bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atopic dermatitis or eczema? Consequences of ambiguity in disease name for biomedical literature mining
Authors: Frainay Clément , Pitarch Yoann , Filippi Sarah , Evangelou Marina , Custovic Adnan 
Published: July 2021

AbstractBackgroundBiomedical research increasingly relies on computational approaches to extract relevant information from large corpora of publications.ObjectiveTo investigate the consequence of the ambiguity between the use of terms “Eczema” and “Atopic Dermatitis” (AD) from the Information Retrieval perspective, and its impact on meta‐analyses, systematic reviews and text mining.MethodsArticles were retrieved by querying the PubMed using terms ‘eczema’ (D003876) and “dermatitis, atopic” (D004485). We used machine learning to investigate the differences between the contexts in which each term is used. We used a decision tree approach and trained model to predict if an article would be indexed with eczema or AD tags. We used text‐mining tools to extract biological entities associated with eczema and AD, and investigated the discrepancy regarding the retrieval of key findings according to the terminology used.ResultsAtopic dermatitis query yielded more articles related to veterinary science, biochemistry, cellular and molecular biology; the eczema query linked to public health, infectious disease and respiratory system. Medical Subject Headings terms associated with “AD” or “Eczema” differed, with an agreement between the top 40 lists of 52%. The presence of terms related to cellular mechanisms, especially allergies and inflammation, characterized AD literature. The metabolites mentioned more frequently than expected in articles with AD tag differed from those indexed with eczema. Fewer enriched genes were retrieved when using eczema compared to AD query.Conclusions and Clinical RelevanceThere is a considerable discrepancy when using text mining to extract bio‐entities related to eczema or AD. Our results suggest that any systematic approach (particularly when looking for metabolites or genes related to the condition) should be performed using both terms jointly. We propose to use decision tree learning as a tool to spot and characterize ambiguity, and provide the source code for disambiguation at https://github.com/cfrainay/ResearchCodeBase.
Post‐extubation dysphagia and dysphonia amongst adults with COVID‐19 in the Republic of Ireland: A prospective multi‐site observational cohort study
Authors: Regan Julie , Walshe Margaret , Lavan Sarah , Horan Eanna , Gillivan Murphy Patricia , Healy Anne , Langan Caoimhe , Malherbe Karen , Flynn Murphy Breda , Cremin Maria , Hilton Denise , Cavaliere Jenni , Whyte Alice 
Published: July 2021

AbstractObjectivesThis study aims to (i) investigate post‐extubation dysphagia and dysphonia amongst adults intubated with SARS‐COV‐2 (COVID‐19) and referred to speech and language therapy (SLT) in acute hospitals across the Republic of Ireland (ROI) between March and June 2020; (ii) identify variables predictive of post‐extubation oral intake status and dysphonia and (iii) establish SLT rehabilitation needs and services provided to this cohort.DesignA multi‐site prospective observational cohort study.ParticipantsOne hundred adults with confirmed COVID‐19 who were intubated across eleven acute hospital sites in ROI and who were referred to SLT services between March and June 2020 inclusive.Main Outcome MeasuresOral intake status, level of diet modification and perceptual voice quality.ResultsBased on initial SLT assessment, 90% required altered oral intake and 59% required tube feeding with 36% not allowed oral intake. Age (OR 1.064; 95% CI 1.018–1.112), proning (OR 3.671; 95% CI 1.128–11.943) and pre‐existing respiratory disease (OR 5.863; 95% CI 1.521–11.599) were predictors of oral intake status post‐extubation. Two‐thirds (66%) presented with dysphonia post‐extubation. Intubation injury (OR 10.471; 95% CI 1.060–103.466) and pre‐existing respiratory disease (OR 24.196; 95% CI 1.609–363.78) were predictors of post‐extubation voice quality. Thirty‐seven per cent required dysphagia intervention post‐extubation, whereas 20% needed intervention for voice. Dysphagia and dysphonia persisted in 27% and 37% cases, respectively, at hospital discharge.DiscussionPost‐extubation dysphagia and dysphonia were prevalent amongst adults with COVID‐19 across the ROI. Predictors included iatrogenic factors and underlying respiratory disease. Prompt evaluation and intervention is needed to minimise complications and inform rehabilitation planning.
LID study: Plasma lidocaine levels following airway topicalisation for paediatric microlaryngobronchoscopy (MLB)
Authors: Doherty Catherine , Quinn Natalie , Mistry Sara , Diacono Jacques , Walker Robert , Harrison Anna , Bateman Neil , Bruce Iain 
Published: July 2021

