bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Atomic Partial Charges Arboretum: Trying to See the Forest for the Trees
Authors: Cho Minsik , Sylvetsky Nitai , Eshafi Sarah , Santra Golokesh , Efremenko Irena , Martin Jan M. L. 
Published: February 2020

AbstractAtomic partial charges are among the most commonly used interpretive tools in quantum chemistry. Dozens of different ‘population analyses’ are in use, which are best seen as proxies (indirect gauges) rather than measurements of a ‘general ionicity’. For the GMTKN55 benchmark of nearly 2,500 main‐group molecules, which span a broad swathe of chemical space, some two dozen different charge distributions were evaluated at the PBE0 level near the 1‐particle basis set limit. The correlation matrix between the different charge distributions exhibits a block structure; blocking is, broadly speaking, by charge distribution class. A principal component analysis on the entire dataset suggests that nearly all variation can be accounted for by just two ‘principal components of ionicity’: one has all the distributions going in sync, while the second corresponds mainly to Bader QTAIM vs. all others. A weaker third component corresponds to electrostatic charge models in opposition to the orbital‐based ones. The single charge distributions that have the greatest statistical similarity to the first principal component are iterated Hirshfeld (Hirshfeld‐I) and a minimal‐basis projected modification of Bickelhaupt charges. If three individual variables, rather than three principal components, are to be identified that contain most of the information in the whole dataset, one representative for each of the three classes of Corminboeuf et al. is needed: one based on partitioning of the density (such as QTAIM), a second based on orbital partitioning (such as NPA), and a third based on the molecular electrostatic potential (such as HLY or CHELPG).
Redox Mechanisms in Li and Mg Batteries Containing Poly(phenanthrene quinone)/Graphene Cathodes using Operando ATR‐IR Spectroscopy
Authors: Vizintin Alen , Bitenc Jan , Kopač Lautar Anja , Grdadolnik Jože , Randon Vitanova Anna , Pirnat Klemen 
Published: February 2020

AbstractThe redox reaction mechanism of a poly(phenanthrene quinone)/graphene composite (PFQ/rGO) was investigated using operando attenuated total reflection infrared (ATR‐IR) spectroscopy during cycling of Li and Mg batteries. The reference phenanthrene quinone and the Li and Mg salts of the hydroquinone monomers were synthesized and their IR spectra were measured. Additionally, IR spectra were calculated using DFT. A comparison of all three spectra allowed us to accurately assign the C=O and C−O− vibration bands and confirm the redox mechanism of the quinone/Li salt of hydroquinone, with radical anion formation as the intermediate product. PFQ/rGO also showed exceptional performance in an Mg battery: A potential of 1.8 V versus Mg/Mg2+, maximum capacity of 186 mAh g−1 (335 Wh kg−1 of cathode material), and high capacity retention with only 8 % drop/100 cycles. Operando ATR‐IR spectroscopy was performed in a Mg/organic system, revealing an analogous redox mechanism to a Li/organic cell.
CD163+ tumor‐associated macrophage accumulation in breast cancer patients reflects both local differentiation signals and systemic skewing of monocytes
Authors: Ramos Rodrigo Nalio , Rodriguez Céline , Hubert Margaux , Ardin Maude , Treilleux Isabelle , Ries Carola H , Lavergne Emilie , Chabaud Sylvie , Colombe Amélie , Trédan Olivier , Guedes Henrique Gomes , Laginha Fábio , Richer Wilfrid , Piaggio Eliane , Barbuto José Alexandre M , Caux Christophe , Ménétrier‐Caux Christine , Bendriss‐Vermare Nathalie 
Published: February 2020

