bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Value of Artificial Intelligence in Laboratory Medicine
Authors: Paranjape Ketan , Schinkel Michiel , Hammer Richard D , Schouten Bo , Nannan Panday R S , Elbers Paul W G , Kramer Mark H H , Nanayakkara Prabath 
Published: August 2020

AbstractObjectivesAs laboratory medicine continues to undergo digitalization and automation, clinical laboratorians will likely be confronted with the challenges associated with artificial intelligence (AI). Understanding what AI is good for, how to evaluate it, what are its limitations, and how it can be implemented are not well understood. With a survey, we aimed to evaluate the thoughts of stakeholders in laboratory medicine on the value of AI in the diagnostics space and identify anticipated challenges and solutions to introducing AI.MethodsWe conducted a web-based survey on the use of AI with participants from Roche’s Strategic Advisory Network that included key stakeholders in laboratory medicine.ResultsIn total, 128 of 302 stakeholders responded to the survey. Most of the participants were medical practitioners (26%) or laboratory managers (22%). AI is currently used in the organizations of 15.6%, while 66.4% felt they might use it in the future. Most had an unsure attitude on what they would need to adopt AI in the diagnostics space. High investment costs, lack of proven clinical benefits, number of decision makers, and privacy concerns were identified as barriers to adoption. Education in the value of AI, streamlined implementation and integration into existing workflows, and research to prove clinical utility were identified as solutions needed to mainstream AI in laboratory medicine.ConclusionsThis survey demonstrates that specific knowledge of AI in the medical community is poor and that AI education is much needed. One strategy could be to implement new AI tools alongside existing tools.
Effect of Correcting the Postnatal Age of Preterm-Born Children on Measures of Associations Between Infant Length-for-Age z Scores and Mid-Childhood Outcomes
Authors: Perumal Nandita , Roth Daniel E , Cole Donald C , Zlotkin Stanley H , Perdrizet Johnna , Barros Aluisio J D , Santos Ina S , Matijasevich Alicia , Bassani Diego G 
Published: August 2020

Abstract
Child growth standards are commonly used to derive age- and sex-standardized anthropometric indices but are often inappropriately applied to preterm-born children (&lt;37 weeks of gestational age (GA)) in epidemiology studies. Using the 2004 Pelotas Birth Cohort, we examined the impact of correcting for GA in the application of child growth standards on the magnitude and direction of associations in 2 a priori–selected exposure-outcome scenarios: infant length-for-age z score (LAZ) and mid-childhood body mass index (scenario A), and infant LAZ and mid-childhood intelligence quotient (scenario B). GA was a confounder that had a strong (scenario A) or weak (scenario B) association with the outcome. Compared with uncorrected postnatal age, using GA-corrected postnatal age attenuated the magnitude of associations, particularly in early infancy, and changed inferences for associations at birth. Although differences in the magnitude of associations were small when GA was weakly associated with the outcome, model fit was meaningfully improved using corrected postnatal age. When estimating population-averaged associations with early childhood growth in studies where preterm- and term-born children are included, incorporating heterogeneity in GA at birth in the age scale used to standardize anthropometric indices postnatally provides a useful strategy to reduce standardization errors.
Occupational Skin Disease in Physicians: A Review of the Literature
Authors: Henning Mattias A S , Jemec Gregor B , Ibler Kristina S 
Published: August 2020

AbstractObjectivesOccupational skin disease (OSD) arises from work-related activity. However, there is a paucity of literature on OSD in physicians. The aim of the this review was therefore to examine and summarize what types of symptomatic OSD physicians experience.MethodsWe conducted a systematic literature search on Cochrane Library, Embase, and Pubmed.ResultsContact dermatitis from formaldehyde and glutaraldehyde were found in 11.5 and 13.5% of cases, respectively. In total 2.4–14.9% had latex allergy. The reported standardized incidence ratio of squamous cell carcinoma and melanoma was up to 2.15 [95% confidence interval (CI) 1.57–1.95] and 3.2 (95% CI 1.38–6.31). Transmission of human papilloma virus (HPV) particles during carbon dioxide laser wart ablation were found in 70% of samples collected from protective gloves and in 52% of samples from vapors.ConclusionsThe most frequently reported OSD in physicians is contact dermatitis from allergens in disinfectants and rubber gloves. There is also a risk of cutaneous reactions to latex. The incidence of skin cancer was higher in physicians than in the general population, and the reason for this remains unexplained and potentially biased. There are no reports of transmission of patient HPV to surgeons during wart ablation, possibly because of proper use of protective equipment.
Irreconcilable perspectives like in an Escher’s drawing? Extension of an arbitration agreement to a non-signatory state and attribution of state entities’ conduct: privity of contract in Swiss and investment arbitral tribunals’ case law
Authors: Magnarelli Martina , Ziegler Andreas R 
Published: August 2020

