bluuebunny/crossref_metadata_2025_split huggingface dataset:
DpgC‐Catalyzed Peroxidation of 3,5‐Dihydroxyphenylacetyl‐CoA (DPA‐CoA): Insights into the Spin‐Forbidden Transition and Charge Transfer Mechanisms**
Authors: Ortega Pablo , Zanchet Alexandre , Sanz‐Sanz Cristina , Gómez‐Carrasco Susana , González‐Sánchez Lola , Jambrina Pablo G. 
Published: September 2020

AbstractDespite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O2 at room temperature because O2 is a diradical whereas most organic molecules are closed‐shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non‐relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor‐independent oxidation of 3,5‐dihydroxyphenylacetyl‐CoA (DPA‐CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet–singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical‐pair between dioxygen and enolate is enough to promote spin‐forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.
Quadruplex–Duplex Junction: A High‐Affinity Binding Site for Indoloquinoline Ligands
Authors: Vianney Yoanes Maria , Preckwinkel Pit , Mohr Swantje , Weisz Klaus 
Published: September 2020

AbstractA parallel quadruplex derived from the Myc promoter sequence was extended by a stem‐loop duplex at either its 5′‐ or 3′‐terminus to mimic a quadruplex–duplex (Q–D) junction as a potential genomic target. High‐resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q–D hybrids with a very high affinity in the order Ka≈107 m−1 irrespective of the duplex location at the quadruplex 3′‐ or 5′‐end. NMR chemical shift perturbations identified the tetrad face of the Q–D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3′‐ or 5′‐terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3′‐Q–D junction, whereas non‐hydrophobic entropic contributions favor binding with formation of a 2:1 ligand‐quadruplex complex in case of the 5′‐Q–D hybrid.
High‐Efficiency FRET Processes in BODIPY‐Functionalized Quantum Dot Architectures
Authors: Panniello Annamaria , Trapani Mariachiara , Cordaro Massimiliano , Dibenedetto Carlo Nazareno , Tommasi Raffaele , Ingrosso Chiara , Fanizza Elisabetta , Grisorio Roberto , Collini Elisabetta , Agostiano Angela , Curri Maria Lucia , Castriciano Maria Angela , Striccoli Marinella 
Published: September 2020

AbstractEfficient FRET systems are developed combining colloidal CdSe quantum dots (QDs) donors and BODIPY acceptors. To promote effective energy transfer in FRET architectures, the distance between the organic fluorophore and the QDs needs to be optimized by a careful system engineering. In this context, BODIPY dyes bearing amino‐terminated functionalities are used in virtue of the high affinity of amine groups in coordinating the QD surface. A preliminary QD surface treatment with a short amine ligand is performed to favor the interaction with the organic fluorophores in solution. The successful coordination of the dye to the QD surface, accomplishing a short donor–acceptor distance, provides effective energy transfer already in solution, with efficiency of 76 %. The efficiency further increases in the solid state where the QDs and the dye are deposited as single coordinated units from solution, with a distance between the fluorophores down to 2.2 nm, demonstrating the effectiveness of the coupling strategy.
Improvement of Molecular Diagnosis Using Domain‐Level Single‐Nucleotide Variants by Eliminating Unexpected Secondary Structures
Authors: Tan Yun , Zhong Weiye , Tang Weiyang , Fan Jin , Zhang Xiaohui , Guo Donghua , Wu Xiaolong , Liu Yizhen 
Published: September 2020

