bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Ultrasound-Guided Fine-Needle Aspiration of Thyroid Bed Lesions and Clinical Predictors of Recurrent Papillary Thyroid Carcinoma
Authors: Yuan Lisi , Jebastin Thangaiah Judith , Chute Deborah J 
Published: July 2020

Abstract

Objectives
Fine-needle aspiration (FNA) of thyroid bed lesions after thyroidectomy is challenging to evaluate. We determined the sensitivity, specificity, and positive and negative predicative value of thyroid bed FNA (TB-FNA) for detecting local recurrence of thyroid carcinoma.

Methods
A retrospective search was conducted for TB-FNAs from patients with a prior thyroid resection and subsequent ipsilateral FNA from the thyroid bed. Clinical and pathologic data were retrieved from the medical record. Patients were ultimately classified as “malignant” or “benign” based on the worst pathology identified and follow-up available.

Results
Forty-two cases were included, and the prior thyroidectomy pathology included 36 papillary thyroid carcinomas, two follicular carcinomas, one medullary carcinoma, and three benign cases. TB-FNA was adequate in 38 (90.5%) cases and interpreted as positive for malignancy (n = 22; 52.4%), suspicious for follicular neoplasm (n = 3; 7.1%), atypia of unknown significance (n = 2; 4.8%), and benign (n = 10; 23.8%). Twenty-seven patients had histologic follow-up, and 24 (87.5%) showed recurrent malignancy. The cytology sensitivity, specificity, positive predictive value, negative predictive value, and accuracy were 96%, 100%, 100%, 92.3%, and 97.4%, respectively, for identification of recurrent malignancy.

Conclusions
Most TB-FNA cases ultimately were diagnosed with malignancy on follow-up, although there may be sampling bias, as not all clinically benign cases had surgical follow-up.
Ensuring that the outcome domains proposed for use in burns research are relevant to adult burn patients: a systematic review of qualitative research evidence
Authors: Mathers Jonathan , Moiemen Naiem , Bamford Amy , Gardiner Fay , Tarver Joanne 
Published: July 2020

Abstract

Background
There have been several attempts to define core outcome domains for use in research focused on adult burns. Some have been based in expert opinion, whilst others have used primary qualitative research to understand patients’ perspectives on outcomes. To date there has not been a systematic review of qualitative research in burns to identify a comprehensive list of patient-centred outcome domains. We therefore conducted a systematic review of qualitative research studies in adult burns.

Methods
We searched multiple databases for English-language, peer-reviewed, qualitative research papers. We used search strategies devised using the SPIDER tool for qualitative synthesis. Our review utilized an iterative three-step approach: (1) outcome-focused coding; (2) development of descriptive accounts of outcome-relevant issues; and (3) revisiting studies and the broader theoretical literature in order to frame the review findings.

Results
Forty-one articles were included. We categorized papers according to their primary focus. The category with the most papers was adaptation to life following burn injury (n = 13). We defined 19 outcome domains across the 41 articles: (1) sense of self; (2) emotional and psychological morbidity; (3) sensory; (4) scarring and scar characteristics; (5) impact on relationships; (6) mobility and range of joint motion; (7) work; (8) activities of daily living and self-care; (9) treatment burden; (10) engagement in activities; (11) wound healing and infection; (12) other physical manifestations; (13) financial impact; (14) impact on spouses and family members; (15) analgesia and side effects; (16) cognitive skills; (17) length of hospital stay; (18) access to healthcare; and (19) speech and communication. We suggest that sense of self is a core concern for patients that, to date, has not been clearly conceptualized in the burns outcome domain literature.