Abstract
A matter of perspective? When a dispute arises and on the government’s side a non-signatory to the arbitration agreement or investment treaty adopted the contested action, privity of contract and rules of attribution of conduct may apply. Both have been interpreted in different manners. When one put all these interpretations together, the result is a picture of impossible spaces and irreconcilable scenarios like in a drawing of Escher. If Escher expressed his artistic inspiration by challenging gravity and visual logic, practitioners may nowadays find challenging solving the dilemma of when and how an arbitration agreement can be extended to a non-signatory state or the conduct of a state entity be attributed to the state.
In its recent decision 4 A_636/2018, the Swiss Supreme Court confirmed its case law that exceptions to the doctrine of privity of contract exist under Swiss law, but these are limited in number and scope. The same applies regardless of whether private or public entities are concerned. This article will examine decision 4 A_636/2018 in light of Swiss case law and draw a comparison with investment arbitral tribunals’ jurisprudence applying rules of attribution of conduct of customary international law when privity of contract lacks on the government’s side.
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
Authors: Deutekom Eva S , Snel Berend , van Dam Teunis J P 
Published: August 2020

Abstract
Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets or expanding the analyses to larger scales. Automated orthology inference should allow such large-scale analyses, but substantial differences between orthologous groups generated by different approaches are observed.
We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regard to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes), the last eukaryotic common ancestor’s gene content, pervasiveness of gene loss and the overlap with manually determined orthologous groups. Moreover, we compare the inferred orthologies to each other.
We find that most orthology methods reconstruct a large last eukaryotic common ancestor, with substantial gene loss, and can predict interacting proteins reasonably well when applying phylogenetic co-occurrence. At the same time, derived orthologous groups show imperfect overlap with manually curated orthologous groups. There is no strong indication of which orthology method performs better than another on individual or all of these aspects. Counterintuitively, despite the orthology methods behaving similarly regarding large-scale evaluation, the obtained orthologous groups differ vastly from one another.
Availability and implementation The data and code underlying this article are available in github and/or upon reasonable request to the corresponding author: https://github.com/ESDeutekom/ComparingOrthologies.
Unveiling COVID-19-associated organ-specific cell types and cell-specific pathway cascade
Authors: Dey Ashmita , Sen Sagnik , Maulik Ujjwal 
Published: August 2020

Abstract
The novel coronavirus or COVID-19 has first been found in Wuhan, China, and became pandemic. Angiotensin-converting enzyme 2 (ACE2) plays a key role in the host cells as a receptor of Spike-I Glycoprotein of COVID-19 which causes final infection. ACE2 is highly expressed in the bladder, ileum, kidney and liver, comparing with ACE2 expression in the lung-specific pulmonary alveolar type II cells. In this study, the single-cell RNAseq data of the five tissues from different humans are curated and cell types with high expressions of ACE2 are identified. Subsequently, the protein–protein interaction networks have been established. From the network, potential biomarkers which can form functional hubs, are selected based on k-means network clustering. It is observed that angiotensin PPAR family proteins show important roles in the functional hubs. To understand the functions of the potential markers, corresponding pathways have been researched thoroughly through the pathway semantic networks. Subsequently, the pathways have been ranked according to their influence and dependency in the network using PageRank algorithm. The outcomes show some important facts in terms of infection. Firstly, renin-angiotensin system and PPAR signaling pathway can play a vital role for enhancing the infection after its intrusion through ACE2. Next, pathway networks consist of few basic metabolic and influential pathways, e.g. insulin resistance. This information corroborate the fact that diabetic patients are more vulnerable to COVID-19 infection. Interestingly, the key regulators of the aforementioned pathways are angiontensin and PPAR family proteins. Hence, angiotensin and PPAR family proteins can be considered as possible therapeutic targets. Contact: sagnik.sen2008@gmail.com, umaulik@cse.jdvu.ac.in Supplementary information: Supplementary data are available online.
Modular arrangements of sequence motifs determine the functional diversity of KDM proteins
Authors: Wang Zerong , Liu Dongyang , Xu Baofang , Tian Ruixia , Zuo Yongchun 
Published: August 2020

Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
CARE: context-aware sequencing read error correction
Authors: Kallenborn Felix , Hildebrandt Andreas , Schmidt Bertil 
Published: August 2020

Abstract

Motivation
Error correction is a fundamental pre-processing step in many Next-Generation Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false-positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes.