AbstractObjectivesA dose of 5 mg/kg lidocaine is considered appropriate for paediatric airway topicalisation. Existing literature suggests that younger children are susceptible to toxic lidocaine plasma levels and achieve this at a faster rate.Main outcome measuresThe primary outcome of this study was to ascertain peak plasma lidocaine levels after topicalisation for airway endoscopy. Secondary endpoints included: time to peak lidocaine plasma levels, signs of lidocaine toxicity (restricted to ECG changes or seizures when under anaesthesia) and clinical adverse events of laryngospasm, coughing or desaturation during the procedure.SettingData were collected prospectively over 18 months at Royal Manchester Children's Hospital.ParticipantsChildren aged 0–8 years undergoing elective diagnostic or therapeutic airway endoscopy were included within the study.DesignStandardised 2% lidocaine was used for airway topicalisation. Dose varied depending upon the practitioner's usual practice. Venous bloodsampling occurred at 5, 10, 15 and 20 min post‐administration and plasma lidocaine levels (ng/ml) were analysed.ResultsA significant relationship exists between higher peak plasma levels and ages <18 months (p = .00973). Strong linear correlation exists between body weight and age for our cohort (r = .88). Higher peak plasma lidocaine levels occur with total dose volumes between 2 and 3 mls of 2% lidocaine local anaesthetic (p = .03) compared with <2 ml total dose volumes. Data suggest a potential relationship of lower body weights achieving higher peak plasma levels (p = .0516). Reduced interquartile variation of peak plasma lidocaine levels exists when lidocaine dosing is <5 mg/kg.ConclusionsAge and total dose volume of topicalised lidocaine have a significant relationship with plasma lidocaine levels. A dose of 5 mg/kg topicalised lidocaine for paediatric airway endoscopy is safe and provides good operating conditions. Lower patient body weights trend towards higher peak lidocaine plasma concentrations and require further investigation.
Model‐Based Wisdom of the Crowd for Sequential Decision‐Making Tasks
Authors: Thomas Bobby , Coon Jeff , Westfall Holly A. , Lee Michael D. 
Published: July 2021

AbstractWe study the wisdom of the crowd in three sequential decision‐making tasks: the Balloon Analogue Risk Task (BART), optimal stopping problems, and bandit problems. We consider a behavior‐based approach, using majority decisions to determine crowd behavior and show that this approach performs poorly in the BART and bandit tasks. The key problem is that the crowd becomes progressively more extreme as the decision sequence progresses, because the diversity of opinion that underlies the wisdom of the crowd is lost. We also consider model‐based approaches to each task. This involves inferring cognitive models for each individual based on their observed behavior, and using these models to predict what each individual would do in any possible task situation. We show that this approach performs robustly well for all three tasks and has the additional advantage of being able to generalize to new problems for which there are no behavioral data. We discuss potential applications of the model‐based approach to real‐world sequential decision problems and discuss how our approach contributes to the understanding of collective intelligence.
Towards a Cognitive Theory of Cyber Deception
Authors: Cranford Edward A. , Gonzalez Cleotilde , Aggarwal Palvi , Tambe Milind , Cooney Sarah , Lebiere Christian 
Published: July 2021

AbstractThis work is an initial step toward developing a cognitive theory of cyber deception. While widely studied, the psychology of deception has largely focused on physical cues of deception. Given that present‐day communication among humans is largely electronic, we focus on the cyber domain where physical cues are unavailable and for which there is less psychological research. To improve cyber defense, researchers have used signaling theory to extended algorithms developed for the optimal allocation of limited defense resources by using deceptive signals to trick the human mind. However, the algorithms are designed to protect against adversaries that make perfectly rational decisions. In behavioral experiments using an abstract cybersecurity game (i.e., Insider Attack Game), we examined human decision‐making when paired against the defense algorithm. We developed an instance‐based learning (IBL) model of an attacker using the Adaptive Control of Thought‐Rational (ACT‐R) cognitive architecture to investigate how humans make decisions under deception in cyber‐attack scenarios. Our results show that the defense algorithm is more effective at reducing the probability of attack and protecting assets when using deceptive signaling, compared to no signaling, but is less effective than predicted against a perfectly rational adversary. Also, the IBL model replicates human attack decisions accurately. The IBL model shows how human decisions arise from experience, and how memory retrieval dynamics can give rise to cognitive biases, such as confirmation bias. The implications of these findings are discussed in the perspective of informing theories of deception and designing more effective signaling schemes that consider human bounded rationality.
Continuous expression of reprogramming factors induces and maintains mouse pluripotency without specific growth factors and signaling inhibitors
Authors: Mao Yihuan , Wang Libin , Zhong Bei , Yang Ning , Li Zhikun , Cui Tongtong , Feng Guihai , Li Wei , Zhang Ying , Zhou Qi 
Published: July 2021