AbstractIdentification of single‐nucleotide variants (SNVs) is of great significance in molecular diagnosis. The problem that should not be ignored in the identification process is that the unexpected secondary structure of the target nucleic acid may greatly affect the detection accuracy. Herein, we proposed a conditional domain‐level SNV diagnosis strategy, in which the subsequent SNV detection can only be carried out after eliminating the unexpected secondary structure of target DNA. Specifically, the target DNA is assembled into a rigid double strand, which makes folding the target DNA difficult and the unexpected secondary structure is eliminated. Based on this double‐stranded structure, specially designed probes are used to detect double‐stranded properties and report abundant domain‐level oligonucleotide information to improve the effective information in the detection results and complete domain‐level SNV diagnosis. If the unexpected secondary structure is not eliminated, the detector will first detect it and feed back to us, ensuring the accuracy of the subsequent detection results. With the occurrence (or not) of SNV and the change of the SNV site, in the proof‐of‐concept experiment, we successfully identified the four homologous sequences to be tested related to BRAF gene.
Push–Pull Bisnaphthyridylamine Supramolecular Nanoparticles: Polarity‐Induced Aggregation and Crystallization‐Induced Emission Enhancement and Fluorescence Resonance Energy Transfer
Authors: Hagihara Ryusuke , Umeno Tomohiro , Ueki Shoji , Yoshihara Daisuke , Fuchi Yasufumi , Usui Kazuteru , Sakuma Masaomi , Yamada Ken‐ichi , Karasawa Satoru 
Published: September 2020

AbstractEmissive push–pull‐type bisnaphthyridylamine derivatives (BNA‐X: X=Me, Et, Bzl, Ph, BuBr, and BuTEMPO) aggregate in aqueous methanol. Furthermore, a two‐step emission and aggregation process is controllable by varying the methanol‐to‐water ratio. At 2:3 MeOH/H2O, crystallization‐induced emission enhancement (CIEE) occurs via formation of an emissive crystal phase, whereas, at 1:9 MeOH/H2O, aggregation‐induced emission enhancement (AIEE) occurs, induced by emissive supramolecular nanoparticles (NPs). For BNA‐Ph, the emission quantum yield was 25 times higher in aqueous methanol than that in pure methanol. Despite the high hydrophobicity of BNA‐X (C log P=6.1–8.0), the spherical NPs were monodisperse (polydispersity indices <0.2). Moreover, the emissive NPs exhibited fluorescence resonance energy transfer (FRET) with pyrene; however, for BNA‐X bearing the TEMPO radical (BNA‐BuTEMPO), no FRET was observed because of quenching. In particular, the BNA‐BuTEMPO NPs have a slow rotational correlation time (1.3 ns), suggesting applications as magnetic resonance imaging contrast agents with large relaxivity.
Cucurbit[n]urils for Supramolecular Catalysis
Authors: Tang Bohan , Zhao Jiantao , Xu Jiang‐Fei , Zhang Xi 
Published: September 2020

AbstractThe control over chemical reactivity and selectivity are always pursued. Using non‐covalent interactions to achieve efficient and selective catalysis is an essential goal of supramolecular catalysis. Supramolecular catalysis based on cucurbit[n]urils (CB[n]s) possesses distinct characteristics for the unique structure of CB[n]s. CB[n]s are a family of pumpkin‐shaped host molecules with various molecular sizes, rigid structures, electronegative portals and wealthy host‐guest chemistry. Herein, we summarize the three major mechanisms of CB[n]s based supramolecular catalysis. Owing to the structural properties of CB[n]s, CB[n]s can serve as nanoreactors and steric hindrance to modulate the reactivity of substrates. They can also catalyze the reactions by modulating the reactivity of ionized intermediates. Recent progresses on the CB[n]s based supramolecular catalysis are introduced in this Minireview and the future development in this field is discussed. It is anticipated that this review provides insights into the mechanism of CB[n]s based supramolecular catalysis and may help scientists find new opportunities in this field.
Lignin from Annual Plants as Raw Material Source for Flavors and Basic Chemicals
Authors: Jahn Annika , Hoffmann Anton , Blaesing Luisa , Kunde Fabian , Bertau Martin , Bremer Martina , Fischer Steffen 
Published: September 2020

AbstractThe enzymatic conversion of lignins, possibly in combination with electrochemical oxidation, makes aromatics such as syringol, guaiacol, vanillin and catechol available in the qualities required by the fragrance industry. The lignins were obtained by soda digestion from wheat straw and Miscanthus, characterized and then converted with laccases. The overall yield amounted up to 9 wt % with a product spectrum confined to four substances. Catechol was the major product, with a fraction of ≈75 %. It can easily be isolated by extraction with acetone.
A Cytochrome c‐Chlorotoxin Hybrid Protein as a Possible Antiglioma Drug
Authors: Delinois Louis J. , Peón Harold , Villalobos‐Santos Juan C. , Ramírez‐Paz Josell , Miller Jennifer , Griebenow Kai H. , Tinoco Arthur D. 
Published: September 2020