Conclusions
This outcome domain framework identifies domains that are not covered in previous attempts to outline core outcome domains for adult burn research. It does so with reference to existing theoretical perspectives from the sociology and psychology of medicine. We propose that this framework can be used as a basis to ensure that outcome assessment is patient-centred. Sense of self requires further consideration as a core outcome domain.
Oncogene HSPH1 modulated by the rs2280059 genetic variant diminishes EGFR-TKIs efficiency in advanced lung adenocarcinoma
Authors: Li Yankang , Zhang Nasha , Zhang Li , Song Yemei , Liu Jie , Yu Jinming , Yang Ming 
Published: July 2020

Abstract
Although epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) therapy is effective for most advanced non-small-cell lung cancer (NSCLC) patients with mutant EGFR, some patients show little or no response. Germline variations, such as single-nucleotide polymorphisms (SNPs), have been proved to be involved in disease progression after EGFR-TKI therapy. In this study, we hypothesized that the functional HSPH1 SNP may affect gene expression and, thus, prognosis of NSCLC patients treated with EGFR-TKIs. We systematically examined impacts of HSPH1 SNPs on NSCLC survival in two independent cohorts consisted of 319 EGFR-TKI treated stage IIIB/IV NSCLC patients. The promoter rs2280059 polymorphism was significantly associated with patient survival in both cohorts. In vitro and In vivo assays elucidated that rs2280059 G allele shows higher capability to drive HSPH1 promoter activities. Silencing HSPH1 significantly increases the antineoplastic effects of gefitinib on NSCLC cells. Our findings demonstrated potential implications of HSPH1 in clinic, which may lead to better understanding and outcome assessment of EGFR-TKI treatment.
A Randomized, Double-blind, Multicenter Trial Comparing Efficacy and Safety of Imipenem/Cilastatin/Relebactam Versus Piperacillin/Tazobactam in Adults With Hospital-acquired or Ventilator-associated Bacterial Pneumonia (RESTORE-IMI 2 Study)
Authors: Titov Ivan , Wunderink Richard G , Roquilly Antoine , Rodríguez Gonzalez Daniel , David-Wang Aileen , Boucher Helen W , Kaye Keith S , Losada Maria C , Du Jiejun , Tipping Robert , Rizk Matthew L , Patel Munjal , Brown Michelle L , Young Katherine , Kartsonis Nicholas A , Butterton Joan R , Paschke Amanda , Chen Luke F 
Published: July 2020

Abstract

Background
Imipenem combined with the β-lactamase inhibitor relebactam has broad antibacterial activity, including against carbapenem-resistant gram-negative pathogens. We evaluated efficacy and safety of imipenem/cilastatin/relebactam in treating hospital-acquired/ventilator-associated bacterial pneumonia (HABP/VABP).

Methods
This was a randomized, controlled, double-blind phase 3 trial. Adults with HABP/VABP were randomized 1:1 to imipenem/cilastatin/relebactam 500 mg/500 mg/250 mg or piperacillin/tazobactam 4 g/500 mg, intravenously every 6 hours for 7–14 days. The primary endpoint was day 28 all-cause mortality in the modified intent-to-treat (MITT) population (patients who received study therapy, excluding those with only gram-positive cocci at baseline). The key secondary endpoint was clinical response 7–14 days after completing therapy in the MITT population.

Results
Of 537 randomized patients (from 113 hospitals in 27 countries), the MITT population comprised 264 imipenem/cilastatin/relebactam and 267 piperacillin/tazobactam patients; 48.6% had ventilated HABP/VABP, 47.5% APACHE II score ≥15, 24.7% moderate/severe renal impairment, 42.9% were ≥65 years old, and 66.1% were in the intensive care unit. The most common baseline pathogens were Klebsiella pneumoniae (25.6%) and Pseudomonas aeruginosa (18.9%). Imipenem/cilastatin/relebactam was noninferior (P &lt; .001) to piperacillin/tazobactam for both endpoints: day 28 all-cause mortality was 15.9% with imipenem/cilastatin/relebactam and 21.3% with piperacillin/tazobactam (difference, −5.3% [95% confidence interval {CI}, −11.9% to 1.2%]), and favorable clinical response at early follow-up was 61.0% and 55.8%, respectively (difference, 5.0% [95% CI, −3.2% to 13.2%]). Serious adverse events (AEs) occurred in 26.7% of imipenem/cilastatin/relebactam and 32.0% of piperacillin/tazobactam patients; AEs leading to treatment discontinuation in 5.6% and 8.2%, respectively; and drug-related AEs (none fatal) in 11.7% and 9.7%, respectively.

