bluuebunny/crossref_metadata_2025_split huggingface dataset:
New enzymes for peptide biosynthesis in microorganisms
Authors: Ogasawara Yasushi 
Published: December 2018

ABSTRACT
Peptides, biologically occurring oligomers of amino acids linked by amide bonds, are essential for living organisms. Many peptides isolated as natural products have biological functions such as antimicrobial, antivirus and insecticidal activities. Peptides often possess structural features or modifications not found in proteins, including the presence of nonproteinogenic amino acids, macrocyclic ring formation, heterocyclization, N-methylation and decoration by sugars or acyl groups. Nature employs various strategies to increase the structural diversity of peptides. Enzymes that modify peptides to yield mature natural products are of great interest for discovering new enzyme chemistry and are important for medicinal chemistry applications. We have discovered novel peptide modifying enzymes and have identified: (i) a new class of amide bond forming-enzymes; (ii) a pathway to biosynthesize a carbonylmethylene-containing pseudodipeptide structure; and (iii) two distinct peptide epimerases. In this review, an overview of our findings on peptide modifying enzymes is presented.
Final report: key comparison EURAMET.AUV.A-K5
Authors: Avison Janine , Harris Peter , Robinson Stephen , Rodrigues Dominique , Guglielmone Claudio , Hof Christian , Sadikoglu Enver , Chushkov Marin , Zelenika Slobodan , Rosenkrantz Peter , Andersson Håkan , Fedtke Thomas , Koch Christian , Martin Nieves Medina , Ruiz Salustiano , Shawky Hany 
Published: December 2018

This is the final (Draft B) report for key comparison EURAMET.AUV.A-K5 on the pressure calibration of laboratory standard microphones in the frequency range from 2 Hz to 10 kHz. Twelve national metrology institutes took part in the key comparison and the National Physical Laboratory piloted the project. Two travelling standard microphones were circulated to the participants and results in the form of regular calibration certificates were collected throughout the project. The analysis used the results for one of the microphones only and values for both sensitivity level and sensitivity phase and have been linked to the CCAUV.A K5 key comparison reference value (KCRV) via two linking laboratories (NPL and INRIM).
KEY WORDS FOR SEARCH
acoustics, microphones, metrology, key comparison, pressure calibration

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCAUV, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
How to take fractional-order derivative experimentally?
Authors: Stupin D D , Lihachev A I , Nashchekin A V 
Published: December 2018

Abstract
In this study we demonstrate a simple and compact implementation of the fractional-order differentiator. At the heart of the proposed approach lies the “universal power law” of the capacitance dispersion of the interface between nanoporous TiN micro-electrode and NaCl 0.9% solution. Using of this phenomenon we take experimentally 0.68- and 0.77-order derivatives of various functions.
The G-protein coupled receptor ChemR23 determines smooth muscle cell phenotypic switching to enhance high phosphate-induced vascular calcification
Authors: Carracedo Miguel , Artiach Gonzalo , Witasp Anna , Clària Joan , Carlström Mattias , Laguna-Fernandez Andres , Stenvinkel Peter , Bäck Magnus 
Published: December 2018

Abstract

Aims
Vascular calcification, a marker of increased cardiovascular risk, is an active process orchestrated by smooth muscle cells. Observational studies indicate that omega-3 fatty acids protect against vascular calcification, but the mechanisms are unknown. The G-protein coupled receptor ChemR23 transduces the resolution of inflammation induced by the omega-3-derived lipid mediator resolvin E1. ChemR23 also contributes to osteoblastic differentiation of stem cells and bone formation, but its role in vascular calcification is unknown. The aim of this study was to establish the role of ChemR23 in smooth muscle cell fate and calcification

Methods and results
Gene expression analysis in epigastric arteries derived from patients with chronic kidney disease and vascular calcification revealed that ChemR23 mRNA levels predicted a synthetic smooth muscle cell phenotype. Genetic deletion of ChemR23 in mice prevented smooth muscle cell de-differentiation. ChemR23-deficient smooth muscle cells maintained a non-synthetic phenotype and exhibited resistance to phosphate-induced calcification. Moreover, ChemR23-deficient mice were protected against vitamin D3-induced vascular calcification. Resolvin E1 inhibited smooth muscle cell calcification through ChemR23. Introduction of the Caenorhabditis elegans Fat1 transgene, leading to an endogenous omega-3 fatty acid synthesis and hence increased substrate for resolvin E1 formation, significantly diminished the differences in phosphate-induced calcification between ChemR23+/+ and ChemR23−/− mice.

