bluuebunny/crossref_metadata_2025_split huggingface dataset:
An in vitro mimic of in‐cell solvation for protein folding studies
Authors: Davis Caitlin M. , Deutsch Jonathan , Gruebele Martin 
Published: January 2020

AbstractFicoll, an inert macromolecule, is a common in vitro crowder, but by itself it does not reproduce in‐cell stability or kinetic trends for protein folding. Lysis buffer, which contains ions, glycerol as a simple kosmotrope, and mimics small crowders with hydrophilic/hydrophobic patches, can reproduce sticking trends observed in cells but not the crowding. We previously suggested that the proper combination of Ficoll and lysis buffer could reproduce the opposite in‐cell folding stability trend of two proteins: variable major protein‐like sequence expressed (VlsE) is destabilized in eukaryotic cells and phosphoglycerate kinase (PGK) is stabilized. Here, to discover a well‐characterized solvation environment that mimics in‐cell stabilities for these two very differently behaved proteins, we conduct a two‐dimensional scan of Ficoll (0–250 mg/ml) and lysis buffer (0–75%) mixtures. Contrary to our previous expectation, we show that mixtures of Ficoll and lysis buffer have a significant nonadditive effect on the folding stability. Lysis buffer enhances the stabilizing effect of Ficoll on PGK and inhibits the stabilizing effect of Ficoll on VlsE. We demonstrate that a combination of 150 mg/ml Ficoll and 60% lysis buffer can be used as an in vitro mimic to account for both crowding and non‐steric effects on PGK and VlsE stability and folding kinetics in the cell. Our results also suggest that this mixture is close to the point where phase separation will occur. The simple mixture proposed here, based on commercially available reagents, could be a useful tool to study a variety of cytoplasmic protein interactions, such as folding, binding and assembly, and enzymatic reactions.Significance StatementThe complexity of the in‐cell environment is difficult to reproduce in the test tube. Here we validate a mimic of cellular crowding and sticking interactions in a test tube using two proteins that are differently impacted by the cell: one is stabilized and the other is destabilized. This mimic is a starting point to reproduce cellular effects on a variety of protein and biomolecular interactions, such as folding and binding.
Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46
Authors: Yan Yumeng , He Jiahua , Feng Yuyu , Lin Peicong , Tao Huanyu , Huang Sheng‐You 
Published: January 2020

AbstractProtein‐protein docking plays an important role in the computational prediction of the complex structure between two proteins. For years, a variety of docking algorithms have been developed, as witnessed by the critical assessment of prediction interactions (CAPRI) experiments. However, despite their successes, many docking algorithms often require a series of manual operations like modeling structures from sequences, incorporating biological information, and selecting final models. The difficulties in these manual steps have significantly limited the applications of protein‐protein docking, as most of the users in the community are nonexperts in docking. Therefore, automated docking like a web server, which can give a comparable performance to human docking protocol, is pressingly needed. As such, we have participated in the blind CAPRI experiments for Rounds 38‐45 and CASP13‐CAPRI challenge for Round 46 with both our HDOCK automated docking web server and human docking protocol. It was shown that our HDOCK server achieved an “acceptable” or higher CAPRI‐rated model in the top 10 submitted predictions for 65.5% and 59.1% of the targets in the docking experiments of CAPRI and CASP13‐CAPRI, respectively, which are comparable to 66.7% and 54.5% for human docking protocol. Similar trends can also be observed in the scoring experiments. These results validated our HDOCK server as an efficient automated docking protocol for nonexpert users. Challenges and opportunities of automated docking are also discussed.
Inhibition of the type III secretion system of Pseudomonas syringae pv. tomato DC3000 by resveratrol oligomers identified in Vitis vinifera L
Authors: Kang Ji Eun , Jeon Byeong Jun , Park Min Young , Yang Hye Ji , Kwon Jaeyoung , Lee Dong Ho , Kim Beom Seok 
Published: January 2020