Conclusions
Imipenem/cilastatin/relebactam is an appropriate treatment option for gram-negative HABP/VABP, including in critically ill, high-risk patients.

Clinical Trials Registration
NCT02493764.
Similarity of Sentences With Contradiction Using Semantic Similarity Measures
Authors: Krishna Siva Prasad M , Sharma Poonam 
Published: July 2020

AbstractShort text or sentence similarity is crucial in various natural language processing activities. Traditional measures for sentence similarity consider word order, semantic features and role annotations of text to derive the similarity. These measures do not suit short texts or sentences with negation. Hence, this paper proposes an approach to determine the semantic similarity of sentences and also presents an algorithm to handle negation. In sentence similarity, word pair similarity plays a significant role. Hence, this paper also discusses the similarity between word pairs. Existing semantic similarity measures do not handle antonyms accurately. Hence, this paper proposes an algorithm to handle antonyms. This paper also presents an antonym dataset with 111-word pairs and corresponding expert ratings. The existing semantic similarity measures are tested on the dataset. The results of the correlation proved that the expert ratings are in order with the correlation obtained from the semantic similarity measures. The sentence similarity is handled by proposing two algorithms. The first algorithm deals with the typical sentences, and the second algorithm deals with contradiction in the sentences. SICK dataset, which has sentences with negation, is considered for handling the sentence similarity. The algorithm helped in improving the results of sentence similarity.
VE-PTP inhibition elicits eNOS phosphorylation to blunt endothelial dysfunction and hypertension in diabetes
Authors: Siragusa Mauro , Oliveira Justo Alberto Fernando , Malacarne Pedro Felipe , Strano Anna , Buch Akshay , Withers Barbara , Peters Kevin G , Fleming Ingrid 
Published: July 2020

Abstract

Aims
Receptor-type vascular endothelial protein tyrosine phosphatase (VE-PTP) dephosphorylates Tie-2 as well as CD31, VE-cadherin, and vascular endothelial growth factor receptor 2 (VEGFR2). The latter form a signal transduction complex that mediates the endothelial cell response to shear stress, including the activation of the endothelial nitric oxide (NO) synthase (eNOS). As VE-PTP expression is increased in diabetes, we investigated the consequences of VE-PTP inhibition (using AKB-9778) on blood pressure in diabetic patients and the role of VE-PTP in the regulation of eNOS activity and vascular reactivity.

Methods and results
In diabetic patients AKB-9778 significantly lowered systolic and diastolic blood pressure. This could be linked to elevated NO production, as AKB increased NO generation by cultured endothelial cells and elicited the NOS inhibitor-sensitive relaxation of endothelium-intact rings of mouse aorta. At the molecular level, VE-PTP inhibition increased the phosphorylation of eNOS on Tyr81 and Ser1177 (human sequence). The PIEZO1 activator Yoda1, which was used to mimic the response to shear stress, also increased eNOS Tyr81 phosphorylation, an effect that was enhanced by VE-PTP inhibition. Two kinases, i.e. abelson-tyrosine protein kinase (ABL)1 and Src were identified as eNOS Tyr81 kinases as their inhibition and down-regulation significantly reduced the basal and Yoda1-induced tyrosine phosphorylation and activity of eNOS. VE-PTP, on the other hand, formed a complex with eNOS in endothelial cells and directly dephosphorylated eNOS Tyr81 in vitro. Finally, phosphorylation of eNOS on Tyr80 (murine sequence) was found to be reduced in diabetic mice and diabetes-induced endothelial dysfunction (isolated aortic rings) was blunted by VE-PTP inhibition.

