bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basin Evolution and Shale Tectonics on an Obliquely Convergent Margin: The Bahia Basin, Offshore Colombian Caribbean
Authors: Galindo Pedro A. , Lonergan Lidia 
Published: January 2020

AbstractOblique convergent margins accumulate strike‐slip deformation that controls basin formation and evolution. The Bahia Basin is located offshore, proximal to major strike‐slip fault systems that affect northern Colombia. It lies behind the toe of the modern accretionary prism, where the Caribbean Plate is being subducted obliquely beneath South America. This is the first attempt using 3‐D seismic reflection data to interpret a complex strike‐slip basin at the western end of the southern margin of the Caribbean Plate. Detailed 2‐D and 3‐D seismic mapping of regional unconformities and faults is used to describe the structural geometry, timing, and evolution of extensional and strike‐slip faults, which controlled the formation of the basin. Analysis of the fault zones is coupled with a description of the seismic‐stratigraphic units observed within the Bahia Basin to reconstruct the spatial and temporal evolution of deformation and to evaluate the influence of the pervasive shale tectonics observed in the area. The results, presented as a series of structural‐paleogeographic maps, illustrate an initial stage of transtension that controlled the formation of shale‐withdrawal minibasins from late Oligocene to late Miocene times. The continuous deformation and northward expulsion of the Santa Marta Massif resulted in transpression during Pliocene times, leading to basin inversion and ultimate closure of the basin. Basin evolution along the southern Caribbean oblique, convergent margin, shows the occurrence of a complex interaction between subduction and major‐onshore strike‐slip fault systems and illustrates how strain‐partitioning led to the break‐up and lateral displacement of early accretionary prisms formed along the margin.
Structural basis for itraconazole-mediated NPC1 inhibition
Authors: Long Tao , Qi Xiaofeng , Hassan Abdirahman , Liang Qiren , De Brabander Jef K. , Li Xiaochun 
Published: January 2020

AbstractNiemann-Pick C1 (NPC1), a lysosomal protein of 13 transmembrane helices (TMs) and three lumenal domains, exports low-density-lipoprotein (LDL)-derived cholesterol from lysosomes. TMs 3–7 of NPC1 comprise the Sterol-Sensing Domain (SSD). Previous studies suggest that mutation of the NPC1-SSD or the addition of the anti-fungal drug itraconazole abolishes NPC1 activity in cells. However, the itraconazole binding site and the mechanism of NPC1-mediated cholesterol transport remain unknown. Here, we report a cryo-EM structure of human NPC1 bound to itraconazole, which reveals how this binding site in the center of NPC1 blocks a putative lumenal tunnel linked to the SSD. Functional assays confirm that blocking this tunnel abolishes NPC1-mediated cholesterol egress. Intriguingly, the palmitate anchor of Hedgehog occupies a similar site in the homologous tunnel of Patched, suggesting a conserved mechanism for sterol transport in this family of proteins and establishing a central function of their SSDs.
Chiral recognition and enantiomer excess determination based on emission wavelength change of AIEgen rotor
Authors: Hu Ming , Yuan Ying-Xue , Wang Weizhou , Li Dong-Mi , Zhang Hong-Chao , Wu Bai-Xing , Liu Minghua , Zheng Yan-Song 
Published: January 2020

AbstractChiral recognition, such as enantioselective interactions of enzyme with chiral agents, is one of the most important issues in the natural world. But artificial chiral receptors are much less efficient than natural ones. For tackling the chiral recognition and enantiomer excess (ee) analysis, up until now all the fluorescent receptors have been developed based on fluorescence intensity changes. Here we report that the chiral recognition of a large number of chiral carboxylic acids, including chiral agrochemicals 2,4-D, is carried out based on fluorescent colour changes rather than intensity changes of AIEgen rotors. Moreover, the fluorescence wavelength of the AIEgen rotor linearly changes with ee of the carboxylic acid, enabling the ee to be accurately measured with average absolute errors (AAE) of less than 2.8%. Theoretical calculation demonstrates that the wavelength change is ascribed to the rotation of the AIEgen rotor upon interaction with different enantiomers.
Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS
Authors: Bian Yangyang , Zheng Runsheng , Bayer Florian P. , Wong Cassandra , Chang Yun-Chien , Meng Chen , Zolg Daniel P. , Reinecke Maria , Zecha Jana , Wiechmann Svenja , Heinzlmeir Stephanie , Scherr Johannes , Hemmer Bernhard , Baynham Mike , Gingras Anne-Claude , Boychenko Oleksandr , Kuster Bernhard 
Published: January 2020