AbstractObjectivesDerivation and maintenance of pluripotent stem cells (PSCs) generally require optimized and complex culture media, which hinders the derivation of PSCs from various species. Expression of Oct4, Sox2, Klf4, and c‐Myc (OSKM) can reprogram somatic cells into induced PSCs (iPSCs), even for species possessing no optimal culture condition. Herein, we explored whether expression of OSKM could induce and maintain pluripotency without PSC‐specific growth factors and signaling inhibitors.MethodsThe culture medium of Tet‐On‐OSKM/Oct4‐GFP mouse embryonic stem cells (ESCs) was switched from N2B27 with MEK inhibitor, GSK3β inhibitor, and leukemia inhibitory factor (LIF) (2iL) to N2B27 with doxycycline. Tet‐On‐OSKM mouse embryonic fibroblast (MEF) cells were reprogrammed in N2B27 with doxycycline. Cell proliferation was traced. Pluripotency was assessed by expression of ESC marker genes, teratoma, and chimera formation. RNA‐Seq was conducted to analyze gene expression.ResultsVia continuous expression of OSKM, mouse ESCs (OSKM‐ESCs) and the resulting iPSCs (OSKM‐iPSCs) reprogrammed from MEF cells propagated stably, expressed pluripotency marker genes, and formed three germ layers in teratomas. Transcriptional landscapes of OSKM‐iPSCs resembled those of ESCs cultured in 2iL and were more similar to those of ESCs cultured in serum/LIF. Furthermore, OSKM‐iPSCs contributed to germline transmission.ConclusionsExpression of OSKM could induce and maintain mouse pluripotency without specific culturing factors. Importantly, OSKM‐iPSCs could produce gene‐modified animals through germline transmission, with potential applications in other species.
Investigation of new biomarkers of kidney injury in renal transplant recipients undergoing graft biopsy
Authors: Michon Arthur , Durrbach Antoine , Gautier Jean‐Charles , Benain Xavier , Lunven Catherine , Jagerschmidt Alexandre , Aubert Catherine , Poetz Oliver , Joos Thomas , Gury Thierry , Becquemont Laurent 
Published: July 2021

ABSTRACTAimUrinary and blood kidney biomarkers (BM) remain insufficient for early kidney injury detection. We aimed to compare new kidney BM with histopathological data in kidney allograft recipients.MethodsBlood and urine samples were collected from consecutive adult patients just before graft biopsy. All kidney samples were classified according to the Banff 2007 classification. The diagnostic performance of 16 new BM was compared to those of urinary proteins, blood urea nitrogen, eGFR, and serum creatinine to identify histopathological groups.ResultsTwo hundred and twenty‐three patients were analyzed. Microalbuminuria and urinary proteins performed well to discriminate glomerular injury from slightly modified renal parenchyma (SMRP). Urinary neutrophil gelatinase‐associated lipocalin (NGAL) had the best performance relative to SMRP (AUROC .93) for acute tubular necrosis (ATN) diagnosis. Other BM had a slightly lower AUROC (.89). For the comparison of ATN to acute rejection, several new urinary BM (NGAL, cystatin C, MCP1) and classical BM (eGFR, serum creatinine) gave similar AUROC values (from .80 to .85). Urinary NGAL values in patients with ATN were 10‐time higher than those with acute rejection (P=.0004).ConclusionThe new BM did not outperform classical BM in the context of renal transplantation. Urinary NGAL may be useful for distinguishing between ATN and acute rejection.
Periodontal ligament repair after active splinting of replanted dogs' teeth
Authors: Silva Raquel Assed Bezerra , Vieira Heloísa Aparecida Orsini , de Gregorio César , Cohenca Nestor , Lucisano Marília Pacífico , Pucinelli Carolina Maschietto , Paula‐Silva Francisco Wanderley Garcia , Nelson‐Filho Paulo , Romano Fábio Lourenço , Assed Bezerra Silva Lea 
Published: July 2021