AbstractBACKGROUNDThe bacterial type III secretion system (T3SS) is one of the virulence determinants of Gram‐negative bacteria through which various effector and virulence proteins are translocated into host cells.RESULTSWe constructed an assay system to screen inhibitors of hrpA gene expression (a structural gene of Hrp pili) in Pseudomonas syringae pv. tomato DC3000. In a plant extract library screening, the root extract of Vitis vinifera L. displayed the most prominent activity. Three resveratrol oligomers, hopeaphenol, isohopeaphenol and ampelopsin A, were identified in grapevine root extract, which significantly reduced the transcription levels of the hrpA, hrpL and hopP1 genes without growth retardation. Additional resveratrol derivatives identified in other plant extracts were also examined for their inhibitory effect on hrpA expression. Another resveratrol oligomer, kobophenol A, also inhibited the transcription of the hrpA gene and other T3SS‐related genes, while resveratrol monomers (resveratrol and piceatannol) were not effective. The severity of bacterial specks was reduced by each hopeaphenol, isohopeaphenol and ampelopsin A treatment.CONCLUSIONThese results show the potential of resveratrol derivatives as anti‐virulence agents for the control of plant diseases.
Associations between riparian plant morphological guilds and fluvial sediment dynamics along the regulated Colorado River in Grand Canyon
Authors: Butterfield Bradley J. , Grams Paul E. , Durning Laura E. , Hazel Joseph , Palmquist Emily C. , Ralston Barbara E. , Sankey Joel B. 
Published: January 2020

AbstractEffects of riparian vegetation on fluvial sediment dynamics depend on morphological traits of the constituent species. Determining the effects of different morphological guilds on sedimentation rates, as influenced by multiple aspects of dam operations, can help identify viable strategies for streamflow and vegetation management to achieve riparian resource goals. Plants of increasing size and branching density or complexity have been found to have greater effects on sedimentation in free‐flowing systems; however, this relationship could differ in regulated rivers. We tested the hypothesis that plant guilds of increasing height and branching complexity would be positively associated with sedimentation rates on 23 sandbars deposited in zones of recirculating flow (eddies) along the Colorado River in Grand Canyon. We used an image‐based vegetation classification and digital elevation models from annual topographic surveys to track associations between six plant morphological guilds and topographic change over 5 years. Vegetation had significant associations with deposition after accounting for geomorphic setting, but the ordinal guild scale was not positively correlated with deposition magnitude. Instead, low‐statured rhizomatous and herbaceous guilds were particularly effective at capturing sediment in the separation zone of sandbars, whereas tall herbs and large shrubs were most effective at capturing sediment in reattachment zones. These nuanced interactions between geomorphic position and morphological guild may be a direct consequence of flow regulation through modifications to physical deposition and erosion processes. Flow regulation may also select for a narrow subset of morphological guilds, reducing the diversity of vegetation feedbacks on sedimentation and emphasizing geomorphic drivers.
Identifying the Activation Mechanism and Boosting Electrocatalytic Activity of Layered Perovskite Ruthenate
Authors: Li Qun , Wang Dewen , Lu Qingqing , Meng Tian , Yan Mengxia , Fan Libing , Xing Zhicai , Yang Xiurong 
Published: January 2020

AbstractSrRuO3 as a rare conductive perovskite ruthenate has attracted increasing attention for application in energy conversion. Here, the electrocatalytic activity for the hydrogen evolution reaction (HER) of thermally synthesized layered SrRuO3 is investigated and shows a considerable activation during cathodic polarization in alkaline solution. The analysis demonstrates the electrode activation is caused by the increased hydrophilicity of SrRuO3 surface, revealing the influence of the surface properties on HER performance. For further improving the catalytic activity of perovskite ruthenate, the RuO2/SrRuO3 (RSRO) heterostructure is fabricated in situ by reducing the thermal decomposition temperature of 1000 °C for SrRuO3 to 600 °C. The appropriate lattice parameter of SrRuO3 ensures a good lattice match, which results in a strong interaction between SrRuO3 and RuO2. Hence, the RSRO substantially outperforms the corresponding single‐component oxides. In addition, the increased active sites induced by the rapid improvement of hydrophilicity of RSRO surface further highlight its structural advantage for catalytic hydrogen generation. The experimental and theoretical computation results consistently validate the positive synergistic effect among SrRuO3 and RuO2 in tuning the atomic and electronic configuration.
A High‐Temperature Na‐Ion Battery: Boosting the Rate Capability and Cycle Life by Structure Engineering
Authors: Zhou Yanping , Zhang Xianghua , Liu Yanjing , Xie Xinxin , Rui Xianhong , Zhang Xiong , Feng Yuezhan , Zhang Xiaojun , Yu Yan , Huang Kama 
Published: January 2020

