bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photometry, spectroscopy, and polarimetry of distant comet C/2014 A4 (SONEAR)
Authors: Ivanova Oleksandra , Luk’yanyk Igor , Kolokolova Ludmilla , Das Himadri Sekhar , Husárik Marek , Rosenbush Vera , Afanasiev Viktor , Svoreň Ján , Kiselev Nikolai , Krushinsky Vadim 
Published: April 2019

Context.The study of distant comets, which are active at large heliocentric distances, is important for a better understanding of their physical properties and mechanisms of long-lasting activity.Aims.We analyzed the dust environment of the distant comet C/2014 A4 (SONEAR), with a perihelion distance near 4.1 au, using comprehensive observations obtained by different methods.Methods.We present an analysis of spectroscopy, photometry, and polarimetry of comet C/2014 A4 (SONEAR), which were performed on November 5–7, 2015, when its heliocentric distance was 4.2 au and phase angle was 4.7°. Long-slit spectra and photometric and linear polarimetric images were obtained using the focal reducer SCORPIO-2 attached to the prime focus of the 6 m telescope BTA (SAO RAS, Russia). We simulated the behavior of color and polarization in the coma presenting the cometary dust as a set of polydisperse polyshapes rough spheroids.Results.No emission features were detected in the 3800–7200 Å wavelength range. The continuum showed a reddening effect with the normalized gradient of reflectivity 21.6 ± 0.2% per 1000 Å within the 4650–6200 Å wavelength region. The fan-like structure in the sunward hemisphere was detected. The radial profiles of surface brightness differ forr-sdss andg-sdss filters, indicating a predominance of submicron and micron-sized particles in the cometary coma. The dust color (g–r) varies from 0.75 ± 0.05mto 0.45 ± 0.06malong the tail. For an aperture radius near 20 000 km, the dust productions in various filters were estimated asAfρ= 680 ± 18 cm (r-sdss) and 887 ± 16 cm (g-sdss). The polarization map shows spatial variations in polarization over the coma from about −3% near the nucleus to −8% at a cometocentric distance of about 150 000 km. Our simulations show that the dust particles are dominated (or covered) by ice and tholin-like organics. Spatial changes in the color and polarization can be explained by particle fragmentation.
Quercus ilex Extract Ameliorates Acute TNBS-Induced Colitis in Rats
Authors: Castejón Maria Luisa , Rosillo Maria Ángeles , Villegas Isabel , Sánchez-Hidalgo Marina , Hadidi Lila , Zaidi Farid , Alarcón-de-la-Lastra Catalina 
Published: April 2019

Abstract
Quercus ilex L. (Fagaceae) is one of the most commonly used plants in folk medicine in the Mediterranean region to treat gastrointestinal disorders. The aim of the present study was to evaluate the effects of a polyphenol extract from mature leaves of Q. ilex on acute 2,4,6-trinitrobenzene sulfonic acid-induced colitis in rats. A polyphenol extract from mature leaves of Q. ilex (250 and 500 mg/kg/day) was administered by gavage 48, 24, and 1 h prior to the induction of colitis with 2,4,6-trinitrobenzene sulfonic acid as well as 24 h later. The inflammation response was assessed by histology, myeloperoxidase activity, and Th1 proinflammatory cytokine production. The protein expression of cyclooxygenase-2 and inducible nitric oxide synthase, and signaling pathways were studied by Western blotting in the colon tissues. The polyphenol extract from mature leaves of Q. ilex decreased neutrophil infiltration, interleukin-1β and TNF-α production, and proinflammatory proteins cyclooxygenase-2 and inducible nitric oxide synthase overexpression. Also, the polyphenol extract from mature leaves of Q. ilex was capable of blocking the activation of mitogen-activated protein kinases and nuclear transcription factor-kappa B. Furthermore, the reduction of inflammation by polyphenol extract from mature leaves of Q. ilex treatment was accompanied by a recovery of Nrf2 and heme oxygenase-1 protein expression levels. In conclusion, this study demonstrates that a polyphenol extract from mature leaves of Q. ilex improves 2,4,6-trinitrobenzene sulfonic acid-induced colitis, probably through mitogen-activated protein kinase/nuclear transcription factor-kappa B inhibition and Nrf2/heme oxygenase-1 activation signaling pathways, thus reducing the production of Th1 proinflammatory cytokines and cyclooxygenase-2 and inducible nitric oxide synthase overexpression.
A New Wave of Amide Bond Formations for Peptide Synthesis
Authors: Hollanders Karlijn , Maes Bert , Ballet Steven 
Published: April 2019