AbstractBackground/AimThe high rate of root resorption resulting from tooth replantation represents a serious clinical problem. In order to prevent ankylosis and replacement resorption, the contemporary literature highlights the importance of using a flexible stabilization for traumatized teeth. For this purpose, orthodontic devices may be promising for obtaining a better prognosis and periodontal repair. The aim of this study was to evaluate the effect of an active splinting protocol with controlled force in dog's teeth following replantation.Material and MethodsSixty premolar roots from three dogs were used. They were submitted to endodontic treatment, hemisected, atraumatically extracted and subsequently replanted. They were divided into four groups: Passive Stabilization (n = 20)‐after 20 min in a dry medium; Active Stabilization (n = 20)‐after 20 min in a dry medium; Negative control (n = 10)‐immediate replantation and passive Stabilization; and Positive control (n = 10)‐90 min of extra‐alveolar time and passive Stabilization. The samples were collected and submitted to histologic processing. They were then evaluated for the count of inflammatory cells, expression of neurotrophin 4, osteoclasts, apoptotic cells and collagen fibres. The results were submitted to ANOVA or Kruskal‐Wallis statistical tests followed by Tukey or Dunn post‐tests (α = 5%).ResultsPassive Stabilization with orthodontic brackets without traction used after replantation had the highest number of inflammatory cells (p = .0122), osteoclasts (p = .0013) and percentage of collagen fibres in the periodontal ligament (p < .0001) when compared to Active Stabilization with orthodontic brackets applying amild tensile force. Neurotrophin 4 had no statistically significant difference (p = .05), regardless of the treatment. The apoptotic cells count revealed statistical differences (p < .0001) between Active Stabilization (189.70 ± 47.99) and Positive Control (198.90 ± 88.92) when compared to Passive Stabilization (21.19 ± 32.94).ConclusionThe active splinting protocol using orthodontic appliances generating a light and controlled force favoured periodontal ligament repair of replanted teeth.
On inorganic N uptake by vascular plants: Can 15N tracer techniques resolve the NH4+ versus NO3− “preference” conundrum?
Authors: Chalk Phillip , Smith Christopher 
Published: July 2021

AbstractThe relative uptake by plants of the two ionic nitrogen (N) forms, ammonium (NH4+) and nitrate (NO3−), has been the subject of much interest during the past 50 years, resulting in a considerable scientific literature. The general idea is that plants have choice, resulting in preference for either one mineral N form or the other. Unfortunately, there is no specific definition of preference or agreement on how it should be measured. In this review, we critically examine the alternative techniques that have been used to measure the relative uptake of NH4+ and NO3− by plants, including those based on unlabelled sources, 15N‐enriched mineral N forms and variations in the 15N natural abundance of mineral N sources. The main difficulty with using unlabelled N is the antecedent N in plant tissue prior to the imposition of treatments. Although 15N‐enrichment overcomes this obstacle, it is nevertheless difficult to separate uptake as 15NH4+, uptake as 15NO3− and uptake as 15NO3− derived from the nitrification of 15NH4+. With 15N natural abundance, isotopic fractionation during plant uptake complicates the interpretation of data. There is increasing evidence that plants exhibit flexibility or plasticity with respect to the use of mineral N forms rather than preference.Highlights
The concept of plant preference for NH4+ or NO3− forms of mineral N is examined
Experiments using 15N‐enrichment and 15N natural abundance are reviewed
The direct uptake of 15NO3− is confounded with the uptake of 15NO3− derived from nitrified 15NH4+
Plants exhibit plasticity rather than preference in the acquisition of ammonium and nitrate
The cyclin‐dependent kinase inhibitor AT7519 augments cisplatin's efficacy in ovarian cancer via multiple oncogenic signaling pathways
Authors: Wang Ling , Chen Yan , Li Hui , Xu Qiqi , Liu Rong 
Published: July 2021