AbstractHigh‐temperature sodium ion batteries (SIBs) have drawn significant heed recently for large‐scale energy storage. Yet, conventional SIBs are in the depths of inferior charge/discharge efficiency and cyclability at elevated temperatures. Rational structure design is highly desirable. Hence, a 3D hierarchical flower architecture self‐assembled by carbon‐coated Na3V2(PO4)3 (NVP) nanosheets (NVP@C‐NS‐FL) is fabricated via a microwave‐assisted glycerol‐mediated hydrothermal reaction combined with a post heat‐treatment. The growth mechanism of NVP@C‐NS‐FL is systematically investigated, by forming a microspherical glycerol/polyglycerol‐NVP complex initially and then converting into flower‐like architecture during the subsequent annealing at a low temperature ramping rate. Benefiting from the integrated structure, fast Na+ transportation, and highly effective heat transfer, the as‐obtained NVP@C‐NS‐FL exhibits an excellent high‐temperature SIB performance, e.g., 65 mAh g−1 (100 C) after 1000 cycles under 60 °C. When coupled with NaTi2(PO4)3 anode, the full cell can still display superior power capability of 1.4 kW kg−1 and long‐term cyclability (2000 cycles) under 60 °C.
Multifunctional Antimicrobial Biometallohydrogels Based on Amino Acid Coordinated Self‐Assembly
Authors: Song Jingwen , Yuan Chengqian , Jiao Tifeng , Xing Ruirui , Yang Mengyao , Adams Dave J. , Yan Xuehai 
Published: January 2020

AbstractThere is a real need for new antibiotics against self‐evolving bacteria. One option is to use biofriendly broad‐spectrum and mechanically tunable antimicrobial hydrogels that can combat multidrug‐resistant microbes. Whilst appealing, there are currently limited options. Herein, broad‐spectrum antimicrobial biometallohydrogels based on the self‐assembly and local mineralization of Ag+‐coordinated Fmoc‐amino acids are reported. Such biometallohydrogels have the advantages of localized delivery and sustained release, reduced drug dosage and toxicity yet improved bioavailability, prolonged drug effect, and tunable mechanical strength. Furthermore, they can directly interact with the cell walls and membrane, resulting in the detachment of the plasma membrane and leakage of the cytoplasm. This leads to cell death, triggering a significant antibacterial effect against both Gram‐negative (Escherichia coli) and Gram‐positive (Staphylococcus aureus) bacteria in cells and mice. This study paves the way for developing a multifunctional integration platform based on simple biomolecules coordinated self‐assembly toward a broad range of biomedical applications.
Pomegranate extract inhibits migration and invasion of oral cancer cells by downregulating matrix metalloproteinase‐2/9 and epithelial‐mesenchymal transition
Authors: Peng Sheng‐Yao , Hsiao Chien‐Chou , Lan Ting‐Hsun , Yen Ching‐Yui , Farooqi Ammad A. , Cheng Chih‐Mei , Tang Jen‐Yang , Yu Tzu‐Jung , Yeh Yun‐Chiao , Chuang Ya‐Ting , Chiu Chien‐Chih , Chang Hsueh‐Wei 
Published: January 2020

AbstractDiscovering drug candidates for the modulation of metastasis is of great importance in inhibiting oral cancer malignancy. Although most pomegranate extract applications aim at the antiproliferation of cancer cells, its antimetastatic effects remain unclear, especially for oral cancer cells. The aim of this study is to evaluate the change of two main metastasis characters, migration and invasion of oral cancer cells. Further, we want to explore the molecular mechanisms of action of pomegranate extract (POMx) at low cytotoxic concentration. We found that POMx ranged from 0 to 50 μg/mL showing low cytotoxicity to oral cancer cells. In the case of oral cancer HSC‐3 and Ca9‐22 cells, POMx inhibits wound healing migration, transwell migration, and matrix gel invasion. Mechanistically, POMx downregulates matrix metalloproteinase (MMP)‐2 and MMP‐9 activities and expressions as well as epithelial‐mesenchymal transition (EMT) signaling. POMx upregulates extracellular signal‐regulated kinases 1/2 (ERK1/2), but not c‐Jun N‐terminal kinase (JNK) and p38 expression. Addition of ERK1/2 inhibitor (PD98059) significantly recovered the POMx‐suppressed transwell migration and MMP‐2/−9 activities in HSC‐3 cells. Taken together, these findings suggest to further test low cytotoxic concentrations of POMx as a potential antimetastatic therapy against oral cancer cells.
CROSS RATIOS ON BOUNDARIES OF SYMMETRIC SPACES AND EUCLIDEAN BUILDINGS
Authors: BEYRER J. 
Published: January 2020