AbstractObjectivesThe accumulation of tumor‐associated macrophages (TAMs) is correlated with poor clinical outcome, but the mechanisms governing their differentiation from circulating monocytes remain unclear in humans.MethodsUsing multicolor flow cytometry, we evaluated TAMs phenotype in 93 breast cancer (BC) patients. Furthermore, monocytes from healthy donors were cultured in the presence of supernatants from dilacerated primary tumors to investigate their differentiation into macrophages (MΦ) in vitro. Additionally, we used transcriptomic analysis to evaluate BC patients’ blood monocytes profiles.ResultsWe observed that high intra‐tumor CD163‐expressing TAM density is predictive of reduced survival in BC patients. In vitro, M‐CSF, TGF‐β and VEGF from primary tumor supernatants skewed the differentiation of healthy donor blood monocytes towards CD163highCD86lowIL‐10high M2‐like MΦ that strongly suppressed CD4+ T‐cell expansion via PD‐L1 and IL‐10. In addition, blood monocytes from about 40% of BC patients displayed an altered response to in vitro stimulation, being refractory to type‐1 MΦ (M1‐MΦ) differentiation and secreting higher amounts of immunosuppressive, metastatic‐related and angiogenic cytokines. Aside from showing that monocyte transcriptome is significantly altered by the presence of BC, we also demonstrated an overall metabolic de‐activation in refractory monocytes of BC patients. In contrast, monocytes from sensitive BC patients undergoing normal M1‐MΦ differentiation showed up‐regulation of IFN‐response genes and had no signs of metabolic alteration.ConclusionAltogether, our results suggest that systemic factors skew BC patient blood monocytes towards a pro‐metastatic profile, resulting in the accumulation of further polarised CD163high TAMs resembling type‐2 MΦ (M2‐MΦ) in the local BC microenvironment. These data indicate that monitoring circulating monocytes in BC patients may provide an indication of early systemic alterations induced by cancer and, thus, be instrumental in the development of improved personalised immunotherapeutic interventions.
The clinical and cytomorphological spectrum of hydatid disease
Authors: Kapatia Gargi , Tom Jesty P. , Rohilla Manish , Gupta Parikshaa , Gupta Nalini , Srinivasan Radhika , Rajwanshi Arvind , Dey Pranab 
Published: February 2020

AbstractIntroductionHydatid disease (HD) is caused by the tapeworm of the genus Echinococcus. Fine‐needle aspiration cytology (FNAC) is an expedient diagnostic technique that may be used for its rapid diagnosis.AimTo study the clinical and cytomorphological spectrum of HD diagnosed by cytology.Material and methodsA total of 24 patients diagnosed with HD on FNAC and fluid were studied over a period of 5.5 years. May Grunwald Giemsa, Periodic acid Schiff, and Haematoxylin and Eosin stained smears were studied and analysed for the cytomorphological spectrum of HD.ResultsAmongst the 24 patients studied, the mean age was 29.8 years (range 6‐64 years). There was equal sex preponderance with 12 males and 12 females. The most common organ involved was lung (54.1% of cases) followed by liver (25% of cases). Presence of laminated membranes (n‐20, 83.3%) followed by presence of hooklets (n‐13, 54.1%) were the common cytological features. Scolices and protoscolices representing endocyst were seen in 37.5% of cases (n‐9).ConclusionClinicians and pathologists should be aware of the clinical and morphological spectrum of HD respectively for immediate diagnosis followed by prompt management.
Early childhood cumulative risk is associated with decreased global brain measures, cortical thickness, and cognitive functioning in school‐age children
Authors: Chad‐Friedman Emma , Botdorf Morgan , Riggins Tracy , Dougherty Lea R. 
Published: February 2020

AbstractChildren exposed to multiple risk factors early in life are increasingly more likely to suffer from a host of cognitive impairments across development. However, little work has identified the neurobiological mechanisms linking early cumulative risk and cognitive functioning. The current study examined the impact of cumulative risk assessed during early childhood on neural and cognitive outcomes measured 3 years later when children were school‐aged. Participants included 63 children assessed during preschool (age: M = 4.23 years, SD = 0.84) and 3 years later (age: M = 7.19 years, SD = 0.89). Early cumulative risk was defined by the presence of low family income, a single parent household, low parental education, child exposure to parental depression, child exposure to high parental hostility, and high levels of stressful life events. Children's exposure to stressors in the past year, cognitive abilities, and brain structure were assessed at follow‐up. Early cumulative risk was prospectively associated with reduced total gray matter volume, cortex volume, right superior parietal and inferior parietal thickness, and poorer attention shifting and memory. Right superior parietal thickness mediated associations between early risk and recall memory. Results highlight neural variations associated with early cumulative risk and suggest potential neural pathways from early risk to later childhood cognitive impairments.
Timing, frequency, and duration of incubation recesses in dabbling ducks
Authors: Croston Rebecca , Hartman C. Alex , Herzog Mark P. , Casazza Michael L. , Feldheim Cliff L. , Ackerman Joshua T. 
Published: February 2020