AbstractAlthough cisplatin is the most active drug for the treatment of ovarian cancer, majority of patients develop resistance and ultimately relapse. Enhancing the efficacy of cisplatin could represent a promising strategy to improve the clinical outcome of patients with ovarian cancer. AT7519 is a multitargeted cyclin‐dependent kinase (CDK) inhibitor and displays potent anticancer activities. In this work, we show that the combination of AT7519 with cisplatin is much more superior to cisplatin alone in inhibiting ovarian cancer. AT7519 at nanomolar concentrations inhibits proliferation and migration and induces apoptosis of multiple ovarian cancer cell lines. In contrast, AT7519 at the same concentrations either does not affect survival or is significantly less effective in inhibiting proliferation and migration in normal ovarian cells and fibroblast cells. AT7519 significantly augments the inhibitory effects of cisplatin in ovarian cancer cells in a dose‐dependent manner. Mechanistic studies suggest that AT7519 (i) inhibits proliferation via decreasing activities of CDK1 and 2, and via inhibiting RNA transcription; (ii) inhibits migration via suppressing epithelial–mesenchymal transition (EMT); and (iii) induces apoptosis via decreasing Mcl‐1 and increasing Bim in ovarian cancer cells. Using a human ovarian cancer xenograft mouse model, we confirm the in vivo efficacy of AT7519 alone, and the synergistic effects of AT7519 and cisplatin in combination, at doses that cause minimal toxicity in mice. Our findings provide systematic preclinical evidence to support the initialization of clinical trials of the AT7519 and cisplatin combination for the treatment of ovarian cancer.
Microtubule inhibitors identified through nonbiased screening enhance DNA transfection efficiency by delaying p62‐dependent ubiquitin recruitment
Authors: Tsuchiya Megumi , Ogawa Hidesato , Watanabe Kento , Koujin Takako , Mori Chie , Nunomura Kazuto , Lin Bangzhong , Tani Akiyoshi , Hiraoka Yasushi , Haraguchi Tokuko 
Published: July 2021

AbstractEctopic gene expression is an indispensable tool in biology and medicine, but is often limited by the low efficiency of DNA transfection. We previously reported that depletion of the autophagy receptor p62/SQSTM1 enhances DNA transfection efficiency by preventing the degradation of transfected DNA. Therefore, p62 is a potential target for drugs to increase transfection efficiency. To identify such drugs, a nonbiased high‐throughput screening was applied to over 4,000 compounds from the Osaka University compound library, and their p62 dependency was evaluated. The top‐scoring drugs were mostly microtubule inhibitors, such as colchicine and vinblastine, and all of them showed positive effects only in the presence of p62. To understand the p62‐dependent mechanisms, the time required for p62‐dependent ubiquitination, which is required for autophagosome formation, was examined using polystyrene beads that were introduced into cells as materials that mimicked transfected DNA. Microtubule inhibitors caused a delay in ubiquitination. Furthermore, the level of phosphorylated p62 at S405 was markedly decreased in the drug‐treated cells. These results suggest that microtubule inhibitors inhibit p62‐dependent autophagosome formation. Our findings demonstrate for the first time that microtubule inhibitors suppress p62 activation as a mechanism for increasing DNA transfection efficiency and provide solutions to increase efficiency.
The changing face of trigeminal neuralgia—A narrative review
Authors: Maarbjerg Stine , Benoliel Rafael 
Published: July 2021

AbstractObjectiveThis narrative review aims to update the reader on the new classification of trigeminal neuralgia (TN), clinical signs, pathophysiologic evidence, and their implications on management. This review is based on the authors’ collective experience and knowledge of the literature in addition to a literature search.BackgroundIn recent years, the phenotype of TN has been intensively studied leading to discrete groups of patients. These include patients with TN with additional continuous pain, and patients with and without neurovascular compression of the trigeminal dorsal root entry zone. A number of associated clinical signs such as tearing and sensory changes need further research.MethodsThe literature on TN was searched in PubMed with the aims of providing evidence for the recently published third edition of the International Classification of Headache Disorders (ICHD) and update the clinical phenotype and management of the TN subcategories.ResultsThe ICHD's new classification for TN is based on reliable clinical data, imaging, and neurophysiologic studies. The TN classification reflects current knowledge and has improved the possibility for clinicians to choose adequate management options. However, there is a lack of effective, safe drugs for the management of TN and sparse, robust data on neurosurgical options.ConclusionResearch into all aspects of TN—diagnosis, pharmacotherapy, surgery, long‐term management prognosis, and natural history—is needed. Research should adhere to the ICHD's schema for TN. Improved drugs are needed along with rigorous research into surgical options and their efficacy for different subtypes of TN.