Conclusion
This study identifies ChemR23 as a previously unrecognized determinant of synthetic and osteoblastic smooth muscle cell phenotype, favouring phosphate-induced vascular calcification. This effect may be of particular importance in the absence of ChemR23 ligands, such as resolvin E1, which acts as a calcification inhibitor under hyperphosphatic conditions.
Trimodality therapy for superior sulcus tumour: experience of a single institution over 19 years
Authors: Uchida Shinsuke , Yoshida Yukihiro , Ohe Yuichiro , Nakayama Yuko , Motoi Noriko , Kobayashi Aki , Asakura Keisuke , Nakagawa Kazuo , Watanabe Shun-ichi 
Published: December 2018

AbstractOBJECTIVESInduction chemoradiotherapy followed by surgery is the standard treatment for superior sulcus tumours (SSTs). However, the protocols, chemotherapy agents and cycles used as well as the mode and intensity of radiotherapy vary between institutions. Thus, the objective of the study was to investigate the effects of trimodality therapy on the outcomes of patients with SSTs.METHODSSixty patients with SSTs were enrolled between January 1999 and December 2017. Induction therapy consisted primarily of 2 cycles of mitomycin–vindesine–cisplatin or cisplatin–vinorelbine delivered concurrently to the tumour with 40–45 Gy of radiation. Surgery was performed 2–6 weeks after completion of induction therapy.RESULTSFifty-four (90%) patients underwent radical surgical resection. Complete pathological resection was achieved in 44 patients (81%). There was no 30-day mortality. After a median follow-up of 57.0 months, 19 (35%) patients experienced recurrence, and 8 (15%) patients showed brain metastasis. A pathological complete response (PCR) was observed in 12 (22%) patients. The 5-year survival rate for the entire population (n = 54) was 69% (95% confidence interval 55–81%). The survival rate was better for patients who underwent complete resection than for those who underwent incomplete resection (73% vs 51%, P = 0.46). A better survival rate was evident in patients with PCR than in those without PCR (92% vs 62%, P = 0.12).CONCLUSIONSTrimodality therapy for SSTs was efficacious and associated with favourable outcomes, with acceptable morbidity and mortality. PCR in patients with resected SSTs reveals promising long-term survival prospects with the trimodality therapy.
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
Authors: Xu Gui-Cai , Xu Tian-Jun , Zhu Rui , Zhang Yan , Li Shang-Qi , Wang Hong-Wei , Li Jiong-Tang 
Published: December 2018

Abstract

Background
Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes.

Findings
We developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps faster and with a lower error rate and a much lower memory usage than two existing, state-of-the art tools. This tool utilized raw reads to fill more gaps than when using error-corrected reads. It is applicable to gaps in the assemblies by different approaches and from large and complex genomes. After performing gap-closure using this tool, the contig N50 size of the human CHM1 genome was improved from 143 kb to 19 Mb, a 132-fold increase. We also closed the gaps in the Triticum urartu genome, a large genome rich in repeats; the contig N50 size was increased by 40%. Further, we evaluated the contiguity and correctness of six hybrid assembly strategies by combining the optimal TGS-based and next-generation sequencing-based assemblers with LR_Gapcloser. A proposed and optimal hybrid strategy generated a new human CHM1 genome assembly with marked contiguity. The contig N50 value was greater than 28 Mb, which is larger than previous non-reference assemblies of the diploid human genome.