AbstractNano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. Here we show that micro-flow LC–MS/MS using a 1 × 150 mm column shows excellent reproducibility of chromatographic retention time (<0.3% coefficient of variation, CV) and protein quantification (<7.5% CV) using data from >2000 samples of human cell lines, tissues and body fluids. Deep proteome analysis identifies >9000 proteins and >120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. The system identifies >30,000 phosphopeptides in 12 h and protein-protein or protein-drug interaction experiments can be analyzed in 20 min per sample. We show that the same column can be used to analyze >7500 samples without apparent loss of performance. This study demonstrates that micro-flow LC–MS/MS is suitable for a broad range of proteomic applications.
Evolving parsec-scale radio structure in the most distant blazar known
Authors: An Tao , Mohan Prashanth , Zhang Yingkang , Frey Sándor , Yang Jun , Gabányi Krisztina É. , Gurvits Leonid I. , Paragi Zsolt , Perger Krisztina , Zheng Zhenya 
Published: January 2020

AbstractBlazars are a sub-class of quasars with Doppler boosted jets oriented close to the line of sight, and thus efficient probes of supermassive black hole growth and their environment, especially at high redshifts. Here we report on Very Long Baseline Interferometry observations of a blazar J0906 + 6930 at z = 5.47, which enabled the detection of polarised emission and measurement of jet proper motion at parsec scales. The observations suggest a less powerful jet compared with the general blazar population, including lower proper motion and bulk Lorentz factor. This coupled with a previously inferred high accretion rate indicate a transition from an accretion radiative power to a jet mechanical power based transfer of energy and momentum to the surrounding gas. While alternative scenarios could not be fully ruled out, our results indicate a possibly nascent jet embedded in and interacting with a dense medium resulting in a jet bending.
Two-dimensional higher-order topology in monolayer graphdiyne
Authors: Lee Eunwoo , Kim Rokyeon , Ahn Junyeong , Yang Bohm-Jung 
Published: January 2020

AbstractBased on first-principles calculations and tight-binding model analysis, we propose monolayer graphdiyne as a candidate material for a two-dimensional higher-order topological insulator protected by inversion symmetry. Despite the absence of chiral symmetry, the higher-order topology of monolayer graphdiyne is manifested in the filling anomaly and charge accumulation at two corners. Although its low energy band structure can be properly described by the tight-binding Hamiltonian constructed by using only the pz orbital of each atom, the corresponding bulk band topology is trivial. The nontrivial bulk topology can be correctly captured only when the contribution from the core levels derived from px,y and s orbitals are included, which is further confirmed by the Wilson loop calculations. We also show that the higher-order band topology of a monolayer graphdyine gives rise to the nontrivial band topology of the corresponding three-dimensional material, ABC-stacked graphdiyne, which hosts monopole nodal lines and hinge states.
Bile acid bio-nanoencapsulation improved drug targeted-delivery and pharmacological effects via cellular flux: 6-months diabetes preclinical study
Authors: Mooranian Armin , Raj Wagle Susbin , Kovacevic Bozica , Takechi Ryu , Mamo John , Lam Virginie , Watts Gerald F. , Mikov Momir , Golocorbin-Kon Svetlana , Stojanovic Goran , Al-Sallami Hesham , Al-Salami Hani 
Published: January 2020

AbstractThe antilipidemic drug, probucol (PB), has demonstrated potential applications in Type 2 diabetes (T2D) through its protective effects on pancreatic β-cells. PB has poor solubility and bioavailability, and despite attempts to improve its oral delivery, none has shown dramatic improvements in absorption or antidiabetic effects. Preliminary data has shown potential benefits from bile acid co-encapsulation with PB. One bile acid has shown best potential improvement of PB oral delivery (ursodeoxycholic acid, UDCA). This study aimed to examine PB and UDCA microcapsules (with UDCA microcapsules serving as control) in terms of the microcapsules’ morphology, biological effects ex vivo, and their hypoglycemic and antilipidemic and anti-inflammatory effects in vivo. PBUDCA and UDCA microcapsules were examined in vitro (formulation studies), ex vivo and in vivo. PBUDCA microcapsules exerted positive effects on β-cells viability at hyperglycemic state, and brought about hypoglycemic and anti-inflammatory effects on the prediabetic mice. In conclusion, PBUDCA co-encapsulation have showed beneficial therapeutic impact of dual antioxidant-bile acid effects in diabetes treatment.
SWeeP: representing large biological sequences datasets in compact vectors
Authors: De Pierri Camilla Reginatto , Voyceik Ricardo , Santos de Mattos Letícia Graziela Costa , Kulik Mariane Gonçalves , Camargo Josué Oliveira , Repula de Oliveira Aryel Marlus , de Lima Nichio Bruno Thiago , Marchaukoski Jeroniza Nunes , da Silva Filho Antonio Camilo , Guizelini Dieval , Ortega J. Miguel , Pedrosa Fabio O. , Raittz Roberto Tadeu 
Published: January 2020