AbstractMalignant gliomas are the most lethal form of primary brain tumors. Despite advances in cancer therapy, the prognosis of glioma patients has remained poor. Cytochrome c (Cytc), an endogenous heme‐based protein, holds tremendous potential to treat gliomas because of its innate capacity to trigger apoptosis. To this end, a hybrid cytochrome c‐chlorotoxin (Cytc‐CTX) protein was biosynthesized to enable cellular uptake of the cell impenetrable Cytc using CTX transporters. A nucleotide sequence containing 1 : 1 Cytc and CTX was constructed and separated by a hexahistidine‐tag and an enterokinase cleavage site. The sequence was cloned into a pBTR1 plasmid, expressed in Escherichia coli, purified via 2‐dimensional chromatography. The identity and size of the protein were determined by Western blot and mass spectrometry. Cytc in this soluble hybrid protein has similar structure and stability as human Cytc and the hybrid protein is endocytosed into a glioma cell line, while displaying potent cytotoxicity and a favorable therapeutic index. Its facile, low‐cost, and high yield synthesis, biocompatibility, and robustness suggest that the hybrid protein is a promising candidate for antiglioma drug evaluation.
Curability of patients with lymph node metastases from extremity soft‐tissue sarcoma
Authors: Basile Georges , Mattei Jean‐Camille , Alshaygy Ibrahim , Griffin Anthony M. , Catton Charles N. , Chung Peter W. , Shultz David B. , Razak Albiruni R. A. , Demicco Elizabeth G. , Ferguson Peter C. , Wunder Jay S. 
Published: September 2020

BackgroundLymph node metastases (LNM) rarely occur in adult extremity soft‐tissue sarcoma (STS), affecting approximately 5% of patients. To the authors' knowledge, few studies to date have evaluated the prognosis and survival of patients with LNM.MethodsA retrospective review was performed of a single‐center, prospectively collected STS database. Demographic, treatment, and oncologic data for patients with STS of the extremity with LNM were obtained from clinical and radiographic records.ResultsOf 2689 patients with extremity STS, a total of 120 patients (4.5%) were diagnosed with LNM. LNM occurred most frequently among patients diagnosed with clear cell sarcoma (27.6%), epithelioid sarcoma (21.9%), rhabdomyosarcoma (17.3%), angiosarcoma (14.0%), and extraskeletal myxoid chondrosarcoma (9.3%). A total of 98 patients (81.7%) underwent LNM surgical resection. Patients with isolated LNM had a greater 5‐year overall survival (57.3%) compared with patients with American Joint Committee on Cancer (AJCC) eighth edition stage IV STS with only systemic metastases (14.6%) or both LNM and systemic disease (0%; P < .0001). Patients with isolated LNM had an overall survival rate (52.9%) similar to that of patients with localized AJCC stage III tumors (ie, large, high‐grade tumors) (49.3%) (P = .8). Patients with late, isolated, metachronous LNM had a 5‐year overall survival rate (61.2%) that was similar to that of patients with isolated synchronous LNM at the time of presentation (53.6%) (P = .4).ConclusionsMany different types of STS develop LNM. Patients with extremity STS with isolated LNM should not be considered as having stage IV disease as they are according to the current AJCC eighth edition classification because they have significantly better survival than those with systemic metastases. Patients with isolated, late, metachronous LNM have a survival similar to that of patients with isolated synchronous LNM at the time of presentation.Lay Summary

The results of the current study demonstrated that patients diagnosed with isolated lymph node metastases have a prognosis similar to that of patients diagnosed with localized American Joint Committee on Cancer stage III soft‐tissue sarcomas, which also equates to a significantly better overall survival compared with patients with systemic metastases.