Conclusions
VE-PTP inhibition enhances eNOS activity to improve endothelial function and decrease blood pressure indirectly, through the activation of Tie-2 and the CD31/VE-cadherin/VEGFR2 complex, and directly by dephosphorylating eNOS Tyr81. VE-PTP inhibition, therefore, represents an attractive novel therapeutic option for diabetes-induced endothelial dysfunction and hypertension.
Trapped Factors and China’s Impact on Global Growth
Authors: Bloom Nicholas , Romer Paul , Terry Stephen J , Van Reenen John 
Published: July 2020

AbstractAfter a recent increase in Chinese import competition, European firms increased innovation. We present and rationalise these patterns using ‘trapped factors’ at the micro level within a stylised equilibrium model of product-cycle trade and growth. Trade integration of the magnitude observed between the OECD and low-wage nations as a whole can considerably increase the long-run growth rate and welfare. In the short run exposed firms devote trapped factors to increased innovation, leading both to increased innovation at these individual firms as well as to a small amount of extra transitional growth overall. China accounts for half of the dynamic trade gains.
Skewed CD39/CD73/adenosine pathway contributes to B-cell hyperactivation and disease progression in patients with chronic hepatitis B
Authors: Zhou Shuang-Nan , Zhang Ning , Liu Hong-Hong , Xia Peng , Zhang Chao , Song Jin-Wen , Fan Xing , Shi Ming , Jin Lei , Zhang Ji-Yuan , Wang Fu-Sheng 
Published: July 2020

Abstract

Background
The mechanisms underlying B-cell hyperactivation in patients with chronic hepatitis B virus (HBV) infection remain largely undefined. The present study assessed the clinical characteristics of the CD39/CD73/adenosine pathway in patients with chronic hepatitis B (CHB).

Methods
We examined CD39 and CD73 expression and adenosine production by B-cells from 202 HBV-infected patients. B-cell-activation phenotypes were assessed by flow cytometry after CpG+CD40 ligand stimulation with or without blockade and activation of the adenosine pathway.

Results
CD39 and CD73 expression on circulating B-cells was decreased in CHB patients with high HBV DNA, HBeAg positivity, high HBsAg levels, and active liver inflammation, and was hierarchically restored in complete responders according to HBeAg seroconversion or HBsAg reduction. However, CD39 and CD73 expression on activated memory and tissue-like memory B-cell subsets in complete responders was not increased despite effective antiviral treatments. Furthermore, CD39 and CD73 expression on intra-hepatic B-cells was decreased in inflammatory livers. In vitro, B-cells from CHB patients showed a markedly reduced capacity to generate CD39/CD73-dependent extracellular adenosine and expressed increased levels of activation markers after adenosine-production blockade. Contrastingly, metformin significantly reduced activation-marker expression via regulating AMP-activated protein kinase.

Conclusions
The skewed CD39 and CD73 expression on B-cells was associated with a high viral burden, liver inflammation, and antiviral efficacy in CHB patients, and the skewed CD39/CD73/adenosine pathway contributed to B-cell hyperactivation. Regulation of the CD39/CD73/adenosine pathway using metformin may represent a therapeutic option to reverse HBV-induced immune pathogenesis.
Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences
Authors: Kryukov Kirill , Ueda Mahoko Takahashi , Nakagawa So , Imanishi Tadashi 
Published: July 2020

Abstract

Background
Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available.

Findings
We systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results.

Conclusion
We found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.
Time-domain elastic Gauss–Newton full-waveform inversion: a matrix-free approach
Authors: Chen Ke , Sacchi Mauricio D 
Published: July 2020

SUMMARYWe present a time-domain matrix-free elastic Gauss–Newton full-waveform inversion (FWI) algorithm. Our algorithm consists of a Gauss–Newton update with a search direction calculated via elastic least-squares reverse time migration (LSRTM). The conjugate gradient least-squares (CGLS) method solves the LSRTM problem with forward and adjoint operators derived via the elastic Born approximation. The Hessian of the Gauss–Newton method is never explicitly formed or saved in memory. In other words, the CGLS algorithm solves for the Gauss–Newton direction via the application of implicit-form forward and adjoint operators which are equivalent to elastic Born modelling and elastic reverse time migration, respectively. We provide numerical examples to test the proposed algorithm where we invert for P- and S-wave velocities simultaneously. The proposed algorithm performs positively on mid-size problems where we report solutions of slight improvement than those computed using the conventional non-linear conjugate gradient method. In spite of the aforementioned limited gain, the theory developed in this paper contributes to a better understanding of time-domain elastic Gauss–Newton FWI.
Schizophrenic agendas in the EU's external actions in Mali
Authors: Cold-Ravnkilde Signe Marie , Nissen Christine 
Published: July 2020