AbstractVectoral and alignment-free approaches to biological sequence representation have been explored in bioinformatics to efficiently handle big data. Even so, most current methods involve sequence comparisons via alignment-based heuristics and fail when applied to the analysis of large data sets. Here, we present “Spaced Words Projection (SWeeP)”, a method for representing biological sequences using relatively small vectors while preserving intersequence comparability. SWeeP uses spaced-words by scanning the sequences and generating indices to create a higher-dimensional vector that is later projected onto a smaller randomly oriented orthonormal base. We constructed phylogenetic trees for all organisms with mitochondrial and bacterial protein data in the NCBI database. SWeeP quickly built complete and accurate trees for these organisms with low computational cost. We compared SWeeP to other alignment-free methods and Sweep was 10 to 100 times quicker than the other techniques. A tool to build SWeeP vectors is available at https://sourceforge.net/projects/spacedwordsprojection/.
Shortening injection matrix for serial crystallography
Authors: Nam Ki Hyun 
Published: January 2020

AbstractSerial crystallography allows crystal structures to be determined at room temperature through the steady delivery of crystals to the X-ray interaction point. Viscous delivery media are advantageous because they afford efficient sample delivery from an injector or syringe at a low flow rate. Hydrophobic delivery media, such as lipidic cubic phase (LCP) or grease, provide a stable injection stream and are widely used. The development of new hydrophobic delivery materials can expand opportunities for future SX studies with various samples. Here, I introduce fat-based shortening as a delivery medium for SX experiments. This material is commercially available at low cost and is straightforward to handle because its phase (i.e., solid or liquid) can be controlled by temperature. Shortening was extruded from a syringe needle in a stable injection stream even below 200 nl/min. X-ray exposed shortening produced several background scattering rings, which have similar or lower intensities than those of LCP and contribute negligibly to data processing. Serial millisecond crystallography was performed using two shortening delivery media, and the room temperature crystal structures of lysozyme and glucose isomerase were successfully determined at resolutions of 1.5–2.0 Å. Therefore, shortening can be used as a sample delivery medium in SX experiments.
γ-AApeptides–based Small Molecule Ligands That Disaggregate Human Islet Amyloid Polypeptide
Authors: Bolarinwa Olapeju , Li Chunpu , Khadka Nawal , Li Qi , Wang Yan , Pan Jianjun , Cai Jianfeng 
Published: January 2020

AbstractThe abnormal folding and aggregation of functional proteins into amyloid is a typical feature of many age-related diseases, including Type II diabetes. Growing evidence has revealed that the prevention of aggregate formation in culprit proteins could retard the progression of amyloid diseases. Human Amylin, also known as human islet amyloid polypeptide (hIAPP), is the major factor for categorizing Type II diabetes as an amyloid disease. Specifically, hIAPP has a great aggregation potential, which always results in a lethal situation for the pancreas. Many peptide inhibitors have been constructed from the various segments of the full-length hIAPP peptide; however, only a few have their origin from the screening of combinatorial peptidomimetic library. In this study, based on HW-155, which was previously discovered from a one–bead–one compound (OBOC) library to inhibit Aβ40 aggregation, we investigated eight (8) analogues and evaluated their amyloid-prevention capabilities for inhibiting fibrillization of hIAPP. Characterization studies revealed that all analogues of HW-155, as well as HW-155, were effective inhibitors of the fibril formation by hIAPP.
Modeling of the irradiation effect on some physicochemical properties of metoprolol tartrate for safe medical uses
Authors: Ouerfelli Najoua , Vrinceanu Narcisa , Mliki Ezzedine , Homeida Abdelgadir M. , Amin Kamal A. , Ogrodowczyk Magdalena , Alshehri Fawziah S. , Ouerfelli Noureddine 
Published: January 2020

