bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination
Authors: McGurk Kathryn A , Dagliati Arianna , Chiasserini Davide , Lee Dave , Plant Darren , Baricevic-Jones Ivona , Kelsall Janet , Eineman Rachael , Reed Rachel , Geary Bethany , Unwin Richard D , Nicolaou Anna , Keavney Bernard D , Barton Anne , Whetton Anthony D , Geifman Nophar 
Published: November 2019

Abstract

Motivation
Data-independent acquisition mass spectrometry allows for comprehensive peptide detection and relative quantification than standard data-dependent approaches. While less prone to missing values, these still exist. Current approaches for handling the so-called missingness have challenges. We hypothesized that non-random missingness is a useful biological measure and demonstrate the importance of analysing missingness for proteomic discovery within a longitudinal study of disease activity.

Results
The magnitude of missingness did not correlate with mean peptide concentration. The magnitude of missingness for each protein strongly correlated between collection time points (baseline, 3 months, 6 months; R = 0.95–0.97, confidence interval = 0.94–0.97) indicating little time-dependent effect. This allowed for the identification of proteins with outlier levels of missingness that differentiate between the patient groups characterized by different patterns of disease activity. The association of these proteins with disease activity was confirmed by machine learning techniques. Our novel approach complements analyses on complete observations and other missing value strategies in biomarker prediction of disease activity.

Supplementary information
Supplementary data are available at Bioinformatics online.
The pelvis as an anatomical indicator for facultative bipedality and substrate use in lepidosaurs
Authors: Grinham Luke R , Norman David B 
Published: November 2019

AbstractFacultative bipedality is regarded as an enigmatic middle ground in the evolution of obligate bipedality and is associated with high mechanical demands in extant lepidosaurs. Traits linked with this phenomenon are largely associated with the caudal end of the animal: hindlimbs and tail. The articulation of the pelvis with both of these structures suggests a morphofunctional role in the use of a facultative locomotor mode. Using a three-dimensional geometric morphometric approach, we examine the pelvic osteology and associated functional implications for 34 species of extant lepidosaur. Anatomical trends associated with the use of a bipedal locomotor mode and substrate preferences are correlated and functionally interpreted based on musculoskeletal descriptions. Changes in pelvic osteology associated with a facultatively bipedal locomotor mode are similar to those observed in species preferring arboreal substrates, indicating shared functionality between these ecologies.
Using hand maps to understand how intersecting inequalities affect possibilities for community safety in Cape Town
Authors: Black Gillian F , Liedeman Rory , Ryklief Farida 
Published: November 2019

Abstract
Knowledge about what builds and what blocks pathways to accountability in South African townships could be strengthened by better understanding the role of intersectionality in these settings. This article describes our use of a novel hand mapping method to explore identity and inequality among a collective of community members from the township of Delft in Cape Town. We share new insights about the effect of intersecting inequalities on the capacity of activists and concerned young citizens to take part in building accountability for safer spaces in South Africa. Although we gained a deeper understanding about some of the ways that intersecting inequalities play out in the lives of Delft residents, we also learnt lessons about the limits to facilitated accountability struggles. Some of these struggles relate directly to the inequalities that this study has highlighted, and some reflect the highly fluid socioeconomic and political environment in which our work was situated. This article is divided into eight main sections. We begin by introducing the theory of intersectionality and provide a rationale for using participatory visual methods as tools for intersectionality research. We then summarize the study context and describe the hand mapping method that was used. The following four sections present our results through discussions of identity and personal experiences of inequality, unpacking intersecting inequalities, the possibilities and constraints of advancing accountability, and balancing accountability with the conditions of collective action. The paper ends with a summary of the insights and conclusions we have reached through facilitating this action research process.
Predictors of Primary Response to Biologic Treatment [Anti-TNF, Vedolizumab, and Ustekinumab] in Patients With Inflammatory Bowel Disease: From Basic Science to Clinical Practice
Authors: Gisbert Javier P , Chaparro María 
Published: November 2019