Conclusions
LR_Gapcloser is a fast and efficient tool that can be used to close gaps and improve the contiguity of genome assemblies. A proposed hybrid assembly including this tool promises reference-grade assemblies. The software is available at http://www.fishbrowser.org/software/LR_Gapcloser/.
Evaluating visual analytics for health informatics applications: a systematic review from the American Medical Informatics Association Visual Analytics Working Group Task Force on Evaluation
Authors: Wu Danny T Y , Chen Annie T , Manning John D , Levy-Fix Gal , Backonja Uba , Borland David , Caban Jesus J , Dowding Dawn W , Hochheiser Harry , Kagan Vadim , Kandaswamy Swaminathan , Kumar Manish , Nunez Alexis , Pan Eric , Gotz David 
Published: December 2018

AbstractObjectiveThis article reports results from a systematic literature review related to the evaluation of data visualizations and visual analytics technologies within the health informatics domain. The review aims to (1) characterize the variety of evaluation methods used within the health informatics community and (2) identify best practices.MethodsA systematic literature review was conducted following PRISMA guidelines. PubMed searches were conducted in February 2017 using search terms representing key concepts of interest: health care settings, visualization, and evaluation. References were also screened for eligibility. Data were extracted from included studies and analyzed using a PICOS framework: Participants, Interventions, Comparators, Outcomes, and Study Design.ResultsAfter screening, 76 publications met the review criteria. Publications varied across all PICOS dimensions. The most common audience was healthcare providers (n = 43), and the most common data gathering methods were direct observation (n = 30) and surveys (n = 27). About half of the publications focused on static, concentrated views of data with visuals (n = 36). Evaluations were heterogeneous regarding setting and measurements used.DiscussionWhen evaluating data visualizations and visual analytics technologies, a variety of approaches have been used. Usability measures were used most often in early (prototype) implementations, whereas clinical outcomes were most common in evaluations of operationally-deployed systems. These findings suggest opportunities for both (1) expanding evaluation practices, and (2) innovation with respect to evaluation methods for data visualizations and visual analytics technologies across health settings.ConclusionEvaluation approaches are varied. New studies should adopt commonly reported metrics, context-appropriate study designs, and phased evaluation strategies.
Neurologic Manifestations of Influenza A(H3N2) Infection in Children During the 2016–2017 Season
Authors: Rao Suchitra , Martin Jan , Ahearn M Alex , Osborne Christina , Moss Angela , Dempsey Amanda , Dominguez Samuel R , Weinberg Adriana , Messacar Kevin B 
Published: December 2018

Abstract
Among 182 children with influenza infection in 2016–2017, 18% had neurologic manifestations of influenza (NMI), including seizures and encephalopathy; 85% of these children were infected with the H3N2 strain. Children with NMI had 3.5-times-higher odds of having a neurologic comorbidity than those without NMI and a 10-fold increased odds of hospitalization.
Typological features of grammaticalization in Semitic
Authors: Esseesy Mohssen 
Published: December 2018

AbstractThis study highlights some notable typological features of ancient and modern Semitic languages. It sheds light on a number of shared intragenetic similarities and parallels within Semitic in the processes and outcomes of grammaticalization. Specifically, it examines the emergence and evolution of prepositionals from certain body-part terms; the shift from synthetic towards more analytic possessive strategies; and independent personal pronouns becoming inherently bound agreement markers as prefixes and suffixes on the imperfective and perfective verb stems, respectively. Moreover, with supporting evidence from corpus data, this study argues for the primacy of third-person pronouns, which assume expanded grammatical functions as copulas, expletives, and discourse-related functions. Finally, this study draws attention to the sociolinguistic factors, such as native speakers’ attitudinal stance, which directly impinge on language change within the diglossic nature of Arabic, and calls for consideration of sociolinguistic factors in the study of language evolution by grammaticalization.
The Unexpected Activeness of Passive Investors: A Worldwide Analysis of ETFs
Authors: Cheng Si , Massa Massimo , Zhang Hong 
Published: December 2018

Abstract
The global ETF industry provides more complicated investment vehicles than low-cost index trackers. Instead, we find that the real investments of ETFs may deviate from their benchmarks to leverage informational advantages (which leads to a surprising stock-selection ability) and to help affiliated OEFs through cross-trading. These effects are more prevalent in ETFs domiciled in Europe. Moreover, ETF flows seem to respond to additional risk. These results have important normative implications for consumer protection and financial stability.
Received March 18, 2017; Editorial decision October 14, 2018 by Editor Raman Uppal. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
MWDS-2016: THE SLOW DISSOLUTION RATE FOR PLUTONIUM NITRATE INTAKES AT THE MAYAK FACILITY
Authors: Bull R K , Puncher M 
Published: December 2018

