bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary trade‐offs in the chemical defense of floral and fruit tissues across genus Cornus
Authors: De La Pascua Danielle R. , Smith‐Winterscheidt Corrinne , Dowell Jordan A. , Goolsby Eric W. , Mason Chase M. 
Published: September 2020

PremiseDefense investment in plant reproductive structures is relatively understudied compared to the defense of vegetative organs. Here the evolution of chemical defenses in reproductive structures is examined in light of the optimal defense, apparency, and resource availability hypotheses within the genus Cornus using a phylogenetic comparative approach in relation to phenology and native habitat environmental data.MethodsIndividuals representing 25 Cornus species were tracked for reproductive phenology over a full growing season at the Arnold Arboretum of Harvard University. Floral, fruit, and leaf tissue was sampled to quantify defensive chemistry as well as fruit nutritional traits relevant to bird dispersal. Native habitat environmental characteristics were estimated using locality data from digitized herbarium records coupled with global soil and climate data sets.ResultsThe evolution of later flowering was correlated with increased floral tannins, and the evolution of later fruiting was correlated with increased total phenolics. Leaves were found to contain the highest tannin activity, while inflorescences contained the highest total flavonoids. Multiple aspects of fruit defensive chemistry were correlated with fruit nutritional traits. Floral and fruit defensive chemistry were evolutionarily correlated with aspects of native habitat temperature, precipitation, and soil characteristics.ConclusionsResults provide tentative support for the apparency hypothesis with respect to both flower and fruit phenology, while relative concentrations of secondary metabolites across organs provide mixed support for the optimal defense hypothesis. The evolution of reproductive defense with native habitat provides, at best, mixed support for the resource availability hypothesis.
Comparison of point transect distance and traditional acoustic point‐count sampling of hoolock gibbons in Htamanthi Wildlife Sanctuary, Myanmar
Authors: Brockelman Warren Y. , Tun Aung Ye , Pan Su , Naing Hla , Htun Saw 
Published: September 2020

AbstractEffective conservation demands more accurate and reliable methods of survey and monitoring of populations. Surveys of gibbon populations have relied mostly on mapping of groups in “listening areas” using acoustical point‐count data. Traditional methods of estimating density in have usually used counts of gibbon groups within fixed‐radius areas or areas bounded by terrain barriers to sound transmission, and have not accounted for possible decline in detectability with distance. In this study we sampled the eastern hoolock gibbon (Hoolock leucogenys) population in Htamanthi Wildlife Sanctuary (WS), Myanmar, using two methods: the traditional point‐count method with fixed‐radius listening areas, and a newer method using point‐transect Distance analysis from a sample point established in the center of each listening point array. The basic data were obtained by triangulating on singing groups from four LPs for 4 days, in 10 randomly selected sample areas within the sanctuary. The point transect method gave an average density of 3.13 groups km−2, higher than the estimates of group density within fixed‐radius areas without correction for detectability. A new method of analysis of singing probability per day (p[1]) gave an estimate of 0.547. Htamanthi WS is an important conservation area containing an estimated 7000 (95% confidence interval: 5000–10,000) hoolock groups. Surveys at Htamanthi WS and locations in the Hukaung Valley suggest that the extensive evergreen forests in northern Myanmar have the capacity to support 2–4 (average about 3) groups of hoolock gibbons per km2, but most forests in its range have yet to be surveyed.
Highly Diastereo‐ and Enantioselective Synthesis of 3,6′‐Bisboryl‐anti‐1,2‐oxaborinan‐3‐enes: An Entry to Enantioenriched Homoallylic Alcohols with A Stereodefined Trisubstituted Alkene
Authors: Chen Jichao , Miliordos Evangelos , Chen Ming 
Published: September 2020

AbstractA Cu‐catalyzed regio‐, diastereo‐, and enantioselective carboboration of 1,1‐bisboryl‐1,3‐butadiene is developed to generate enantioenriched 3,6′‐bisboryl‐anti‐1,2‐oxaborinan‐3‐enes. DFT calculations indicate that the initial diene 1,2‐borocupration forms a 3η‐allylic copper as the most stable intermediate. Subsequent aldehyde addition, however, operates under Curtin–Hammett control via a more reactive α,α‐bisboryl tertiary allylcopper species to furnish products with high enantioselectivities. The three boryl groups in the products are properly differentiated and can undergo a variety of chemoselective transformations to produce enantioenriched homoallylic alcohols with a stereodefined trisubstituted alkene.
Hin zur Kontrolle lumineszenter, optisch‐aktiver 3D‐Architekturen
Authors: Hindenberg Philip , Rominger Frank , Romero‐Nieto Carlos 
Published: September 2020