AbstractThe effect of gamma-irradiation and ionizing radiation (high-energy electrons beam) on the physicochemical properties of metoprolol tartrate at the solid phase and aqueous solution, has been investigated in the present study to model some properties affected by absorbed doses and to reveal some interesting mutual causal correlation. The proposed some interesting models can be adapted to other experimental conditions, and the newly obtained values of the adjustable parameters could be an excellent criterion of the state quality of the metoprolol tartrate or for other additional interpretations. The peculiar behaviour of variation of physicochemical properties against dose leads us to confirm the suggested optimized doses mentioned in previous work, for sterilization and safe medical uses.
Geochemistry and tectonic significance of late Paleoproterozoic A-type granites along the southern margin of the North China Craton
Authors: Wang Yan , Yang Yi-Zeng , Siebel Wolfgang , Zhang He , Zhang Yuan-Shuo , Chen Fukun 
Published: January 2020

AbstractThe Longwangzhuang pluton is a typical example of Paleoproterozoic A-type granite intrusions at the southern margin of the North China Craton. This pluton is composed of arfvedsonite granite and minor aegirine–augite granites. Samples from both granite types display similar zircon U-Pb ages with 207U-206Pb ages of 1612 ± 19 Ma [mean square weighted deviation (MSWD) = 0.66] and 1609 ± 24 Ma (MSWD = 0.5), respectively. The granites exhibit similar high silica (SiO2 = 71.1–73.4 wt.%), high alkaline (Na2O + K2O = 8.10–9.26 wt.%, K2O/Na2O > 1), and low Al2O3 (11.8–12.8 wt. %) contents and metaluminous to weakly peraluminous bulk chemistry. The chemical variations of the Longwangzhuang pluton suggest the effects of mineral fractionation. In addition, all samples show typical characteristics of A-type granites, such as high 10000Ga/Al ratios (4.10–7.28), high FeOtot/(FeOtot + MgO) ratios (0.88–0.99), and high Zr (484–1082 ppm), Ce (201–560 ppm), and Y (78–156 ppm) contents. The εNd(t) values and the (206Pb/204Pb)t, (207Pb/204Pb)t, and (208Pb/204Pb)t ratios of the arfvedsonite granite samples vary from −4.6 to –5.3, 15.021 to 17.349, 15.241 to 15.472, and 33.206 to 36.905, respectively, and those for the aegirine–augite granite sample amount at −0.2, 14.421, 15.175, and 33.706. The distinct and variable Nd and Pb isotope values indicate the presence of heterogeneous protoliths. Based on its geochemistry, its low initial Pb isotope ratios, and its enrichment in Nd isotopes, we infer that the Longwangzhuang A-type granite is the partial melting product of basement rocks such as the Taihua Group gneisses accompanied by some involvement of juvenile material from the mantle. Together with published data from other Paleoproterozoic A-type granite plutons exposed at the southern margin of the craton, our findings suggest that these granites had a similar origin. Furthermore, geochemically, they can be divided into two groups: A2-type, which formed earlier (~1.8–1.6 Ga), and A1-type, which formed later (~1.6–1.5 Ga). Combining this information with the variations in whole-rock Nd and zircon Hf isotopic composition at ca. 1.6 Ga, we propose that tectonic transformation from post-orogenic to anorogenic magmatism occurred at the southern margin of the North China Craton at that time.
Group task-related component analysis (gTRCA): a multivariate method for inter-trial reproducibility and inter-subject similarity maximization for EEG data analysis
Authors: Tanaka Hirokazu 
Published: January 2020

AbstractEEG is known to contain considerable inter-trial and inter-subject variability, which poses a challenge in any group-level EEG analyses. A true experimental effect must be reproducible even with variabilities in trials, sessions, and subjects. Extracting components that are reproducible across trials and subjects benefits both understanding common mechanisms in neural processing of cognitive functions and building robust brain-computer interfaces. This study extends our previous method (task-related component analysis, TRCA) by maximizing not only trial-by-trial reproducibility within single subjects but also similarity across a group of subjects, hence referred to as group TRCA (gTRCA). The problem of maximizing reproducibility of time series across trials and subjects is formulated as a generalized eigenvalue problem. We applied gTRCA to EEG data recorded from 35 subjects during a steady-state visual-evoked potential (SSVEP) experiment. The results revealed: (1) The group-representative data computed by gTRCA showed higher and consistent spectral peaks than other conventional methods; (2) Scalp maps obtained by gTRCA showed estimated source locations consistently within the occipital lobe; And (3) the high-dimensional features extracted by gTRCA are consistently mapped to a low-dimensional space. We conclude that gTRCA offers a framework for group-level EEG data analysis and brain-computer interfaces alternative in complement to grand averaging.
In vivo analysis of FANCD2 recruitment at meiotic DNA breaks in Caenorhabditis elegans
Authors: Germoglio Marcello , Valenti Anna , Gallo Ines , Forenza Chiara , Santonicola Pamela , Silva Nicola , Adamo Adele 
Published: January 2020