AbstractWe generalize the natural cross ratio on the ideal boundary of a rank one symmetric space, or even CAT(−1) space, to higher rank symmetric spaces and (nonlocally compact) Euclidean buildings. We obtain vector valued cross ratios defined on simplices of the building at infinity. We show several properties of those cross ratios; for example that (under some restrictions) periods of hyperbolic isometries give back the translation vector. In addition, we show that cross ratio preserving maps on the chamber set are induced by isometries and vice versa, — motivating that the cross ratios bring the geometry of the symmetric space/Euclidean building to the boundary.
Congruency of intervening events and self-induced action influence prediction of final results
Authors: Kimura Tsukasa , Katayama Jun’ichi 
Published: January 2020

AbstractPredicting self-induced stimuli is easier than predicting externally produced ones and the amplitude of event-related brain potentials (ERP) elicited by self-induced stimuli is smaller than that elicited by externally produced ones. Previous studies reported that these phenomena occurred strong when stimuli were presented immediately after self-induced action. To be able to adapt to changes, however, it is necessary to predict not only an event that follows a self-induced action but also a subsequent final result. We investigated whether congruency among self-induced actions, intervening events, and final results influences the processing of final results. The congruency of an intervening event with self-induced action was task-irrelevant information for the required response to a final result. The results showed that the P1 amplitude elicited by the final result (i.e., somatosensory stimulus) when an intervening event was congruent with self-induced action was smaller than other elicited amplitudes. This suggests that the congruency of an intervening event and self-induced action may facilitate prediction of a final result, even when this congruency is irrelevant to the ongoing task.
Poincaré polynomials of moduli spaces of Higgs bundles and character varieties (no punctures)
Authors: Mellit Anton 
Published: January 2020

AbstractUsing our earlier results on polynomiality properties of plethystic logarithms of generating series of certain type, we show that Schiffmann’s formulas for various counts of Higgs bundles over finite fields can be reduced to much simpler formulas conjectured by Mozgovoy. In particular, our result implies the conjecture of Hausel and Rodriguez-Villegas on the Poincaré polynomials of twisted character varieties and the conjecture of Hausel and Thaddeus on independence of E-polynomials on the degree.
Midlatitude atmospheric transient eddy feedbacks influenced ENSO-associated wintertime Pacific teleconnection patterns in two PDO phases
Authors: Chu Cuijiao , Hu Haibo , Yang Xiu-Qun , Yang Dejian 
Published: January 2020

AbstractThe El Nino-Southern Oscillation (ENSO)-associated wintertime atmospheric teleconnection patterns in two Pacific decadal oscillation (PDO) phases are investigated using ERA-20C reanalysis data for 1950–2010. A strengthened ENSO-associated Pacific-North American (PNA) teleconnection pattern presents in PDO positive phase, while a West Pacific (WP) pattern over Northwestern Pacific and a squeezed PNA pattern coexist when ENSO occurs in PDO negative phase. The dynamical role of atmospheric transient eddy feedbacks to the teleconnection patterns are highlighted in the present study. When ENSO occurs in PDO positive phase, the uniform strengthened westerly jet anomalies downstream of the climatological main body of jet accompany with energetic transient eddy anomalies over Northeastern Pacific. The transient eddy feedbacks largely enhance and favor the strengthened PNA pattern. When ENSO occurs in PDO negative phase, the strengthened westerly jet anomalies appear to separate into two parts, one locating north of the climatological main body of jet and the other at the downstream. The accompanied transient eddy anomalies also split into two parts. Under such conditions, the transient eddy feedbacks are limited over Northeastern Pacific and favor a weak PNA pattern. However, the transient eddy anomalies over Northwestern Pacific strengthen, and the feedbacks also strengthen and largely contribute to the WP pattern. Moreover, the transient eddy anomalies over Northwestern Pacific seem to be anchored along the anomalously poleward strengthened oceanic subarctic frontal zone (SAFZ) in PDO negative phase. The enhanced atmospheric baroclinicity anomalies, coupled with the strengthened SAFZ, energize atmospheric transient eddy anomalies, and work as the potential maintenance in shaping the WP pattern.
Improving the dietary quality of food parcels leads to improved dietary intake in Dutch food bank recipients—effects of a randomized controlled trial
Authors: Neter Judith E. , Dijkstra S. Coosje , Twisk Jos W. R. , Visser Marjolein , Brouwer Ingeborg A. 
Published: January 2020