Abstractπ‐Erweiterte Systeme sind Schlüsselkomponenten für die Entwicklung zukünftiger organisch‐elektronischer Technologien. Während die Konzeption neuer Moleküle mit verbesserten Eigenschaften fundamental für die Evolution der Materialwissenschaft ist, stellt die Kontrolle über deren Anordnung im dreidimensionalen Raum eine stetig wachsende Herausforderung dar. Hier beschreiben wir nun eine synthetische Methode, die in π‐Systemen eingebundenen Kohlenstoffatome durch dissymmetrische Phosphoratome zu ersetzen; im Speziellen ermöglichte uns diese Methode, neuartige kondensierte Phosphapyren‐Derivate mit verbesserten Eigenschaften zu erhalten. Das Vorhandensein dissymmetrischer Phosphoratome verhinderte die Bildung von Excimeren. Die Kristallstrukturanalyse zeigte zudem, dass im Festkörper starke intermolekulare Wechselwirkungen vorherrschen. Die Phosphapyrene photolumineszieren mit hohen Quantenausbeuten im sichtbaren Bereich und sind zudem CD‐aktiv. Darüber hinaus ermöglichte die einzigartige nicht‐planare Geometrie der Phosphoratome die Kontrolle über die 3D‐Anordnung der Moleküle, wodurch lemniskatenartige Strukturen entstanden. Basierend auf unseren Erkenntnissen, streben wir die Konstruktion höher‐geordneter, chiraler 3D‐Architekturen aus größeren phosphorhaltigen π‐Systemen an.
A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex
Authors: Czescik Joanna , Zamolo Susanna , Darbre Tamis , Rigo. Riccardo , Sissi Claudia , Pecina Adam , Riccardi Laura , De Vivo Marco , Mancin Fabrizio , Scrimin Paolo 
Published: September 2020

AbstractSimilarly to enzymes, functionalized gold nanoparticles efficiently catalyze chemical reactions, hence the term nanozymes. Herein, we present our results showing how surface‐passivated gold nanoparticles behave as synthetic nanonucleases, able to cleave pBR322 plasmid DNA with the highest efficiency reported so far for catalysts based on a single metal ion mechanism. Experimental and computational data indicate that we have been successful in creating a catalytic site precisely mimicking that suggested for natural metallonucleases relying on a single metal ion for their activity. It comprises one Zn(II) ion to which a phosphate diester of DNA is coordinated. Importantly, as in nucleic acids‐processing enzymes, a positively charged arginine plays a key role by assisting with transition state stabilization and by reducing the pKa of the nucleophilic alcohol of a serine. Our results also show how designing a catalyst for a model substrate (bis‐p‐nitrophenylphosphate) may provide wrong indications as for its efficiency when it is tested against the real target (plasmid DNA).
The Hair Follicle as an Interdisciplinary Model for Biomedical Research: An Eclectic Literature Synthesis
Authors: Haslam Iain S. , Paus Ralf 
Published: September 2020

AbstractSkin is a comparatively accessible organ possessing many conserved regulatory and signaling pathways, drawing researchers from varied fields toward its study. Hair follicle (HF) biology in particular has expanded rapidly over the preceding decade, helping to shape and develop scientific knowledge across diverse areas of biomedical research, beyond the skin. The hope in compiling this review is to inspire more researchers to utilize the HF as an instructive biological model, bringing with them fresh perspectives and experience from differing fields of study. The authors also wish to further motivate seasoned hair researchers to explore the further reaches of their understanding and the discoveries yet to be made. For this reason, the authors have endeavored to collate an eclectic mix of some of the most thought‐provoking and scientifically intriguing articles associated with the field of HF research, published in the preceding two years.
Long-term prognosis in breast cancer is associated with residual disease after neoadjuvant systemic therapy but not with initial nodal status
Authors: Zetterlund L , Celebioglu F , Hatschek T , Frisell J , de Boniface J 
Published: September 2020

Abstract

Background
This follow-up analysis of a Swedish prospective multicentre trial had the primary aim to determine invasive disease-free (IDFS), breast cancer-specific (BCSS) and overall survival (OS) rates, and their association with axillary staging results before and after neoadjuvant systemic therapy for breast cancer.