AbstractBackgroundInflammatory bowel diseases [IBD]―ulcerative colitis and Crohn’s disease―are commonly treated with biologic drugs. However, only approximately two-thirds of patients have an initial response to these therapies. Personalised medicine has the potential to optimise efficacy, decrease the risk of adverse drug events, and reduce costs by establishing the most suitable therapy for a selected patient.AimThe present study reviews the potential predictors of short-term primary response to biologic treatment, including not only anti-tumour necrosis factor [TNF] agents [such as infliximab, adalimumab, certolizumab, and golimumab] but also vedolizumab and ustekinumab.MethodsWe performed a systematic bibliographical search to identify studies investigating predictive factors of response to biologic therapy.ResultsFor anti-TNF agents, most of the evaluated factors have not demonstrated usefulness, and many others are still controversial. Thus, only a few factors may have a potential role in the prediction of the response, including disease behaviour/phenotype, disease severity, C-reactive protein, albumin, cytokine expression in serum, previous anti-TNF therapy, some proteomic markers, and some colorectal mucosa markers. For vedolizumab, the availability of useful predictive markers seems to be even lower, with only some factors showing a limited value, such as the expression of α4β7 integrin in blood, the faecal microbiota, some proteomic markers, and some colorectal mucosa markers. Finally, in the case of ustekinumab, no predictive factor has been reported yet to be helpful in clinical practice.ConclusionIn summary, currently no single marker fulfils all criteria for being an appropriate prognostic indicator of response to any biologic treatment in IBD.
Colonialism and rural inequality in Sierra Leone: an egalitarian experiment
Authors: Galli Stefania , Rönnbäck Klas 
Published: November 2019

AbstractWe analyze the level of inequality in rural Sierra Leone in the early colonial period. Previous research has suggested that the colony was established under highly egalitarian ideals. We examine whether these ideals also are reflected in the real distribution of wealth in the colony. We employ a newly assembled dataset extracted from census data in the colony in 1831. The results show that rural Sierra Leone exhibited one of the most equal distributions of wealth so far estimated for any preindustrial rural society.
Treatment of Carbapenem-Resistant Enterobacteriaceae Infections in Children
Authors: Chiotos Kathleen , Hayes Molly , Gerber Jeffrey S , Tamma Pranita D 
Published: November 2019

AbstractInfections due to carbapenem-resistant Enterobacteriaceae (CRE) are increasingly prevalent in children and are associated with poor clinical outcomes. Optimal treatment strategies for CRE infections continue to evolve. A lack of pediatric-specific comparative effectiveness data, uncertain pediatric dosing regimens for several agents, and a relative lack of new antibiotics with pediatric indications approved by the US Food and Drug Administration (FDA) collectively present unique challenges for children. In this review, we provide a framework for antibiotic treatment of CRE infections in children, highlighting relevant microbiologic considerations and summarizing available data related to the evaluation of FDA-approved antibiotics (as of September 2019) with CRE activity, including carbapenems, ceftazidime-avibactam, meropenem-vaborbactam, imipenem/cilastatin-relebactam, polymyxins, tigecycline, eravacycline, and plazomicin.
Enhancer of zeste homolog 2 modulates oxidative stress‐mediated pyroptosis in vitro and in a mouse kidney ischemia‐reperfusion injury model
Authors: Liu Hao , Chen Zhiyuan , Weng Xiaodong , Chen Hui , Du Yang , Diao Changhui , Liu Xiuheng , Wang Lei 
Published: November 2019