The construction of peptidic amide bonds has become a daily laboratory practice by virtue of well-established ‘coupling reagents’. Nonetheless, inherent limitations connected to these classical coupling methods in terms of waste, safety and expense have yet to be conquered. Research efforts have been devoted to synthetic methods able to surpass these limitations. This short review focuses on the advances made in these ‘non-classical’ methods for amide bond formation with a specific application in peptide chemistry. It consists of two main sections: (i) novel carboxylic activation reagents, and (ii) carboxylic acid and amine surrogates.1	Introduction2	Alternative Carboxylic acid Activation Reagents3	Carboxylic Acid and Amine Surrogates4	Conclusion and Perspectives
Case Report of an Infrequent Complication of Infective Endocarditis: The Complete Detachment from the Aorta of the Previous Vein Graft Anastomosis
Authors: Varela Barca Laura , López Menéndez Jose , Redondo Palacios Ana , Rodríguez-Roda Stuart Jorge 
Published: April 2019

AbstractThe authors report an unusual complication of acute infective endocarditis found in a 70-year-old man with a previous history of two cardiac surgery procedures. During median sternotomy, a massive bleeding occurred. The bleeding was contained within the mediastinum and originated from the 10-year-old anastomosis of the saphenous vein to a composite graft, which was completely detached due to infective endocarditis of the aortic graft.
Minimally Invasive Craniocervical Decompression for Chiari 1 Malformation: An Operative Technique
Authors: Quillo-Olvera Javier , Navarro-Ramírez Rodrigo , Quillo-Olvera Diego , Quillo-Reséndiz Javier , Kim Jin-Sung 
Published: April 2019

AbstractChiari malformation type 1 (CM-1) is an ectopia of the cerebellar tonsils below the foramen magnum that causes severe disability due to its neurologic symptoms. The treatment of choice for CM-1 is decompression of the craniovertebral junction (CVJ). In some patients only an extradural decompression by removing the atlanto-occipital ligament may be sufficient. In other patients, duraplasty is necessary. In this case, we report the operative technique used to treat a CM-1 in a 16-year-old male patient who presented with severe headache and gait instability. A micro-decompression of the suboccipital bone and posterior arch osteotomy of C1 through a 2-cm midline incision was performed under surgical microscope magnification. A duraplasty was performed through the same approach. The patient was discharged home after 2 days in the hospital and returned to regular activities at school 3 weeks after surgery. The minimally invasive technique presented here is a viable option for the posterior decompression of the CVJ in patients with CM-1 using a low-cost self-retaining retractor.
Using Artificial Intelligence to Identify Factors Associated with Autism Spectrum Disorder in Adolescents with Cerebral Palsy
Authors: Bertoncelli Carlo , Altamura Paola , Vieira Edgar , Bertoncelli Domenico , Solla Federico 
Published: April 2019

AbstractAutism spectrum disorder (ASD) is common in adolescents with cerebral palsy (CP) and there is a lack of studies applying artificial intelligence to investigate this field and this population in particular. The aim of this study is to develop and test a predictive learning model to identify factors associated with ASD in adolescents with CP. This was a multicenter controlled cohort study of 102 adolescents with CP (61 males, 41 females; mean age ± SD [standard deviation] = 16.6 ± 1.2 years; range: 12–18 years). Data on etiology, diagnosis, spasticity, epilepsy, clinical history, communication abilities, behaviors, intellectual disability, motor skills, and eating and drinking abilities were collected between 2005 and 2015. Statistical analysis included Fisher's exact test and multiple logistic regressions to identify factors associated with ASD. A predictive learning model was implemented to identify factors associated with ASD. The guidelines of the “transparent reporting of a multivariable prediction model for individual prognosis or diagnosis” (TRIPOD) statement were followed. Type of spasticity (hemiplegia > diplegia > tri/quadriplegia; OR [odds ratio] = 1.76, SE [standard error] = 0.2785, p = 0.04), communication disorders (OR = 7.442, SE = 0.59, p < 0.001), intellectual disability (OR = 2.27, SE = 0.43, p = 0.05), feeding abilities (OR = 0.35, SE = 0.35, p = 0.002), and motor function (OR = 0.59, SE = 0.22, p = 0.01) were significantly associated with ASD. The best average prediction model score for accuracy, specificity, and sensitivity was 75%. Motor skills, feeding abilities, type of spasticity, intellectual disability, and communication disorders were associated with ASD. The prediction model was able to adequately identify adolescents at risk of ASD.
Emergence of topological electronic phases in elemental lithium under pressure
Authors: Mack Stephanie A. , Griffin Sinéad M. , Neaton Jeffrey B. 
Published: April 2019