Methods
Women who underwent neoadjuvant systemic therapy for clinically node-positive (cN+) or -negative (cN0) primary breast cancer between 2010 and 2015 were included. Patients had a sentinel lymph node biopsy before and/or after neoadjuvant systemic therapy, and all underwent completion axillary lymph node dissection. Follow-up was until February 2019. The main outcome measures were IDFS, BCSS and OS. Univariable and multivariable Cox regression analyses were used to identify independent factors associated with survival.

Results
The study included a total of 417 women. Median follow-up was 48 (range 7–114) months. Nodal status after neoadjuvant systemic therapy, but not before, was significantly associated with crude survival: residual nodal disease (ypN+) resulted in a significantly shorter 5-year OS compared with a complete nodal response (ypN0) (83·3 versus 91·0 per cent; P = 0·017). The agreement between breast (ypT) and nodal (ypN) status after neoadjuvant systemic therapy was high, and more so in patients with cN0 tumours (64 of 66, 97 per cent) than those with cN+ disease (49 of 60, 82 per cent) (P = 0·005). In multivariable analysis, ypN0 (hazard ratio 0·41, 95 per cent c.i. 0·22 to 0·74; P = 0·003) and local radiotherapy (hazard ratio 0·23, 0·08 to 0·64; P = 0·005) were associated with improved IDFS, and triple-negative molecular subtype with worse IDFS.

Conclusion
The present findings underline the prognostic significance of nodal status after neoadjuvant systemic therapy. This confirms the clinical value of surgical axillary staging after neoadjuvant systemic therapy.
Teaching reaction kinetics through isomerization cases with the basis of density‐functional calculations
Authors: Rusydi Febdian , Madinah Roichatul , Puspitasari Ira , Mark‐Lee Wun F. , Ahmad Azizan , Rusydi Andrivo 
Published: September 2020

AbstractThe fundamental mechanism of biochemistry lies on the reaction kinetics, which is determined by the reaction pathways. Interestingly, the reaction pathway is a challenging concept for undergraduate students. Experimentally, it is difficult to observe, and theoretically, it requires some degree of physics knowledge, namely statistical and quantum mechanics. However, students can utilize computational methods to study the reaction kinetics without paying too much attention but not wholly neglecting the comprehension of physics. We hereby provided an approach to study the reaction kinetics based on density‐functional calculations. We particularized the study of the isomerization case involving five molecules at three different temperatures and emphasized the importance of the transition state in the study of reaction kinetics. The results we presented were in good agreement with the experiments and provided useful insights to assist students in the application of their knowledge into their research.
Polydimethylsiloxane/ionic liquid sponge used in headspace solid‐phase extraction coupled with GC–MS for rapid analysis of essential oil in lavender
Authors: Liu Xin , Chen Ping , Wang Lili , Wang Caijuan , Zhao Mengqi , Fu Jihong 
Published: September 2020

AbstractA headspace (HS) solid‐phase extraction (SPE) based on polydimethylsiloxane (PDMS)/ionic liquid (IL) sponge was developed for the extraction of lavender essential oil. The PDMS after loading of 1‐butyl‐3‐methylimidazolium tetrachloroferrate ([BMIM]FeCl4) with a high surface area and excellent adsorption capacity was successfully applied in the SPE process. Microwave distillation (MD) coupled with HS‐PDMS/[BMIM]FeCl4 extraction after GC–MS was proposed. Various experimental parameters were studied. The optimal conditions were as follows: optimal IL, [BMIM]FeCl4; volume ratio of IL to ethanol, 1:5; extraction solvent, n‐hexane; microwave power, 600 W; and irradiation time, 12 min. The limits of detection and quantification of the analytic compounds were in the ranges 4.00–16.32 and 10.00–40.00 ng, respectively. The intra‐day and inter‐day precisions were in the ranges 0.37–1.94% and 1.20–2.45%, respectively. Under the optimized conditions, 13 samples of 3 lavender varieties were analyzed, and 40 compounds were identified. Lavender varieties were distinguished using principal component analysis. The results showed that MD‐HS‐PDMS/IL‐GC–MS is a novel, simple, and sensitive method for the determination of essential oil in complex plant samples.
Acute appendicitis: Clinical anatomy of the new palpation sign
Authors: Marek Vitezslav , Záhorec Roman , Durdík Stefan 
Published: September 2020