AbstractNest attendance is an important determinant of avian reproductive success, and identifying factors that influence the frequency and duration of incubation recesses furthers our understanding of how incubating birds balance their needs with those of their offspring. We characterized the frequency and timing (start time, end time, and duration) of incubation recesses for mallard (Anas platyrhynchos) and gadwall (Mareca strepera) hens breeding in Suisun Marsh, California, USA, and examined the influences of day of year, ambient temperature at the nest, incubation day, and clutch size on recess frequency and timing using linear mixed models. Mallard, on average, took more recesses per day (1.69 ± 0.80, mean ± standard deviation) than did gadwall (1.39 ± 0.69), and 45% of mallard nest‐days were characterized by two recesses, while only 27% of gadwall nest‐days were characterized by two recesses. Mallard morning recesses started at 06:14 ± 02:46 and lasted 106.11 ± 2.01 min, whereas mallard afternoon recesses started at 16:39 ± 02:11 and lasted 155.39 ± 1.99 min. Gadwall morning recesses started at 06:30 ± 02:46 and lasted 91.28 ± 2.32 min, and gadwall afternoon recesses started at 16:31 ± 01:57 and lasted 192.69 ± 1.89 min. Mallard and gadwall started recesses earlier in the day with increasing ambient temperature, but later in the day as the season progressed. Recess duration decreased as the season progressed and as clutch size increased, and increased with ambient temperature at the nest. The impending darkness of sunset appeared to be a strong cue for ending a recess and returning to the nest, because hens returned to their nests earlier than expected when recesses were expected to end after sunset. Within hens, the timing of incubation recesses was repeatable across incubation days and was most repeatable for mallard afternoon recesses and on days in which hens took only one recess. Hens were most likely to be away from nests between 04:00 and 07:00 and between 16:00 and 19:00; therefore, investigators should search for nests between 07:00 and 16:00. Our analyses identified important factors influencing incubation recess timing in dabbling ducks and have important implications for nest monitoring programs.
FOE‐based regularization for optical flow estimation from an in‐vehicle event camera
Authors: Nagata Jun , Sekikawa Yusuke , Hara Kosuke , Aoki Yoshimitsu 
Published: February 2020

AbstractOptical flow estimation from an in‐vehicle camera is an important task in automatic driving and advanced driver‐assistance systems. However, there is a problem that optical flow estimation is mistakable with high contrast and high speed. Event camera can overcome these situations because it reports only the per‐pixel intensity change with high dynamic range and low latency. However, the L1 smoothness regularization in the conventional optical flow estimation method is not suitable for radial optical flow in the driving scene. Therefore, we propose to use the focus of expansion (FOE) for regularization of optical flow estimation in event camera. The FOE is defined as the intersection of the translation vector of the camera and the image plane. The optical flow becomes radial from the FOE excluding the rotational component. Using the property, the optical flow can be regularized in the correct direction in the optimization process. We demonstrated that the optical flow was improved by introducing our regularization using the public dataset.
Gross nitrogen transformation rates in semiarid tropical soils under different salinity and vegetation conditions
Authors: Sharma Niharika , Kumar Sanjeev 
Published: February 2020

AbstractExacerbated inundations and saltwater intrusions due to sea‐level rise can significantly alter the ecology of low‐lying coastal drylands by affecting their nutrient cycling and productivity. During the present study, controls on production and consumption of nitrogen in soils of semiarid tropical climate with different levels of vegetation–salinity–moisture condition were investigated using 15N isotope dilution experiments. For this purpose, soils were collected from five land types including two in salt flat and one each in grassland (GL), wetland (WL), and an agricultural field. Soils with no vegetation, high salinity, and high moisture (salt flats) showed significant decline in gross production of nitrogen (mineralization rate: 0.21 ± 0.10 mg N·kg−1·d−1; nitrification rate: 0.27 ± 0.17 mg N·kg−1·d−1) compared to soils with vegetation, low salinity, and low moisture (GL, WL, and agricultural) (mineralization rate: 2.47 ± 1.74 mg N·kg−1·d−1; nitrification rate: 1.43 ± 1.30 mg N·kg−1·d−1). Backward stepwise regression analysis of the results indicated salinity to be the most important factor controlling nitrogen transformation rates. It is likely that soils undergoing frequent seawater exposure or excessive evaporation may experience slowdown in nitrogen cycling due to salinization leading to reduced nutrient production and consumption. Due to climate change, the areal extent of coastal drylands undergoing such decline in nutrient production is likely to increase, eventually leading to loss of productivity and desertification.
Bone‐strengthening effects and safety of compound peptides from skin of Chiloscyllium plagiosum and Mustelus griseus
Authors: Xu Xin‐Heng , Lv Peng‐Fei , Wang Tong‐Xin , Wang Bao‐Xuan , Shi Yan , Wang Bi‐Xue , Meng Zheng‐Rou , Chen Qing‐Xi , Zhuang Jiang‐Xing , Wang Yule‐Yue 
Published: February 2020