Significance
Lithium forms the lightest metallic phase under standard conditions and undergoes an unusual sequence of phase transitions to lower symmetry structures under pressure. We use density functional theory to study the electronic structure of several predicted high-pressure phases of lithium. At 80 GPa, we find its electronic structure becomes topologically nontrivial, with the electrons behaving as massless fermions. Lithium is unique in that it is a light elemental solid where the topological features of the band structure are well isolated from other bands at the Fermi level. Our results indicate that the electronic structure of lithium has previously unexplored topological properties with pressure, adding another dimension to an already remarkable complex phase diagram for an elemental solid.
Parameters and the design of the Language Faculty
Authors: Manzini Maria Rita 
Published: April 2019

AbstractFollowingBerwick and Chomsky (2011), parameters are degrees of freedom open at the externalization (EXT) of syntactico-semantic structures (SEM) by sensorimotor systems (PHON) (Section 1). Within this framework, inSection 2I focus on a case study concerning Northern Italian subject clitics, also raising the well-known question how to reconcile observable microvariation with the desideratum of a reduced number of (macro)parameters.Sections 3reviews recent relevant models of parameterization, the Rethinking Comparative Syntax model (ReCoS,Biberauer et al. 2014) and the Parameters & Schemata model (Longobardi 2005,2017).Sections 4–5return to the case study, taking the reductionist view that parameters may be just categorial cuts, such as the 1/2P vs 3P split, interacting with externalization and other general principles of grammar.
Mining novel biosynthetic machineries of secondary metabolites from actinobacteria
Authors: Katsuyama Yohei 
Published: April 2019

ABSTRACT
Secondary metabolites produced by actinobacteria have diverse structures and important biological activities, making them a useful source of drug development. Diversity of the secondary metabolites indicates that the actinobacteria exploit various chemical reactions to construct a structural diversity. Thus, studying the biosynthetic machinery of these metabolites should result in discovery of various enzymes catalyzing interesting and useful reactions. This review summarizes our recent studies on the biosynthesis of secondary metabolites from actinobacteria, including the biosynthesis of nonproteinogenic amino acids used as building blocks of nonribosomal peptides, the type II polyketide synthase catalyzing polyene scaffold, the nitrous acid biosynthetic pathway involved in secondary metabolite biosynthesis and unique cytochrome P450 catalyzing nitrene transfer. These findings expand the knowledge of secondary metabolite biosynthesis machinery and provide useful tools for future bioengineering.
Biomass and nitrogen distribution ratios reveal a reduced root investment in temperate lianas vs. self-supporting plants
Authors: Wyka Tomasz P , Zadworny Marcin , Mucha Joanna , Żytkowiak Roma , Nowak Kinga , Oleksyn Jacek 
Published: April 2019

AbstractBackground and AimsThe reliance on external support by lianas has been hypothesized to imply a reduction in the biomass cost of stem construction and root anchorage, and an increased investment in leaves, relative to self-supporting plants. These evolutionary trade-offs have not been adequately tested in an ontogenetic context and on the whole-plant scale. Moreover, the hypothesis may be extended to other potentially limiting resources, such as nitrogen (N.)MethodsPlants belonging to five con-familiar pairs of temperate liana/shrub species were cultivated in 120 L barrels and sequentially harvested over up to three growing seasons. To account for the ontogenetic drift, organ biomass and nitrogen fractions were adjusted for plant biomass and N pool, respectively.Key ResultsLianas invested, on average, relatively less biomass in the root fraction in comparison with shrubs. This was offset by only insignificant increases in leaf or stem investment. Even though liana stems and roots showed higher N concentration in comparison with shrubs, plant N distribution was mostly driven by, and largely matched, the pattern of biomass distribution. Lianas also showed a greater relative growth rate than shrubs. The differences between the growth forms became apparent only when ontogenetic drift was controlled for. These results were confirmed regardless of whether reproductive biomass was included in the analysis.ConclusionsOur results suggest that temperate lianas, in spite of their diverse, species-specific resource distribution patterns, preferentially allocate resources to above-ground organs at the expense of roots. By identifying this trade-off and demonstrating the lack of a general trend for reduction in stem investment in lianas, we significantly modify the prevailing view of liana allocation strategies and evolutionary advantages. Such a resource distribution pattern, along with the cheap unit leaf area and stem unit length construction, situates lianas as a group close to the fast acquisition/rapid growth end of the life strategy spectrum.
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Authors: Kozlov Alexey M , Darriba Diego , Flouri Tomáš , Morel Benoit , Stamatakis Alexandros 
Published: April 2019