AbstractEnhancer of zeste homolog 2 (EZH2), a well‐known methyltransferase, mediates histone H3 lysine 27 trimethylation (H3K27me3) and plays a crucial role in several kidney disease models. However, its role in renal ischemia/reperfusion (I/R) injury still remains unclear. In this study, we found that EZH2 was positively related to renal I/R injury and inhibition of EZH2 with DZNeP alleviated I/R injury and blocked the activation of oxidative stress and pyroptosis in vivo. Similarly, inhibition of EZH2 with either DZNeP or si‐RNA also exerted an inhibitory effect on hypoxia/reoxygenation (H/R)‐induced oxidative stress and pyroptosis in vitro. Moreover, further study revealed that ablation of reactive oxygen species (ROS) with N‐acetyl‐cysteine (NAC) suppressed pyroptosis in human renal proximal tubular epithelial cell line cells exposed to H/R stimulation. Furthermore, Nox4, which was positively related to the generation of ROS, was upregulated during H/R process, while it could be reversed by EZH2 inhibition. Consistently, Nox4‐mediated ROS generation was attenuated upon inhibition of EZH2 with DZNeP or si‐RNA. Additionally, the transcriptional activity of Nox4 was enhanced by the activation of ALK5/Smad2/3 signaling pathway, which was abolished by ALK5 knockdown in vitro. Finally, EZH2 inhibition blocked H/R and I/R‐activated ALK5/Smad2/3 pathway and also resulted in an obvious decrease in the transcriptional activity and protein expression levels of Nox4. In conclusion, our results proved that EZH2 inhibition alleviated renal pyroptosis by blocking Nox4‐dependent ROS generation through ALK5/Smad2/3 signaling pathway, indicating that EZH2 could be a potential therapeutic target for renal I/R injury.
Voluntary versus mandatory non-financial disclosure
Authors: Doni Federica , Bianchi Martini Silvio , Corvino Antonio , Mazzoni Michela 
Published: November 2019

Purpose
The recent European Union Directive 95/2014 enforced a radical shift from voluntary to mandatory disclosure of non-financial information. Given radical changes in reporting practices, there is an urgent need to assess the firms’ attitude to disclose non-financial information regarding the new requirement. This paper aims to investigate whether the quantity and quality of non-financial information, voluntarily disclosed in the years before the directive came into force, were linked to the level of compliance.

Design/methodology/approach
Selecting a sample of 60 Italian companies from the obliged entities, the authors carried out a manual content analysis on corporate reports and developed some research hypotheses to explore if their sustainability practices can affect non-financial disclosures required by the Italian adoption of the European directive (i.e. Legislative Decree 254/2016).

Findings
Evidence showed that prior skills and competencies in non-financial reporting made a significant contribution especially regarding to the presence of business model, but further efforts are expected to improve the quality of non-financial reports.

Practical implications
This study yields an initial assessment of the implementation of the European directive in Italy. It may, therefore, help policymakers to identify ways to improve the harmonization of reporting practices. Preparers can also be supported in choosing different positioning of reporting on non-financial information.

Originality/value
This research provides interesting insights into the ex ante and ex post adoption of the European directive by investigating how Italian companies are reacting to regulatory and institutional requirements. One of the main problems remains the lack of a shared understanding of the term “non-financial”, which can make the communication process difficult and unclear.
The tolerance of anisometropia
Authors: Krarup Therese Grønhøj , Nisted Ivan , Christensen Ulrik , Kiilgaard Jens Folke , la Cour Morten 
Published: November 2019

AbstractPurposeThis study examines aniseikonia, Aniseikonia tolerance range (ATR), anisometropia and patient‐reported outcomes (PRO) in an anisometropic population compared with a non‐anisometropic population. The relationship between anisometropia and aniseikonia is determined, and the correlations between aniseikonia, anisometropia and ATR versus PRO are described.MethodsOne hundred and twenty‐three patients with IOL‐induced anisometropia ≥1 dioptre (D) (the anisometropic group) and 17 patients who had IOL‐induced anisometropia <1 D (the control group) were included. Best corrected visual acuity, aniseikonia, ATR and stereoacuity were examined, and two questionnaires were completed: convergence insufficiency symptom survey (CISS) and Visual Function Questionnaire (VFQ‐39).ResultsOne hundred and thirteen patients had anisometropia >1 and <3 D, and 10 patients had anisometropia >3 D. There was no difference in PRO between the control group and the anisometropic group (Mann–Whitney, p‐values VFQ: 0.96, CISS: 0.06). There was no correlation between anisometropia and PRO (Spearman's rank correlation test p‐values: VFQ: 0.54, CISS: 0.57). Patients with low ATR were more sensitive towards anisometropia and had lower PRO than patients with high ATR (Mann–Whitney, p‐values: VFQ: 0.0008, CISS: 0.11). A large tolerance of aniseikonia was observed.ConclusionNo correlation between PRO and anisometropia or aniseikonia was found. Patients with low ATR are at risk of visual complaints if they are exposed to IOL‐induced anisometropia. ATR might be a future screening tool in cataract patients.
Neurothekeoma: Report of two cases in children and review of the literature
Authors: Massimo José A. , Gasibe Mariana , Massimo Ianina , Damilano Cecilia P. , De Matteo Elena , Fiorentino Jorge 
Published: November 2019