AbstractIntroductionCurrently, diagnosis of acute appendicitis (AA) is challenging. Here, we aim to propose using the new palpation sign to diagnose AA and establish the effectiveness of clinical examination using a proprietary diagnostic palpation procedure.Materials and MethodsWe retrospectively analyzed 2,883 patients of all ages who were examined for suspected AA, of whom 532 patients required surgical intervention, using the new palpation sign. Patients were divided into three age categories. Based on the correlation between clinical data and histological findings, clinical examination finding was defined as false negative, false positive, and positive. Pearson correlation analysis was performed to assess the correlation between patients' sex and age distribution and clinical and histological findings.ResultsThere was a strong correlation (r > .95) for distribution of total number of examined patients (distributed in groups by sex and age) versus false‐positive clinical findings, total number of examined patients (distributed in groups by sex and age) versus positive clinical findings, and total number of examined patients (distributed in groups by age) versus histology in phlegmonous and gangrenous appendicitis. Correlations (r = .94 and .90) were observed for distribution of total number of examined patients (distributed in groups by age) versus negative histological findings and Byron's obliterating appendicopathy. Pearson's chi‐squared test showed no significant difference between expected and observed frequencies of both clinical and histologic findings.ConclusionsThe new palpation sign can be used to diagnose early and later stage appendicitis, especially in children and young women, and is very effective in indicating surgery for AA.
Binding of SARS‐CoV‐2 to Cell Receptors: A Tale of Molecular Evolution
Authors: Gómez Santiago A. , Rojas‐Valencia Natalia , Gómez Sara , Egidi Franco , Cappelli Chiara , Restrepo Albeiro 
Published: September 2020

AbstractThe magnified infectious power of the SARS‐CoV‐2 virus compared to its precursor SARS‐CoV is intimately linked to an enhanced ability in the mutated virus to find available hydrogen‐bond sites in the host cells. This characteristic is acquired during virus evolution because of the selective pressure exerted at the molecular level. We pinpoint the specific residue (in the virus) to residue (in the cell) contacts during the initial recognition and binding and show that the virus⋅⋅⋅cell interaction is mainly due to an extensive network of hydrogen bonds and to a large surface of noncovalent interactions. In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus⋅⋅⋅cell interacting residues yields significant shifts of Δλmax=47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively.
Convolutional neural network for preprocessing‐free bacterial Spectra identification
Authors: Kim Younghoon , Lee Jiyoon , Ahn Gonie , Santos Inês C. , Schug Kevin A. , Kim Seoung Bum 
Published: September 2020

AbstractIdentifying bacterial species is essential to epidemiological surveillance. However, the determination of bacterial species is a tedious and labor‐intensive process. Various machine learning methods have been used for identifying bacterial species with mass spectral fingerprints. Although machine learning methods achieve real‐time identification without human experts, it still requires data preprocessing. To address this issue, we proposed a unified solution for the identification of bacterial species with a convolutional neural network. The neural network automatically determined species according to their mass spectra without the preprocessing steps. The convolutional and pooling layers in the neural network could replace the binning, baseline correction, and scaling procedures. Moreover, because of the explainable structure, the model could identify important regions of spectra to discriminate each bacterial species. We used spectral samples obtained from the fatty acid methyl esters of 10 samples from 16 bacterial species (a total of 16) to demonstrate the usefulness of the proposed method by comparing it with existing classification methods preceded by preprocessing. The comparison results confirmed that the proposed method outperformed the alternatives in terms of classification accuracy and robustness. Moreover, the classification results of the proposed method are interpretable.
Noble‐Metal‐Free Doped Carbon Nanomaterial Electrocatalysts
Authors: Sideri Ioanna K. , Tagmatarchis Nikos 
Published: September 2020