Abstract

Motivation
Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.

Results
We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric.

Availability and implementation
The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/.

Supplementary information
Supplementary data are available at Bioinformatics online.
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database
Authors: Islamaj Rezarta , Wilbur W John , Xie Natalie , Gonzales Noreen R , Thanki Narmada , Yamashita Roxanne , Zheng Chanjuan , Marchler-Bauer Aron , Lu Zhiyong 
Published: April 2019

AbstractThis study proposes a text similarity model to help biocuration efforts of the Conserved Domain Database (CDD). CDD is a curated resource that catalogs annotated multiple sequence alignment models for ancient domains and full-length proteins. These models allow for fast searching and quick identification of conserved motifs in protein sequences via Reverse PSI-BLAST. In addition, CDD curators prepare summaries detailing the function of these conserved domains and specific protein families, based on published peer-reviewed articles. To facilitate information access for database users, it is desirable to specifically identify the referenced articles that support the assertions of curator-composed sentences. Moreover, CDD curators desire an alert system that scans the newly published literature and proposes related articles of relevance to the existing CDD records. Our approach to address these needs is a text similarity method that automatically maps a curator-written statement to candidate sentences extracted from the list of referenced articles, as well as the articles in the PubMed Central database. To evaluate this proposal, we paired CDD description sentences with the top 10 matching sentences from the literature, which were given to curators for review. Through this exercise, we discovered that we were able to map the articles in the reference list to the CDD description statements with an accuracy of 77%. In the dataset that was reviewed by curators, we were able to successfully provide references for 86% of the curator statements. In addition, we suggested new articles for curator review, which were accepted by curators to be added into the reference list at an acceptance rate of 50%. Through this process, we developed a substantial corpus of similar sentences from biomedical articles on protein sequence, structure and function research, which constitute the CDD text similarity corpus. This corpus contains 5159 sentence pairs judged for their similarity on a scale from 1 (low) to 5 (high) doubly annotated by four CDD curators. Curator-assigned similarity scores have a Pearson correlation coefficient of 0.70 and an inter-annotator agreement of 85%. To date, this is the largest biomedical text similarity resource that has been manually judged, evaluated and made publicly available to the community to foster research and development of text similarity algorithms.
Safety, feasibility, and effect of an enhanced nutritional support pathway including extended preoperative and home enteral nutrition in patients undergoing enhanced recovery after esophagectomy: a pilot randomized clinical trial
Authors: Liu K , Ji S , Xu Y , Diao Q , Shao C , Luo J , Zhu Y , Jiang Z , Diao Y , Cong Z , Hu L , Qiang Y , Shen Y 
Published: April 2019