Therefore, the authors recommend modifications to the most recent eighth edition of the American Joint Committee on Cancer staging system to clearly distinguish patients with isolated lymph node metastases to acknowledge their better prognosis compared with those with systemic metastases.
Significant reduction of indeterminate (atypical) diagnosis after implementation of The Paris System for Reporting Urinary Cytology: A single‐institution study of more than 27,000 cases
Authors: Tian Wei , Shore Karen T. , Shah Rajal B. 
Published: September 2020

BackgroundUrinary cytology is a noninvasive and cost‐effective diagnostic and surveillance test in the clinical management of urothelial carcinoma (UC). The Paris System for Reporting Urinary Cytology (TPS), published in 2016, introduced definite diagnostic criteria aimed at improving performance in detecting high‐grade UC (HGUC) and decreasing the indeterminate (atypical) diagnosis.MethodsThe authors retrospectively reviewed and compared urinary cytology diagnoses reported between January 2013 and December 2014 (pre‐TPS, 7658 cases) and between May 2016 and April 2018 (post‐TPS, 20,026 cases) to assess the influence of TPS in their practice. The time in between was used as a learning period. Follow‐up information and correlation with the UroVysion fluorescence in situ hybridization test were obtained when available.ResultsUrinary cytology diagnoses pre‐TPS included negative for UC (NUC) (n = 5293; 69.2%), atypical urothelial cells (AUC) (n = 2227; 29%), and suspicious/positive for HGUC (SHGUC/HGUC) (n = 138; 1.8%). Diagnoses post‐TPS included negative for HGUC (NHGUC) (n = 18,507; 92.4%), AUC (n = 1237; 6.2%), and SHGUC/HGUC (n = 282; 1.4%). Comparing the pre‐TPS and post‐TPS periods, AUC diagnoses decreased from 29% to 6.2% (P < .00001), and the specificity and positive predictive value of AUC to detect HGUC significantly improved from 49% to 86% (P < .00001) and from 9% to 39% (P = .002), respectively. The correlation of an AUC diagnosis with a positive UroVysion test improved from 17% to 38% (P < .00001), whereas overall use of the UroVysion test was decreased.ConclusionsImplementation of TPS resulted in a significant reduction in AUC diagnoses that had a superior correlation with a subsequent biopsy and a UroVysion test, resulting in potential reductions in test use and medical cost.
Topographic gradients define the projection patterns of the claustrum core and shell in mice
Authors: Marriott Brian A. , Do Alison D. , Zahacy Ryan , Jackson Jesse 
Published: September 2020

AbstractThe claustrum is densely connected to the cortex and participates in brain functions such as attention and sleep. Although some studies have reported the widely divergent organization of claustrum projections, others describe parallel claustrocortical connections to different cortical regions. Therefore, the details underlying how claustrum neurons broadcast information to cortical networks remain incompletely understood. Using multicolor retrograde tracing we determined the density, topography, and co‐projection pattern of 14 claustrocortical pathways, in mice. We spatially registered these pathways to a common coordinate space and found that the claustrocortical system is topographically organized as a series of overlapping spatial modules, continuously distributed across the dorsoventral claustrum axis. The claustrum core projects predominantly to frontal‐midline cortical regions, whereas the dorsal and ventral shell project to the cortical motor system and temporal lobe, respectively. Anatomically connected cortical regions receive common input from a subset of claustrum neurons shared by neighboring modules, whereas spatially separated regions of cortex are innervated by different claustrum modules. Therefore, each output module exhibits a unique position within the claustrum and overlaps substantially with other modules projecting to functionally related cortical regions. Claustrum inhibitory cells containing parvalbumin, somatostatin, and neuropeptide Y also show unique topographical distributions, suggesting different output modules are controlled by distinct inhibitory circuit motifs. The topographic organization of excitatory and inhibitory cell types may enable parallel claustrum outputs to independently coordinate distinct cortical networks.
The Interplay of Nanoconfinement and pH from the Perspective of a Dye‐Reporter Molecule
Authors: Brilmayer Robert , Brodrecht Martin , Kaiser Christoph , Breitzke Hergen , Kumari Bharti , Wachtveitl Josef , Buntkowsky Gerd , Andrieu‐Brunsen Annette 
Published: September 2020