Abstract
Purpose
Since food banks have a strong influence on recipients’ diets, and seem to have difficulties in supporting healthy diets, improving the dietary quality of food parcels is important. The aim of our study was to assess whether improving the dietary quality of food parcels, using different strategies, can positively impact the actual dietary intake of Dutch food bank recipients.

Methods
This randomized cross-over controlled trial (Trial ID: ISRCTN40554133) with four intervention conditions [(1) Control (standard food parcel), (2) snacks– (standard food parcel with replacement of unhealthy snacks by staple foods), (3) FV+ (standard food parcel plus the recommended daily amount of fruit and vegetables), (4) snacks– + FV+ (standard food parcel with replacement of unhealthy snacks by staple foods plus the recommended daily amount of fruit and vegetables)] included 163 food bank recipients, from three food banks. At baseline, participants filled in a questionnaire. Dietary intake data were collected through 24-h recalls after both intervention conditions at 4 and 8 weeks follow-up. Primary outcome was daily fruit and vegetable intake, secondary outcomes were daily dietary intakes of food groups and nutrients.

Results
Multi-level linear regression analysis, using a two-level model, showed a higher mean daily fruit intake in participants in the FV+ condition than in participants in the Control condition (delta (δ): 74 [40.3;107.6] g). Both mean daily fruit and vegetable intake were higher in participants in the Snacks– + FV+ condition than in participants in the Control condition (fruit δ: 81.3 [56.5;106.2] g; vegetables δ: 46.2 [17.5;74.9] g), as well as in the Snacks– condition (fruit δ: 70.0 [38.8;101.1] g; vegetables δ: 62.2 [26.2; 98.2] g).

Conclusions
This study shows that improving the dietary quality of food parcels can positively impact the dietary intake of Dutch food bank recipients. With this information we can further develop effective strategies that can be easily applied by food banks, to improve dietary intake of food bank recipients.
Sub-angiographic peripheral emboli in high resolution DWI after endovascular recanalization
Authors: Schönfeld Michael H. , Kabiri Reza , Kniep Helge C. , Meyer Lukas , Sedlacik Jan , Ernst Marielle , Broocks Gabriel , Faizy Tobias D. , Cheng Bastian , Thomalla Götz , Fiehler Jens , Hanning Uta 
Published: January 2020

Abstract
Background and aim
To analyze the incidence of peripheral emboli after successful mechanical thrombectomy (MT) of intracranial large vessel occlusions (LVO).

Methods
We performed a prospective analysis of patients with intracranial LVO who underwent successful MT and received a 1.5 T MRI including diffusion-weighted imaging (DWI) in standard- and high-resolution as well as susceptibility-weighted imaging (SWI) on the day following the intervention. Reperfusion grade was assessed on post-thrombectomy digital subtraction angiography (DSA) using the expanded thrombolysis in cerebral infarction (eTICI) scale. Punctuate DWI lesions distal to the DWI core lesion were classified as peripheral emboli. DWI lesions outside the primary affected vascular territory were classified as emboli into new territories. Additionally, SWI and post-thrombectomy DSA were analyzed and correlated to findings on DWI.

Results
Twenty-eight patients undergoing successful MT met the inclusion criteria. In 26/28 patients (93%), a total of 324 embolic lesions were detected in DWI representing 2.1% of the cumulated ischemic core volume. 151 peripheral emboli were detected in standard-resolution DWI, 173 additional emboli were uncovered in high-resolution DWI. Eight out of nine patients with an eTICI 3 reperfusion had embolic lesions (29 DWI lesions). 9.6% (31/324) of peripheral emboli were observed in vascular territories not affected by the LVO. SWI lesions were observed in close proximity to 10.2% (33/324) of DWI lesions.

Conclusions
Peripheral emboli are frequent after MT even after complete reperfusion. These emboli occur rather in the vascular territory of the occluded vessel than in other territories. A large proportion of peripheral emboli is only detected by high-resolution DWI.