Results
We present CARE—an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors are corrected by detailed inspection of the corresponding alignments. Our performance evaluation shows that CARE generates significantly fewer false-positive corrections than state-of-the-art tools (Musket, SGA, BFC, Lighter, Bcool, Karect) while maintaining a competitive number of true positives. When used prior to assembly it can achieve superior de novo assembly results for a number of real datasets. CARE is also the first multiple sequence alignment-based error corrector that is able to process a human genome Illumina NGS dataset in only 4 h on a single workstation using GPU acceleration.

Availabilityand implementation
CARE is open-source software written in C++ (CPU version) and in CUDA/C++ (GPU version). It is licensed under GPLv3 and can be downloaded at https://github.com/fkallen/CARE.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Relationship between Burnout and Job Satisfaction in a Sample of Spanish Social Workers
Authors: Gómez-García Rogelio , Bayón-Calvo Siro , Lucas-García Jezabel 
Published: August 2020

AbstractBurnout and its relationship with job satisfaction have been addressed extensively. Research has focused mainly on diverse groups such as health care workers, teachers and (more recently) social workers. This study aims to examine the relationships between the dimensions of burnout and job satisfaction amongst social workers. A sample of 947 Spanish social workers was collected. We used a structural equation model using the partial least squares structural equation modelling approach. A series of hypotheses were formulated to analyse the relationship between burnout dimensions and job satisfaction. Emotional exhaustion is associated with high levels of depersonalisation and low levels of personal accomplishment. Different personal and work-related characteristics are significantly associated with various dimensions of burnout and job satisfaction. This study confirms a statistically significant relationship between burnout dimensions and job satisfaction.
Simultaneous Determination of Three Coumarins in Rat Plasma by HPLC-MS/MS for Pharmacokinetic Studies Following Oral Administration of Chimonanthi Radix Extract
Authors: Zhang Jing , Wen Quan , Zhou Meng-ying , Zhong Chen-cong , Feng Yulin , Tan Ting 
Published: August 2020

Abstract
Chimonanthi Radix (CR) is widely used in the treatment of influenza in China. Extensive studies revealed that the major bioactive constituents of CR were coumarins. However, pharmacokinetic study of coumarins in CR has not been fully studied. The purpose of this study was to establish a convenient and effective high-performance liquid chromatography–tandem mass spectrometry method that was used to simultaneously determine scopoletin, scopolin and isofraxidin in rat plasma after oral administration of CR extract using xanthotoxin as the internal standard. The chromatographic separation was carried out on a COSMOCORE C18 column (100 × 2 mm, 2.6 μm), using gradient elution with the mobile phase consisting of 0.1% formic acid (A) and acetonitrile (B). Three coumarins and IS were quantified by positive ion electrospray ionization in multiple reaction monitoring mode. The method was fully validated in terms of specificity, accuracy, precision (intra- and inter-day), matrix effect, recovery as well as the stability of the analytes under various conditions. The results could provide further research foundation for anti-influenza mechanism of three coumarins in CR.
The Communicative Ethics of Racial Identity in Dialogue
Authors: Cooks Leda 
Published: August 2020

Abstract
This article explores the role of narratives about racial identity in constituting ethical performances in dialogue. Specifically, a dialogic communication ethics is described and placed in the context of intergroup dialogue (IGD) and communication approaches to dialogue. Then the focus turns to how these ethical frames and models for conducting dialogue functioned in a large-scale campus dialogue on race and whiteness. The article addresses the ways identities were constructed and deployed in the dialogues by examining how dialogue topics are framed and discussed by facilitators and participants. This discussion of intention and outcome raises theoretical and practical questions in order to facilitate further conversations about identity and ethics in a controversially “Post-racial” era. Finally, the article looks at how communication ethics and dialogue might work to address the discursive power of social group identities in pedagogical discussions of civility, inclusion, merit or a “good” life.
Theorizing From the Global South: Dismantling, Resisting, and Transforming Communication Theory
Authors: Dutta Mohan J , Pal Mahuya 
Published: August 2020

AbstractThis special issue explores what theory looks like from the Global South. Whether it is in the work of the women farmers organized into Sanghams under the umbrella of the Deccan Development Society (DDS) or in the organizing of farmers under the collective formations of La Via Campesina, the emergent work of theory is intrinsically tied to plural practices embedded in community life. We argue that we need to theorize from the narratives embedded in experiences of actors who are disenfranchised from metropolitan/mainstream/Euro-US/neoliberal economics and society. We mark the local politics of the Global South at the intersections of the local and global forces as sites of knowledge in this special issue.
What on Earth do Journalists Know? A New Model of Knowledge Brokers’ Expertise
Authors: Reich Zvi , Lahav Hagar 
Published: August 2020

