markus , Kempf Wolfgang E , Ladwig Karl-Heinz , Hristov Michael , Hulsmans Maarten , Hilgendorf Ingo , Weber Christian , Wenzel Philip , Scheiermann Christoph , Maegdefessel Lars , Soehnlein Oliver , Libby Peter , Nahrendorf Matthias , Schunkert Heribert , Kessler Thorsten , Sager Hendrik B 
Published: June 2021

Abstract

Aims
Mental stress substantially contributes to the initiation and progression of human disease, including cardiovascular conditions. We aim to investigate the underlying mechanisms of these contributions since they remain largely unclear.

Methods and results
Here, we show in humans and mice that leucocytes deplete rapidly from the blood after a single episode of acute mental stress. Using cell-tracking experiments in animal models of acute mental stress, we found that stress exposure leads to prompt uptake of inflammatory leucocytes from the blood to distinct tissues including heart, lung, skin, and, if present, atherosclerotic plaques. Mechanistically, we found that acute stress enhances leucocyte influx into mouse atherosclerotic plaques by modulating endothelial cells. Specifically, acute stress increases adhesion molecule expression and chemokine release through locally derived norepinephrine. Either chemical or surgical disruption of norepinephrine signalling diminished stress-induced leucocyte migration into mouse atherosclerotic plaques.

Conclusion
Our data show that acute mental stress rapidly amplifies inflammatory leucocyte expansion inside mouse atherosclerotic lesions and promotes plaque vulnerability.
Knee osteonecrosis after COVID-19
Authors: Angulo-Ardoy María , Ureña-Aguilera Álvaro 
Published: June 2021

Abstract

Background
COVID-19 is an emergent infection, the long-term complications of which are still under study. While hypercoagulability is a common feature in severe cases, the incidence of ischemic complications such as osteonecrosis remains unknown. Previous studies on SARS-CoV1 found an increase in osteonecrosis 3–36 months after infection, and it is still unclear if this was related to the use of corticosteroids or to the virus itself.

Methods
We introduce a 78-year-old woman who complained of right knee pain and swelling a month after COVID-19 infection onset. Her knee radiography showed no significant changes compared to previous ones. MRI, on the other hand, found osteonecrosis in the internal femoral condyle. No coagulation abnormalities were found in blood tests.

Results
While knee replacement should be her main treatment, it will be long delayed due to the pandemic. In the meantime, we increased her tapentadol and salicylic acid doses and gave her home exercises to improve functionality.

Conclusion
In the follow-up after COVID-19, any muscular or joint pain with unusual characteristics should be carefully examined.
International comparison of guidelines for management of impetigo: a systematic review
Authors: Hall Leanne M , Gorges Hilary J , van Driel Mieke , Magin Parker , Francis Nick , Heal Clare F 
Published: June 2021

AbstractBackgroundImpetigo is a common superficial skin infection that affects people worldwide and is usually treated with antibiotics; therefore, its management has implications for global antibiotic stewardship.ObjectiveThis systematic review and narrative synthesis compares and contrasts international impetigo management guidelines.MethodsGuidelines for treatment of impetigo that were produced by a national authority; available to primary care physicians; and published since 2008 were included. Following a comprehensive search strategy, data extraction from eligible studies was performed independently in duplicate. Details of antiseptic and antibiotic treatment; methicillin-resistant Staphylococcus aureus treatment; and conservative management and preventative measures were tabulated and analysed descriptively.ResultsFifty-one guidelines were included from 42 different countries. All guidelines recommended systemic antibiotics, 78% of these only for widespread lesions or failure of topical antibiotic treatment. The first-line systemic antibiotic treatment was restricted to narrow-spectrum options in 21 (41%) whilst 7 (14%) recommended only broad-spectrum antibiotics first-line. Thirty-four (67%) guidelines included recommendations for topical antibiotic use. Twenty guidelines (39%) did not mention antiseptic treatment for impetigo. Guidelines did not always provide clear indications for different treatment options.ConclusionsDespite potentially equal efficacy to systemic antibiotics, only two-thirds of guidelines include topical antibiotic options. Many fail to include recommendations for non-antibiotic treatments such as antiseptics, preventative measures and conservative management, despite potential for antibiotic-sparing. Provision of clear definitions of disease severity and indications for treatment would enhance the ability of clinicians to adhere to recommendations.Systematic review registrationPROSPERO CRD42018117770
Adaptive evolution of sulfite tolerance inBrettanomyces bruxellensis
Authors: Bartel Caroline , Roach Michael , Onetto Cristobal , Curtin Chris , Varela Cristian , Borneman Anthony 
Published: June 2021