Abstract
The slow dissolution rate of material deposited in the lung plays a key role in determining the eventual radiation dose received by the lung. It is therefore of great importance to establish a reliable value for this parameter, to incorporate into the latest Mayak Worker Dosimetry System (MWDS-2016). Disparate values have been obtained for the slow dissolution rate of plutonium nitrate. A volunteer study performed by Public Health England (PHE) and an analysis of United States Transuranium and Uranium Registries (USTUR) case 0269 have yielded slow dissolution rates in the region of 10–40 × 10−4 d−1. However, autopsies performed on 20 Mayak workers, exposed predominantly to nitrates, have resulted in estimates of slow dissolution rates of around 2.4 × 10−4 d−1. Three hypotheses have been proposed to explain this discrepancy: (1) a slower dissolution rate in the interstitium, (2) a third exponential component in the dissolution function and (3) a small component of oxide in the aerosol to which Mayak ‘nitrate’ workers were exposed. This paper describes tests of these competing hypotheses. Bayesian methods have been applied to the following datasets: PHE volunteer data; Beagle dog data; USTUR cases and Mayak worker data. It is concluded that a mixture of oxide and nitrate material, with the oxide forming ~14% of the intake, best describes the Mayak dissolution rate, without introducing values for other parameters which conflict with other studies.
Genetic advances in gout: potential applications in clinical practice
Authors: Tai Vicky , Merriman Tony R. , Dalbeth Nicola 
Published: December 2018

Purpose of review
Many novel genetic associations in the field of hyperuricaemia and gout have been described recently. This review discusses advances in gout genetics and their potential clinical applications.

Recent findings
Genome-wide association studies have identified approximately 30 serum urate-associated loci, some of which represent targets for drug development in gout. Some genes implicated in initiating the inflammatory response to deposited crystals in gout flares have also been described. In addition, genetic studies have been used to understand the link between hyperuricaemia and other comorbidities, particularly cardiometabolic diseases. ABCG2 has been established as a key genetic determinant in the onset of gout, and plays a role in the progression and severity of disease. Recent pharmacogenetic studies have also demonstrated the association between ABCG2 and poor response to allopurinol, and the link between HLA-B

∗

58:01 genotype and adverse drug reactions to allopurinol.

Summary
Advances in gout genetics have provided important molecular insights into disease pathogenesis, better characterized the pharmacogenetics of allopurinol, and raised the possibility of using genetic testing to provide personalized treatment for patients. Prospective studies are now needed to clarify whether genetic testing in gout provides further benefit when added to established clinical management.
The Outcome of Patients With Localized Undifferentiated Pleomorphic Sarcoma of the Lower Extremity Treated at Stanford University
Authors: Kamat Nikhil V. , Million Lynn , Yao Dong-han , Donaldson Sarah S. , Mohler David G. , van de Rijn Matt , Avedian Raffi S. , Kapp Daniel S. , Ganjoo Kristen N. 
Published: December 2018

Background:
As a diagnosis of exclusion, Undifferentiated Pleomorphic Sarcoma (UPS) has unclear clinical characteristics. The objective of this retrospective cohort study is to investigate which clinical and prognostic factors of primary lower-extremity UPS will determine failure.

Methods:
We retrospectively reviewed 55 primary lower-extremity UPS cases treated at Stanford between 1998 and 2015. Overall Survival (OS) and Disease-Free Survival (DFS) curves were calculated. Univariate Fisher’s Exact Tests were used to examine relationships between disease recurrence, treatment, patient factors, tumor characteristics, and surgical margins.

Results:
5-year DFS and OS rates were 60% (95% CI, 45%-72%) and 68% (95% CI, 53%-79%), respectively. The 5-year DFS rate for patients with positive margins was 33.3% (95% CI, 5%-68%) compared with 63% (95% CI, 47%-76%) for patients with negative margins. (Log-rank, P=0.03). The OS rate for those with disease recurrence was 42% % (95% CI, 16%-67%) compared with 76% (95% CI, 59%-87%) for patients who did not have disease recurrence (log-rank, P=0.021). Local failure occurred more frequently with omission of radiation therapy (Fisher’s exact test, P=0.009).