SUMMARYThe aims of this pilot study are to evaluate the feasibility, safety, and effectiveness of conducting an enhanced nutritional support pathway including extended preoperative nutritional support and one month home enteral nutrition (HEN) for patients who underwent enhanced recovery after esophagectomy. We implemented extended preoperative nutritional support and one month HEN after discharge for patients randomized into an enhanced nutrition group and implemented standard nutritional support for patients randomized into a conventional nutrition group. Except the nutritional support program, both group patients underwent the same standardized enhanced recovery after surgery programs of esophagectomy based on published guidelines. Patients were assessed at preoperative day, postoperative day 7 (POD7), and POD30 for perioperative outcomes and nutritional status. To facilitate the determination of an effect size for subsequent appropriately powered randomized clinical trials and assess the effectiveness, the primary outcome we chose was the weight change before and after esophagectomy. Other outcomes including body mass index (BMI), lean body mass (LBM), appendicular skeletal muscle mass index (ASMI), nutrition-related complications, and quality of life (QoL) were also analyzed. The intention-to-treat analysis of the 50 randomized patients showed that there was no significant difference in baseline characteristics. The weight (−2.03 ± 2.28 kg vs. −4.05 ± 3.13 kg, P = 0.012), BMI (−0.73 ± 0.79 kg/m2 vs. −1.48 ± 1.11 kg/m2, P = 0.008), and ASMI (−1.10 ± 0.37 kg/m2 vs. −1.60 ± 0.66 kg/m2, P = 0.010) loss of patients in the enhanced nutrition group were obviously decreased compared to the conventional nutrition group at POD30. In particular, LBM (48.90 ± 9.69 kg vs. 41.96 ± 9.37 kg, p = 0.031) and ASMI (7.56 ± 1.07 kg/m2 vs. 6.50 ± 0.97 kg/m2, P = 0.003) in the enhanced nutrition group were significantly higher compared to the conventional nutrition group at POD30, despite no significant change between pre- and postoperation. In addition, European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 scores revealed that enhanced nutritional support improved the QoL of patients in physical function (75.13 ± 9.72 vs. 68.33 ± 7.68, P = 0.009) and fatigue symptom (42.27 ± 9.93 vs. 49.07 ± 11.33, P = 0.028) compared to conventional nutritional support. This pilot study demonstrated that an enhanced nutritional support pathway including extended preoperative nutritional support and HEN was feasible, safe, and might be beneficial to patients who underwent enhanced recovery after esophagectomy. An appropriately powered trial is warranted to confirm the efficacy of this approach.
Effects of alirocumab on types of myocardial infarction: insights from the ODYSSEY OUTCOMES trial
Authors: White Harvey D , Steg Ph Gabriel , Szarek Michael , Bhatt Deepak L , Bittner Vera A , Diaz Rafael , Edelberg Jay M , Erglis Andrejs , Goodman Shaun G , Hanotin Corinne , Harrington Robert A , Jukema J Wouter , Lopes Renato D , Mahaffey Kenneth W , Moryusef Angele , Pordy Robert , Roe Matthew T , Sritara Piyamitr , Tricoci Pierluigi , Zeiher Andreas M , Schwartz Gregory G ,   ODYSSEY OUTCOMES Investigators
Published: April 2019

Abstract

Aims
The third Universal Definition of Myocardial Infarction (MI) Task Force classified MIs into five types: Type 1, spontaneous; Type 2, related to oxygen supply/demand imbalance; Type 3, fatal without ascertainment of cardiac biomarkers; Type 4, related to percutaneous coronary intervention; and Type 5, related to coronary artery bypass surgery. Low-density lipoprotein cholesterol (LDL-C) reduction with statins and proprotein convertase subtilisin–kexin Type 9 (PCSK9) inhibitors reduces risk of MI, but less is known about effects on types of MI. ODYSSEY OUTCOMES compared the PCSK9 inhibitor alirocumab with placebo in 18 924 patients with recent acute coronary syndrome (ACS) and elevated LDL-C (≥1.8 mmol/L) despite intensive statin therapy. In a pre-specified analysis, we assessed the effects of alirocumab on types of MI.

Methods and results
Median follow-up was 2.8 years. Myocardial infarction types were prospectively adjudicated and classified. Of 1860 total MIs, 1223 (65.8%) were adjudicated as Type 1, 386 (20.8%) as Type 2, and 244 (13.1%) as Type 4. Few events were Type 3 (n = 2) or Type 5 (n = 5). Alirocumab reduced first MIs [hazard ratio (HR) 0.85, 95% confidence interval (CI) 0.77–0.95; P = 0.003], with reductions in both Type 1 (HR 0.87, 95% CI 0.77–0.99; P = 0.032) and Type 2 (0.77, 0.61–0.97; P = 0.025), but not Type 4 MI.

Conclusion
After ACS, alirocumab added to intensive statin therapy favourably impacted on Type 1 and 2 MIs. The data indicate for the first time that a lipid-lowering therapy can attenuate the risk of Type 2 MI. Low-density lipoprotein cholesterol reduction below levels achievable with statins is an effective preventive strategy for both MI types.