AbstractNeurothekeomas, or simply nerve sheath myxomas, are rare benign skin neoplasms. They are believed to derive from peripheral nerve sheath transformation and are typically more prevalent in females. They tend to be found mainly on the upper limbs as well as head and neck locations. In this report, we detail two children with neurothekeomas, describe the fundamental clinical manifestations, and review the current literature.
Adult attachment and spousal reactions to military deployment separations and reunions
Authors: Wood Valerie M. , MacDonald Tara K. , Charbonneau Danielle , Urban Samantha 
Published: November 2019

AbstractWe explored adult attachment and spousal perceptions of intrapersonal and relationship functioning during military deployments. In Study 1, spouses of military members experiencing a separation were assessed, and in Study Two, spouses of military members experiencing a reunion were assessed. Study 3 entailed a large‐scale survey of relationship perceptions of spouses of military members. In Studies One and Two, attachment dimensions were related to perceptions of intrapersonal and relationship functioning during the separation and reunion, with associations moderated by days separated/reunited. In Study 3, attachment dimensions were related to relationship perceptions, with associations moderated by deployment stages. This research not only contributes to the knowledge of attachment processes in military contexts but also has the potential to inform policies and services supporting military families.
Prospective development of practical screening strategies for diagnosis of asthma–COPD overlap
Authors: Zhou Aiyuan , Luo Lijuan , Liu Nian , Zhang Cheng , Chen Yahong , Yin Yan , Zhang Jing , He Zhiyi , Xie Lihua , Xie Jungang , Li Jinhua , Zhou Zijing , Chen Yan , Chen Ping 
Published: November 2019

ABSTRACTBackground and objectiveACO is a syndrome with high prevalence. However, a pragmatic diagnostic criterion to differentiate ACO is non‐existent. We aimed to establish an effective model for screening ACO.MethodsA multicentre survey was developed to assess the clinical criteria considered important and applicable by pulmonologists for screening ACO. These experts were asked to take the surveys twice. The expert grading method, analytic hierarchy process and ROC curve were used to establish the model, which was then validated by a cross‐sectional study of 1066 patients. The GINA/GOLD document was the gold standard in assessing this model.ResultsIncreased variability of symptoms, paroxysmal wheezing, dyspnoea, historical diagnosis of COPD or asthma, allergic constitution, exposure to risk factors, the FEV1/FVC < 70% and a positive BDT were important for screening ACO. According to the weight of each criterion, we confirmed that patients meeting six or more of these eight criteria should be considered to have ACO. We called this Chinese screening model for ACO ‘CSMA’. It differentiated patients with ACO with a sensitivity of 83.33%, while the sensitivity of clinician‐driven diagnosis had a sensitivity of only 42.73%.ConclusionCSMA is a workable model for screening ACO and provides a simple tool for clinicians to efficiently diagnose ACO.
Oral health and nutritional status of children with cerebral palsy in northeastern peninsular Malaysia
Authors: Ahmad Rathmawati , Rahman Normastura Abd , Hasan Ruhaya , Yaacob Nik Soriani , Ali Siti Hawa 
Published: November 2019

AbstractAimsTo investigate the oral health and nutritional status of children with cerebral palsy (CP).Methods and resultsOral health assessment included dental caries and dental plaque maturity scores (DPMS) while the nutritional assessment included children's height‐for‐age Z‐score (HAZ), body mass index‐for‐age Z‐score (BAZ), mid‐upper‐arm circumference (MUAC), nutrient intake, cariogenic food frequency (CFF) and daily sugar exposure (DSE). Ninety‐three CP children were recruited. The prevalence of caries was 81.7% (95% CI: 72.7%‐88.3%). The median (IQR) of the DMFT and dft scores were 0.5(4.0) and 3.0(8.0), respectively. Most of the participants had acid‐producing plaque (90.3%), severely stunted (81.4%), and 45% were severely thin with acute malnutrition. Intakes of calcium, iron, zinc, vitamin A, vitamin D and total fat were below 77% of the Recommended Nutrient Intakes for Malaysian children (RNI 2017). Nine types of cariogenic foods/drinks were consumed moderately, and DSE indicated that 45% of the children were at moderate risk of dental caries.ConclusionUntreated dental caries, severe stunting and thinness were prevalent, and cariogenic foods/drinks were consumed moderately suggesting a moderate risk of caries. Therefore, controlling cariogenic food intake is crucial, but monitoring daily nutrient intake is needed for the optimum growth of children with CP.
Effects of cover crops sown in autumn on N and P leaching
Authors: Norberg Lisbet , Aronsson Helena 
Published: November 2019