AbstractElectrocatalytic processes, such as oxygen reduction reaction (ORR), oxygen evolution reaction (OER), hydrogen evolution reaction (HER) and carbon dioxide reduction reaction (CO2RR), play key roles in various sustainable energy storage and production devices and their optimization in an ecological manner is of paramount importance for mankind. In this inclusive Review, we aspire to set the scene on doped carbon‐based nanomaterials and their hybrids as precious‐metal alternative electrocatalysts for these critical reactions in order for the research community not only to stay up‐to‐date, but also to get inspired and keep pushing forward towards their practical application in energy conversion.
Human herpesvirus‐8–positive primary effusion lymphoma in HIV‐negative patients: Single institution case series with a multidisciplinary characterization
Authors: Rossi Giovanni , Cozzi Ilaria , Della Starza Irene , De Novi Lucia Anna , De Propris Maria Stefania , Gaeta Aurelia , Petrucci Luigi , Pulsoni Alessandro , Pulvirenti Federica , Ascoli Valeria 
Published: September 2020

BACKGROUNDPrimary effusion lymphoma (PEL) is a very rare non‐Hodgkin lymphoma caused by human herpesvirus‐8 (HHV8) that grows in liquid phase within body cavities. The diagnosis of PEL is based on cytology but requires confirmatory ancillary tests. PEL occurs mainly in association with HIV infection. This study describes 9 cases of PEL in HIV‐negative patients and compares their characteristics with 10 HIV‐associated cases of PEL diagnosed at a single institution in Italy between 1995 and 2019.METHODSClinical records were reviewed for demographic data, comorbidities, laboratory abnormalities, and outcome. PEL samples were evaluated for cytomorphology, immunophenotype, immunoglobulin (IG)/T cell receptor (TR) rearrangements, and HHV8 and Epstein‐Barr virus (EBV) viral loads in effusion supernatants.RESULTSHIV‐unrelated PEL occurred in 8 elderly patients (7 men, 1 woman) and 1 young adult with primary antibody deficiency. Cytology revealed HHV8‐positive lymphoma cells lacking B/T cell antigens and exhibiting 2 cell patterns (polymorphous or monotonous). IG was clonally rearranged in all cases; aberrant TRG occurred in 2 cases. Effusion supernatants had more than 106 HHV8 DNA copies per mL and variable loads of EBV DNA. Compared with HIV‐associated PEL, the HIV‐negative cohort was characterized by older age, less frequent association with Kaposi sarcoma and/or multicentric Castleman disease, comparable but less abnormal laboratory parameters, and a nonsignificant survival benefit. PEL cases with low apoptosis were associated with better prognosis.CONCLUSIONTo the best of our knowledge, our case series of HIV‐unrelated PEL is the largest thus far, expands the spectrum of cytological findings, and supports the need for a multidisciplinary approach in the diagnostic workup.
Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron
Authors: Frank Rupert L. , Seiringer Robert 
Published: September 2020

AbstractWe consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem. © 2020 The Authors. Communications on Pure and Applied Mathematics published by Wiley Periodicals, Inc.
Network Building with the Cytoscape BioGateway App Explained in Five Use Cases
Authors: Puig Rafael Riudavets , Holmås Stian , Mironov Vladimir , Kuiper Martin 
Published: September 2020

AbstractThe BioGateway App is a plugin for the Cytoscape network editor, allowing users to interactively build biological networks by querying the Biogateway Resource Description Framework (RDF) triple store. BioGateway contains information from several curated resources including UniProtKB, IntAct, Gene Ontology Annotations, various datasets containing transcription‐factor regulatory relations to specific target genes, and more. The BioGateway App facilitates the step‐by‐step creation of complex SPARQL queries through an intuitive Graphical User Interface, allowing users to build and explore biological interaction networks to assess, among other things, gene regulatory relationships, gene ontology annotations, and protein‐protein interactions. As the BioGateway information content is most abundant for human proteins and genes, this article describes the utility of the tool through a series of use cases on these human data, starting from the most basic levels and then detailing applications that address some of the rich complexity of the integrated data. Network refinement and display can be further optimized via the selection and filtering possibilities that the Cytoscape framework provides. The use cases also provide examples to explore network information in other species, as they become supported by BioGateway. © 2020 The Authors.Basic Protocol 1: Introducing a node from the canvasBasic Protocol 2: Introducing a node from the query builderBasic Protocol 3: Exploring molecular relationships between diseasesBasic Protocol 4: Find proteins with protein kinase activity involved in a disease and explore the context around themBasic Protocol 5: Exploring the potential downstream effects after targeted inhibition of proteinsSupport Protocol: Installation of the BioGateway plugin through the Cytoscape App Manager and from source