AbstractFish processing produces a lot of by‐products highly containing large amount of proteins which mainly consist of collagen, implying great potential value for application as nutraceutical ingredients. In present study, two kinds of sharks, Chiloscyllium plagiosum and Mustelus griseus, were used as raw material to gain three kinds of “compound peptides” (CPs) by enzymolysis, FCP (CPs from the flesh of C. plagiosum), SCP (CPs from the skin of C. plagiosum), and SMG (CPs from the skin of M. griseus). According to a series of constituent analysis, the molecule weights of FCP, SCP, and SMG were under 800 Da; amino acids composition analysis of FCP, SCP, and SMG showed that there were high glycine, proline, and hydroxyproline and low cysteine contents in SCP and SMG, which is the characteristic of collagen peptides; their total protein contents were 87.500%, 91.875%, and 95.625%, respectively; and heavy metal contents of CPs were all beneath national standards. After three kinds of CPs were administrated intragastrically to C57BL/6 mice at a total dosage of 15 g/kg, bone‐strengthening effects of SCP and SMG were manifested by osteoblasts activity promotion, bone mineral density (BMD) increase, and marrow adipocyte number decrease, yet nonsignificant effects were shown in FCP group. No index showed toxicity of SCP and SMG in subacute toxicology trial, indicating their safety as functional foods. Herein, industrial application foundation of the skins from these two sharks was explored but more efforts should subsequently be implemented for further exploitation.
A 2D hydrodynamic model for shallow water flows with significant infiltration losses
Authors: Ni Yufang , Cao Zhixian , Liu Qing , Liu Qingquan 
Published: February 2020

AbstractInfiltration losses may be significant and warrant proper incorporation into mathematical models for river floods in arid and semi‐arid areas, rainfall‐induced surface runoffs in watersheds and swashes on beaches. Here, a depth‐averaged two‐dimensional hydrodynamic model is presented for such processes based on the cell‐centred finite volume method on unstructured meshes, with the full Green‐Ampt equation evaluating the infiltration rate. A local time stepping strategy is employed along with thread parallelization with Open Multi‐processing and high‐performance computing to reduce model run time and therefore facilitate applications for large‐scale processes. The numerical solutions generally agree with the experimental and field‐measured data for typical cases with significant infiltration losses. The case study shows that neglecting infiltration leads to an overestimated discharge hydrograph, which cannot be compensated by means of varied bed resistance as estimated by Manning roughness, and the infiltration parameters play disparate roles in modifying shallow flows compared with Manning roughness. In addition, infiltration affects bed shear stress, which in turn modifies the critical bed sediment size that could be initiated for incipient motion by the flow and therefore needs to be properly accounted for when sediment transport and morphological evolution are to be resolved.
IMPACT OF HEADWATER HYDROLOGICAL DEFICIT ON THE DOWNSTREAM FLOOD‐BASED FARMING SYSTEM IN NORTHERN ETHIOPIA
Authors: Negash Emnet , Gebresamuel Girmay , Embaye Tesfa‐alem , Nguvulu Alick , Meaza Hailemariam , Gebrehiwot Misgina , Demissie Biadgilgn , Gebreyohannes Tesfaalem , Nyssen Jan , Zenebe Amanuel 
Published: February 2020