AbstractThe article offers a new theoretical model that conceptualizes the “exotic” expertise of journalists and other knowledge-brokers who specialize in particular domains (e.g., teachers, librarians, analysts). The model adapts theories from sociology, pedagogy and philosophy and juxtaposes them against the insights of 14 editors-in-chief from leading Israeli media, in order to validate, refine and illustrate the theoretical generalizations. According to the suggested model, specialized knowledge brokers develop a unique type of expertise that can be modeled across four distinct dimensions: The manifestation of expertise (doing/talking), the mechanism of expertise (interplay between journalistic and domain knowledge), the socio-epistemic position (outsiders/insiders) and the density of expertise (homogenous versus heterogeneous knowledge). Understanding journalists’ expertise is crucial due to the overwhelming assault on experts in “post truth” societies; their role as mega brokers of expert knowledge from all disciplines (outside one’s own expertise) and the ongoing scholarly dispute on the nature of expertise.
Fluoride varnish for white spot lesion prevention during orthodontic treatment: results of a randomized controlled trial 1 year after debonding
Authors: Sonesson Mikael , Brechter Anna , Lindman Rolf , Abdulraheem Salem , Twetman Svante 
Published: August 2020

Summary

Background
Topical fluorides are commonly recommended to prevent the development of white spot lesion (WSL) during treatment with fixed orthodontic appliances (FOAs), but the certainty of evidence is low, and long-term effects of fluoride preventive methods to reduce lesions seem to be rare.

Objective
To evaluate the long-term effectiveness of professional applications of a fluoride varnish containing 1.5% ammonium fluoride in preventing WSL development in adolescents undergoing multi-bracket orthodontic treatment.

Subjects and methods
We performed a randomized controlled trial in which 166 healthy adolescents (12–18 years) from three different clinics were enrolled and randomly allocated to a test or a placebo group. The randomization was performed by a computer program, generating sequence numbers in blocks of 15. The fluoride varnish or the non-fluoride placebo varnish was applied in a thin layer around the bracket base every sixth week during the course of the orthodontic treatment (mean duration 1.7 years). We scored the prevalence of WSL on the labial surfaces of the maxillary incisors, canines and premolars immediately after debonding (baseline) and approximately 1 year after debonding, from digital photos with aid of a four-step score. The examiners were not involved in the treatment of the patients and blinded for the group assignment.

Results
One hundred and forty-eight patients were available at debonding and 142 of them could be re-examined after 1 year (71 in the test and 71 in the placebo group). The 1-year attrition rate was 4.0%. On patient level, the prevalence of post-orthodontic WSLs (score ≥ 2) dropped by over 50% during the follow-up with no significant difference between the groups. On surface level, there were significantly fewer remaining WSLs in the test group compared with the placebo group (4.5% versus 10.4%; relative risk 0.44, 95% confidence interval 0.28–0.68).

Limitations
The compliance with fluoride toothpaste was not checked, and the patients’ general dentists may have instigated additional risk-based preventive measures. No cost–benefit analysis was carried out.

Conclusions
This follow-up study displayed a small beneficial long-term effect of fluoride varnish in reducing WSL development during treatment with FOA.

Registration
NCT03725020.

Protocol
The protocol was not published before trial commencement.
Influences of 1-methylcyclopropene-containing papers on the metabolisms of membrane lipids in Anxi persimmons during storage
Authors: Wang Hui , Chen Guo , Shi Lili , Lin Hetong , Chen Yihui , Lin Yifen , Fan Zhongqi 
Published: August 2020

Abstract

Objectives
The aim of this work was to analyse the effects of 1-methylcyclopropene (1-MCP) treatment on the metabolisms of membrane lipids in postharvest Anxi persimmons during storage.

Materials and methods
Anxi persimmon (Diospyros kaki L. f. cv. Anxi) fruits were treated by paper containing 1-MCP with a concentration of 1.35 μl/l. The cellular membrane permeability was analysed by the electric conductivity meter. The activities of lipoxygenase (LOX), phospholipase (PLD) and lipase were determined by spectrophotometry. The component and relative amounts of membrane fatty acids were determined using gas chromatograph (GC).

Results
The 1-MCP-treated Anxi persimmons manifested a lower electrolyte leakage rate, lower LOX, PLD and lipase activities, higher levels of unsaturated fatty acids (USFAs), higher ratio of USFAs to saturated fatty acids (SFAs) (U/S), higher index of USFAs (IUFA), but lower levels of SFAs.

Conclusions
The degradation and the metabolisms of membrane lipids could be suppressed by 1-MCP treatment, which might be accountable for the delaying softening of postharvest Anxi persimmons during storage.