Abstract
Because of its geographical proximity to the EU, the Sahel region's perceived cross-border security threats of terror, migration and organized crime have become a top European security policy priority. Contributing to existing debates on EU external actions, the article develops the idea that the EU's engagement in the Sahel has become an attempt to construct and confirm the Union's ability to act as a global security actor. Through the analytical lens of ‘translation’ emphasizing the continuous transformation of norms and ideas by actors and contexts, the article examines how EU staff implement shifting policy objectives in their security practices in Mali; the effects these intervention practices produce; and how, in turn, these effects reflect back upon the EU's role as a security actor. The article shows how the EU's actorness and ability to perform security are hampered by the lack of buy-in from their local partners, as narrating success in a context of escalating violence becomes increasingly implausible. Thus, we argue that while the EU's activities in Mali reinforce the idea of the EU as a security actor, the limited character and impact of the EU's activities on the ground also reinforce the idea of it as a limited or even ineffective actor. The article thereby provides fruitful input to discussions of the constitutive effects of everyday practices in interventions and the production of EU security actorness as played out in the Sahel.
Security for whom? Analysing hybrid security governance in Africa's extractive sectors
Authors: Enns Charis , Andrews Nathan , Grant J Andrew 
Published: July 2020

Abstract
In this article, we analyse the factors underpinning the shift towards hybrid security governance in Africa. Extant scholarship largely attributes this shift to broader global processes, such as histories of colonialism, neoliberalism and transformations in global governance, which have served to legitimize the role of private authority in security provision around sites of resource extraction. Our analysis seeks to understand the relative and relational influence of power and rules in international politics by offering empirical insights about what hybrid security arrangements look like ‘on the ground’. Drawing upon recently conducted fieldwork in Kenya, Uganda and Ghana, we examine how hybrid security arrangements affect the lives of those living near sites of natural resource extraction. Our analyses suggest that although hybrid security has emerged as the leading approach to security governance, this approach to security does not uniformly involve or serve the interests of all stakeholders. Rather, we find that hybrid security arrangements aid the security of extractive operations—securing investments in both physical and human capital—while sometimes undermining the security of nearby communities.
Cigarette Smoking, Coffee Consumption, Alcohol Intake, and Risk of Crohn’s Disease and Ulcerative Colitis: A Mendelian Randomization Study
Authors: Georgiou Andrea N , Ntritsos Georgios , Papadimitriou Nikos , Dimou Niki , Evangelou Evangelos 
Published: July 2020

Abstract

Background
Crohn’s disease (CD) and ulcerative colitis (UC) are widely associated with smoking in epidemiological studies, whereas there are conflicting results for the association between CD and UC for both coffee and alcohol consumption. Herein, we aimed to investigate whether cigarette smoking and alcohol and coffee consumption are causally associated with either CD or UC.

Methods
We utilized 540 genome-wide significant single-nucleotide polymorphisms for 3 potentially addictive substances—nicotine, alcohol, and caffeine—to assess the association of smoking, coffee, and alcohol consumption with CD and UC (12,194 CD cases, 12,366 UC cases, and 25,042 controls of European ancestry), using Mendelian randomization analysis. Mendelian randomization estimates were used to evaluate the effect of the exposure factors on CD and UC risk. Sensitivity analysis was employed to test for any directional pleiotropy.

Results
We found evidence for a positive causal association between the age of smoking initiation and UC risk and between alcohol consumption and CD risk, which disappeared after sensitivity analysis for both associations (P &gt; 0.05). No evidence for a causal association between cigarettes per day, smoking initiation, smoking cessation, and coffee consumption variables and UC or CD was found.

Conclusions
We found no clear evidence that either genetically predicted smoking, coffee consumption, or alcohol consumption are causally associated with the risk for CD or UC, although our findings indicate a potential positive association between the age of smoking and UC and between alcohol consumption and CD.