AbstractFlood‐based farming is a means of improving crop production in rain‐deficit lowlands. Such spate irrigation systems are growing in importance, although the effects of headwater hydrological deficit on downstream flood farming are lacking evidence. This study investigates the impacts of headwater hydrological deficit on the extent of spate‐irrigated agriculture in the Guguf spate system. The length of canals and area of spate‐irrigated agriculture to the right and left of the Guguf River for the 1980s and 2010s were tracked using a global positioning system and mapped in a geographic information system interface, while climate data were collected from National Meteorological Agency. Trends of selected hydroclimatic variables were analysed using linear regression and the Pettitt test. The flash floods have shrunk by 7.36 × 106 m3, as a result of which the length of canals and area of spate‐based farms declined by 1.37 km and 1540 ha, i.e. 35 and 57.5%, respectively, in only three decades. This corresponds to an average withdrawal of −44.0 ha yr‾¹. A single 1 million m3 decline in flash floods caused a 366.4 ha decline in spate‐based farms. Moreover, farm fields located next to the river course are less affected, compared to those at the tail of the scheme. If the current trend continues, there is a high risk that the remaining farms currently receiving floods may find themselves outside of the spate systems. Therefore, we suggest that flood management technologies are needed to optimize the efficiency of soil moisture in the spate system. © 2020 John Wiley & Sons, Ltd.
Fabrication and characterization of an electrostatically bonded PEEK‐ hydroxyapatite composites for biomedical applications
Authors: Baştan Fatih Erdem 
Published: February 2020

AbstractIn this study, it was aimed to produce electrostatically induced polyetheretherketone (PEEK) and strontium substituted hydroxyapatite (SrHA) composites. SrHA nanoparticles (5 and 10 vol%) were introduced in the PEEK matrix to increase its mechanical properties and osseointegration. In order to disperse and homogeneously distribute the nanoparticles within the matrix, an electrostatic bond was developed between the PEEK and nanoparticles by wet processing through the attraction of the oppositely charged particles. Particles were pressed and sintered according to the Taguchi Design of experiments (DoE) array. The effects of SrHA reinforcement, sintering temperature and time on the density, crystallinity and crystallite sizes were determined with density test, DSC and XRD, respectively. The disks were also analyzed via SEM, FTIR, compression, microhardness, and nanoindentation tests and were immersed into the simulated body fluid (SBF). The composites produced from electrostatically induced powders presented a homogenous microstructure as SEM analysis illustrated the homogenous dispersion and distribution of the SrHA nanoparticles. The SrHA nanoparticles decreased the relative density and crystallinity of the composite, whereas, the rise in the sintering temperature and time enhanced the relative density, according to the DoE results. SrHA reinforcement improved the reduced modulus and nanoindentation hardness of the PEEK (348.47 MPa, 5.97 GPa) to 392.02 MPa and 6.65 GPa, respectively. SrHA promoted the bioactivity of the composite: an apatite layer covered the surface of PEEK/10SrHA composite after 14 days incubation. These promising results suggest that the electrostatically bonded composite powders would be used to produce homogenous PEEK based bioactive composites.
LncRNA MST1P2/miR‐133b axis affects the chemoresistance of bladder cancer to cisplatin‐based therapy via Sirt1/p53 signaling
Authors: Chen Jia , Li Yuanwei , Li Zhiqiu , Cao Lin 
Published: February 2020

AbstractAlthough bladder cancer is commonly chemosensitive to standard first‐line therapy, the acquisition of the resistance to cisplatin (DDP)‐based therapeutic regimens remains a huge challenge. Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs) and microRNAs, have been reported to play a critical role in cancer resistance to DDP. Here, we attempted to provide a novel mechanism by which the resistance of bladder cancer to DDP treatment could be modulated from the perspective of ncRNA regulation. We demonstrated that lncRNA MST1P2 (lnc‐MST1P2) expression was dramatically upregulated, whereas miR‐133b expression was downregulated in DDP‐resistant bladder cancer cell lines, SW 780/DDP and RT4/DDP. Lnc‐MST1P2 and miR‐133b negatively regulated each other via targeting miR‐133b. Both lnc‐MST1P2 silence and miR‐133b overexpression could resensitize DDP‐resistant bladder cancer cells to DDP treatment. More important, miR‐133b could directly target the Sirt1 3′‐untranslated region to inhibit its expression. Inc‐MST1P2/miR‐133b axis affected the resistance of bladder cancer cells to DDP via Sirt1/p53 signaling. In conclusion, MST1P2 serves as a competing endogenous RNA for miR‐133b to counteract miR‐133b‐induced suppression on Sirt1, therefore enhancing the resistance of bladder cancer cells to DDP. MST1P2/miR‐133b axis affects the resistance of bladder cancer cells to DDP via downstream Sirt1/p53 signaling.