ABSTRACTBrettanomyces bruxellensis is considered one of the most problematic microbes associated with wine production. Sulfur dioxide is commonly used to inhibit the growth of B. bruxellensis and limit the potential wine spoilage. Brettanomyces bruxellensis wine isolates can grow at higher concentrations of this preservative than isolates from other sources. Thus, it has been suggested that the use of sulfite may have selected for B. bruxellensis strains better adapted to survive in the winemaking environment. We utilized laboratory adaptive evolution to determine the potential for this to occur. Three B. bruxellensis strains, representative of known genetic variation within the species, were subjected to increasing sublethal sulfur dioxide concentrations. Individual clones isolated from evolved populations displayed enhanced sulfite tolerance, ranging from 1.6 to 2.5 times higher than the corresponding parental strains. Whole-genome sequencing of sulfite-tolerant clones derived from two of the parental strains revealed structural variations affecting 270 genes. The region containing the sulfite efflux pump encoding gene, SSU1, showed clear copy number variants in all sequenced clones. Regardless of parental strain genetic background, SSU1 copy number changes were reproducibly associated with one SSU1 haplotype. This work clearly demonstrates adaptive evolution of B. bruxellensis when exposed to sublethal sulfites and suggests that, similar to Saccharomyces cerevisiae wine yeast, the mechanism responsible involves the gene SSU1.
Numerical simulation of seismic waves in 3-D orthorhombic poroelastic medium with microseismic source implementation
Authors: Tohti Munirdin , Wang Yibo , Xiao Wenjiao , Di Qingyun , Zhou Kefa , Wang Jinlin , An Shaole , Liao Shibin 
Published: June 2021

SUMMARY
We have carried out microseismic forward modelling in orthorhombic poroelastic medium. The seismic response to isotropic (ISO) source, double couple (DC) source and compensated linear vector dipole (CLVD) source was solved by finite-difference algorithm in time domain, respectively. We used analytical solution to test our numerical algorithm and find that the match between the analytical solutions and numerical solutions is sufficiently close. We then designed several different models to calculate the seismic response and analyse the effect of medium parameters and source mechanism on the propagation of seismic waves. We observed from the modelling results that ISO source excites two kinds of waves in isotropic medium, which are fast longitudinal wave and slow longitudinal wave, while the DC and CLVD sources excite three kinds of waves in isotropic medium, including a transverse wave in addition to the fast and slow longitudinal waves. All of these three kinds of sources generate four kinds of seismic waves in orthorhombic poroelastic medium. These are two separable transverse waves in addition to the fast and slow longitudinal waves. The fluid viscosity and medium tortuosity has an effect on the propagation of the slow longitudinal wave. The slow longitudinal wave appears in propagating mode under the effect of low fluid viscosity and appears at the source location in a static mode under the effect of high fluid viscosity. The wavefield snapshot of the slow longitudinal wave has a circular shape when the tortuosity is isotropic, whereas it has an oval shape when the tortuosity is anisotropic. As far as the anisotropic parameters are concerned, the anisotropy of the fast longitudinal wave is more sensitive to the value of $\varepsilon ( {{\varepsilon _1},{\varepsilon _2}} )$, while the value of ${\rm{\delta }}( {{{\rm{\delta }}_1},{{\rm{\delta }}_2},{{\rm{\delta }}_3}} )$ has more effect on the anisotropic behaviour of the two separable transverse waves.
The policy implications of ‘thinking problematically’: problematizing Big Food’s role in obesity policymaking
Authors: Loughnane Cliona 
Published: June 2021

SummaryPractitioners need to engage with the contested nature of public health policymaking. This study, stemming from a concern that the involvement of Big Food is not widely problematized in health promotion practice, used ‘What’s the Problem Represented to Be?’ discourse analysis to examine how Big Food, as a discursive actor, reacted to and shaped a problem representation of childhood obesity. Analysis of Big Food documents, including Coca-Cola and Burger King, developed during the regulation of broadcast advertising to children in Ireland found that Big Food constructs the problem of childhood obesity in a way which privileges its role as policy actor; it draws on and undermines public health discourses of obesity; and it negates the impact of corporate practices on obesity and on related policymaking. An in-depth analysis of Big Food’s own documents provides access to the processes of knowledge production and governing undertaken by Big Food. The study offers two tools of resistance for health promotion practitioners to interrogate and challenge Big Food—problematization as a policy tool and ‘corporate influence’ as a critical public health discourse.