AbstractFanconi Anemia is a rare genetic disease associated with DNA repair defects, congenital abnormalities and infertility. Most of FA pathway is evolutionary conserved, allowing dissection and mechanistic studies in simpler model systems such as Caenorhabditis elegans. In the present study, we employed C. elegans to better understand the role of FA group D2 (FANCD2) protein in vivo, a key player in promoting genome stability. We report that localization of FCD-2/FANCD2 is dynamic during meiotic prophase I and requires its heterodimeric partner FNCI-1/FANCI. Strikingly, we found that FCD-2 recruitment depends on SPO-11-induced double-strand breaks (DSBs) but not RAD-51-mediated strand invasion. Furthermore, exposure to DNA damage-inducing agents boosts FCD-2 recruitment on the chromatin. Finally, analysis of genetic interaction between FCD-2 and BRC-1 (the C. elegans orthologue of mammalian BRCA1) supports a role for these proteins in different DSB repair pathways. Collectively, we showed a direct involvement of FCD-2 at DSBs and speculate on its function in driving meiotic DNA repair.
Renal damage after liver transplantation
Authors: Feldkamp Thorsten , Bienholz Anja , Paul Andreas , Saner Fuat H. 
Published: January 2020

Abstract
Background: Patients following liver transplantation are at risk to develop acute kidney injury (AKI). The aim of our study was to assess risk factors for the development of AKI and the impact of AKI on the outcome of patients after liver transplantation (OLT).
Patients and methods: In this retrospective study, we analyzed 149 patients undergoing OLT from 1/2004 to 12/2007. AKI was defined according to the KDIGO definition representing the AKIN and the RIFLE classification, and according to the need for renal replacement therapy (RRT).
Results: According to the AKIN criteria alone 14 patients, according to the RIFLE criteria alone no patient and according to both definitions 30 patients developed AKI. RRT was required in 54 patients experiencing AKI, whereas 51 patients did not develop AKI. Pre OLT serum creatinine (SCr) significantly predicted the development of AKI requiring RRT, but not AKI without RRT requirement. Survival rate was significantly inferior after 28 days, one or three years in patients with AKI requiring RRT (70.4, 46.4, 44.4% vs. 100, 92.2, 90.2%, P &lt; 0.001). There was no difference in survival between patients experiencing AKI according to the RIFLE or AKIN criteria without RRT requirement and patients without AKI.
Conclusion: Pre OLT renal dysfunction assessed by SCr was the most important risk factor predicting severe forms of AKI, but not milder forms of AKI. AKI requiring RRT had a detrimental impact on patients’ survival, whereas milder forms of AKI were not associated with a worse outcome.
Integrated 100 V bootstrap diode with enhanced reverse recovery characteristics for eGaN‐field effect transistor gate drivers
Authors: Li Shaohong , Zhu Jing , Sun Weifeng , Zhang Long , Zou Yanqin , Zhu Guichuang , Tian Tian 
Published: January 2020

An integrated 100 V bootstrap diode (DBST) with anode engineering based on the double epitaxial process for enhancement mode gallium nitride (eGaN) transistor gate drivers is first proposed in this Letter. On the anode side, the P + dynamic field limiting ring (PDFLR) and the floating metal electrode (FME) are employed. The PDFLR can greatly suppress the peak electric field on both sides of the device during the reverse recovery period, which leads to a significant improvement in reverse recovery robustness. The FME lowers the anode injection efficiency in on‐state and increases the hole recombination rate during reverse recovery, therefore, a fast reverse recovery is realised. The partial heavy doped N‐type buried layer not only reduces the resistance of the drift region but also shortens the hole extraction path from the drift region to sub‐electrode, as a result, reverse recovery tail current can be greatly shortened. Experiments combined with simulations show that the reverse recovery robustness of the optimised proposed DBST is improved by more than 12 times. Furthermore, the reverse recovery charge (Qrr) of the proposed structure is only 3.2 nC, which is 22% lower than that of the conventional device at the same forward current (IF) of 0.1 A.