AbstractA field experiment with separately tile‐drained plots was used to study the ability of oilseed radish (Rhaphanus sativus L.), as a cover crop sown after harvest of a main crop of cereals or peas, to reduce nitrogen (N) and phosphorus (P) leaching losses from a clay loam in southern Sweden over 6 years. In addition to oilseed radish in pure stand, two cover crop mixtures (hairy vetch (Vicia villosa) and rye (Secale cereale) for 3 years and oilseed radish in mixture with buckwheat (Fagopyrum esculentum) for 2 years) were tested. The cover crop plots (three replicates per treatment) were compared with unplanted plots as a control. Plots cropped with oilseed radish during autumn (August–November) had significantly smaller yearly mean N concentration in drainage water over 5 of 6 years compared with unplanted controls. Mineral N content in the soil profile in autumn was significantly less in oilseed radish plots than for control plots in all years. The cover crop mixtures of hairy vetch and rye or buckwheat and oilseed radish also showed the potential to reduce soil mineral N in autumn and N concentration in drainage water, compared with unplanted controls. The cover crops had no impact on P leaching. In conclusion, oilseed radish has the ability to reduce leaching losses of N, without increasing the risk of P leaching.
The effects of long‐term muscle disuse on neuromuscular function in unilateral transtibial amputees
Authors: Sibley Amy R. , Strike Siobhán , Moudy Sarah C. , Tillin Neale A. 
Published: November 2019

New Findings
What is the central question of this study?
The effects of long‐term muscle disuse on neuromuscular function are unclear because disuse studies are typically short term. In this study, we used a new model (unilateral transtibial amputees) to investigate the effects of long‐term disuse on quadriceps neuromuscular function.

What is the main finding and its importance?
Kinetic analysis (knee‐extension moments during gait) indicated habitual disuse of the amputated limb quadriceps, accompanied by lower quadriceps muscle strength (60–76%) and neural activation (32–44%), slower contractile properties and altered muscle architecture in the amputated limb, which could not be predicted from short‐term disuse studies.

AbstractThe purpose of this study was to determine: (i) whether individuals with unilateral transtibial amputations (ITTAs), who habitually disuse the quadriceps muscles of their amputated limb, provide an effective model for assessing the effects of long‐term muscle disuse; and (ii) the effects of such disuse on quadriceps muscle strength and neuromuscular function in this population. Nine ITTAs and nine control subjects performed isometric voluntary knee extensions of both limbs to assess maximal voluntary torque (MVT) and the rate of torque development (RTD). The interpolated twitch technique and EMG normalized to maximal M‐wave were used to assess neural activation, involuntary (twitch and octet) contractions to assess intrinsic contractile properties, and ultrasound images of the vastus lateralis to assess muscle architecture. Clinical gait analysis was used to measure knee kinetic data during walking at an habitual speed. The ITTAs displayed 54–60% lower peak knee‐extensor moments during walking in the amputated compared with intact/control limbs, but the intact and control limbs were comparable for loading during walking and muscle strength variables, suggesting that the intact limb provides a suitable internal control for comparison with the disused amputated limb. The MVT and RTD were ∼60 and ∼75% lower, respectively, in the amputated than intact/control limbs. The differences in MVT appeared to be associated with ∼40 and ∼43% lower muscle thickness and neural activation, respectively, and the differences in RTD appeared to be associated with the decline in MVT coupled with slowing of the intrinsic contractile properties. These results indicate considerable changes in strength and neuromuscular function with long‐term disuse that could not be predicted from short‐term disuse studies.