AbstractA novel thiazol‐based ratiometric dye for the detection of local pH values is synthesized, and its properties are characterized by a combination of optical spectroscopy, solid‐state NMR and DNP (dynamic nuclear polarization)‐enhanced solid‐state NMR. This novel dye covers a completely different sensitivity range with its acidic pKa value of 3.5 compared to other established dyes for ratiometric pH detection, such as SNARF. The dye is grafted to the surfaces of mesoporous silica materials, which enables, for the first time, direct in situ measurements of the local pH values in silica mesopores by a simple UV‐vis spectroscopy method. The obtained results, which are in good agreement with previous indirect techniques, indicate a background electrolyte‐dependent pKa shift of at least one pH unit under nanoconfined conditions compared to the pKa of the dye in bulk solution.
Density peaks clustering based on k‐nearest neighbors sharing
Authors: Fan Tanghuai , Yao Zhanfeng , Han Longzhe , Liu Baohong , Lv Li 
Published: September 2020

SummaryThe density peaks clustering (DPC) algorithm is a density‐based clustering algorithm. Its density peak depends on the density‐distance model to determine it. The definition of local density for samples used in DPC algorithm only considers distance between samples, while the environments of samples are neglected. This leads to the result that DPC algorithm performs poorly on complex data sets with large difference in density, flow pattern or cross‐winding. In the meantime, the fault tolerance of allocation strategy for samples is relatively poor. Based on the findings, this article proposes a density peaks clustering based on k‐nearest neighbors sharing (DPC‐KNNS) algorithm, which uses the similarity between shared neighbors and natural neighbors to define the local density of samples and the allocation. Comparison between theoretical analysis and experiments on various synthetic and real data reveal that the algorithm proposed in this article can discover the cluster center of complex data sets with large difference in density, flow pattern or cross‐winding. It can also provide effective clustering.
Flavylium Fluorophores as Near‐Infrared Emitters
Authors: Uranga‐Barandiaran Olatz , Casanova David , Castet Frédéric 
Published: September 2020

AbstractThis theoretical work rationalizes the absorption and fluorescence emission properties of conjugated dyes composed of dimethylamino flavylium heterocycles linked by a polymethine chain, which were recently reported to act as efficient shortwave infrared emitters. Density functional theory is used to characterize the electronic structure of the low‐lying excited states as a function of the polymethine chain length. Decomposition of the computed excitations in terms of diabatic states is also performed to deconvolute the excited states wavefunction into charge‐transfer intramolecular excitations. Based on these results, chemical substitution patterns consisting in enhancing the electron‐withdrawing strength of the polymethine bridge and the electron‐donating ability of the lateral flavylium fragments, are proposed to further redshift the photoluminescence of the fluorophores.
Structural and Photophysical Properties of Various Polypyridyl Ligands: A Combined Experimental and Computational Study
Authors: De Bruecker Liesbeth , Everaert Jonas , Van Der Voort Pascal , Stevens Christian V. , Waroquier Michel , Van Speybroeck Veronique 
Published: September 2020

AbstractCovalent triazine frameworks (CTFs) with polypyridyl ligands are very promising supports to anchor photocatalytic complexes. Herein, we investigate the photophysical properties of a series of ligands which vary by the extent of the aromatic system, the nitrogen content and their topologies to aid in selecting interesting building blocks for CTFs. Interestingly, some linkers have a rotational degree of freedom, allowing both a trans and cis structure, where only the latter allows anchoring. Therefore, the influence of the dihedral angle on the UV‐Vis spectrum is studied. The photophysical properties are investigated by a combined computational and experimental study. Theoretically, both static and molecular dynamics simulations are performed to deduce ground‐ and excited state properties based on density functional theory (DFT) and time‐dependent DFT. The position of the main absorption peak shifts towards higher wavelengths for an increased size of the π‐system and a higher π‐electron deficiency. We found that the position of the main absorption peak among the different ligands studied in this work can amount to 271 nm; which has a significant impact on the photophysical properties of the ligands. This broad range of shifts allows modulation of the electronic structure by varying the ligands and may help in a rational design of efficient photocatalysts.