Conclusions:
Positive surgical margins are an important prognostic factor for predicting relapse in UPS. Relapse of any kind led to worse OS. Radiation therapy improved local control of disease but had no statistically significant effect on DFS, highlighting the need for improved diagnostics to identify those at highest risk for hematogenous metastasis and for selection of patients for adjuvant systemic treatment.
Opioid Prescribing Patterns After Micrographic Surgery: A Follow-up Retrospective Chart Review
Authors: Donigan Jessica M. , Franco Abigail I. , Stoddard Gregory J. , Hedderman Amanda , Tristani-Firouzi Payam , Bowen Glen M. , Millican Eric A. , Duffy Keith L. 
Published: December 2018

BACKGROUND
The abuse of opioids has reached epidemic proportions in the United States, and leftover medications are a primary source for nonmedical pain relievers. A past study at the University of Utah showed that micrographic surgeons were likely overprescribing opioids, with 35% of patients receiving a postoperative prescription.

OBJECTIVE
To examine the current opioid prescribing habits of the micrographic surgeons at the University of Utah compared with those in 2010.

METHODS
Retrospective chart review of the patient records of 4 micrographic surgeons between February and May 2017.

RESULTS
Four hundred patient visits were reviewed. An opioid prescription was provided after 12% of encounters, 23% lower than in 2010 (p = .004). Younger patient age, increased number of stages and defect size, repair of the defect, and particular surgeons predicted opioid prescription.

CONCLUSION
The percentage of patients who received an opioid prescription after undergoing micrographic surgery at the University of Utah decreased from 35% in 2010 to 12% in 2017. Reports of the minimal need of opioids after micrographic surgery, the authors' past study showing an institutional tendency to overprescribe, and reports of the national opioid epidemic likely all contributed to the decrease in opioid prescriptions at the authors' institution.
Cannula-Assisted Technique to Unfold Grafts in Descemet Membrane Endothelial Keratoplasty
Authors: Sarnicola Caterina , Sabatino Francesco , Sarnicola Enrica , Perri Paolo , Cheung Albert Y. , Sarnicola Vincenzo 
Published: December 2018

Purpose:
To describe the use of irrigating single-port cannulas to unfold Descemet membrane endothelial keratoplasty (DMEK) grafts when traditional tapping techniques are challenging.

Methods:
This study is a retrospective, comparative, nonrandomized, interventional case series that includes 143 DMEKs performed between February 2014 and November 2015. All eyes were divided into 2 groups: in one group, there were 48 cases that underwent DMEK using tap techniques only (Tapping DMEK group), and in another group, there were 30 cases in which irrigating cannulas were used to unfold the graft as a secondary approach (Cannula DMEK group). Intraocular manipulation time and total graft manipulation time were assessed. Uncorrected visual acuity, best spectacle-corrected visual acuity, and endothelial cell count were evaluated at 6 and 12 months postoperatively. We also reviewed DMEK procedures performed between December 2015 and January 2017 to evaluate the use of irrigating cannulas to unfold the graft.

Results:
All grafts were clear. There was a statistically significant improvement in uncorrected visual acuity and best corrected visual acuity at 6 and 12 months postoperatively in both groups (P < 0.01). Endothelial cell loss was 32.10% and 32.11% at 12 months in the Cannula and Tapping DMEK groups, respectively (P > 0.05). Total graft manipulation time was 3 minutes 40 ± 22 seconds in the Cannula DMEK group and 3 minutes 07 ± 26 seconds in the Tapping DMEK group (P < 0.01). Irrigating cannulas were used as a secondary approach in a smaller percentage of cases between December 2015 and January 2017 (26.2%) compared with DMEK performed during this study (38.5%).

Conclusions:
When it is difficult to unscroll the endothelium–Descemet membrane graft using only tap techniques, the use of Sarnicola cannulas is useful and effective without negatively affecting the postoperative endothelial cell count.