bluuebunny/crossref_metadata_2025_split huggingface dataset:
The usefulness of C-reactive protein and procalcitonin to predict prognosis in septic shock patients: A multicenter prospective registry-based observational study
Authors: Ryoo Seung Mok , Han Kap Su , Ahn Shin , Shin Tae Gun , Hwang Sung Yeon , Chung Sung Phil , Hwang Yoon Jung , Park Yoo Seok , Jo You Hwan , Chang Hyung Lan , Suh Gil Joon , You Kyoung Min , Kang Gu Hyun , Choi Sung-Hyuk , Lim Tae Ho , Kim Won Young ,   Korean Shock Society (KoSS) Investigators, Kim Youn-Jung , Lee Sung Woo , Jo Ik Joon , Kim Min Joung , Kwon Woon Yong , Lee Hui Jai , Shin Jong Hwan , Ko Byuk Sung 
Published: April 2019

AbstractThe objective of this study was to evaluate the prognostic value of C-reactive protein (CRP), procalcitonin (PCT), and their combination for mortality in patients with septic shock. This multicenter, prospective, observational study was conducted between November 2015 and December 2017. A total of 1,772 septic shock patients were included, and the overall 28-day mortality was 20.7%. Although both CRP and PCT were elevated in the non-survivor group, only CRP had statistical significance (11.9 mg/dL vs. 14.7 mg/dL, p = 0.003, 6.4 ng/mL vs. 8.2 ng/mL, p = 0.508). Multivariate analysis showed that CRP and PCT were not independent prognostic markers. In the subgroup analysis of the CRP and PCT combination matrix using their optimal cut-off values (CRP 14.0 mg/dL, PCT 17.0 ng/dL), both CRP and PCT elevated showed significantly higher mortality (Odds ratio 1.552 [95% Confidence intervals 1.184–2.035]) than both CRP and PCT not elevated (p = 0.001) and only PCT elevated (p = 0.007). However, both CRP and PCT elevated was also not an independent predictor in multivariate analysis. Initial levels of CRP and PCT alone and their combinations in septic shock patients had a limitation to predict 28-day mortality. Future research is needed to determine new biomarkers for early prognostication in patients with septic shock.
Linkage-based genome assembly improvement of oil palm (Elaeis guineensis)
Authors: Ong Ai-Ling , Teh Chee-Keng , Kwong Qi-Bin , Tangaya Praveena , Appleton David Ross , Massawe Festo , Mayes Sean 
Published: April 2019

AbstractMeiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.
The interactome of a family of potential methyltransferases in HeLa cells
Authors: Ignatova Valentina V. , Jansen Pascal W. T. C. , Baltissen Marijke P. , Vermeulen Michiel , Schneider Robert 
Published: April 2019

AbstractHuman methytransferase like proteins (METTL) are part of a large protein family characterized by the presence of binding domains for S-adenosyl methionine, a co-substrate for methylation reactions. Despite the fact that members of this protein family were shown or predicted to be DNA, RNA or protein methyltransferases, most METTL proteins are still poorly characterized. Identification of complexes in which these potential enzymes act could help to understand their function(s) and substrate specificities. Here we systematically studied interacting partners of METTL protein family members in HeLa cells using label-free quantitative mass spectrometry. We found that, surprisingly, many of the METTL proteins appear to function outside of stable complexes whereas others including METTL7B, METTL8 and METTL9 have high-confidence interaction partners. Our study is the first systematic and comprehensive overview of the interactome of METTL protein family that can provide a crucial resource for further studies of these potential novel methyltransferases.
Rapid assessment of heavy metal pollution using ion-exchange resin sachets and micro-XRF core-scanning
Authors: Huang Jyh-Jaan Steven , Lin Sheng-Chi , Löwemark Ludvig , Liou Sofia Ya Hsuan , Chang Queenie , Chang Tsun-Kuo , Wei Kuo-Yen , Croudace Ian W. 
Published: April 2019

AbstractConventional pollution monitoring strategies for heavy metals are often costly and unpractical. Innovative sampling and analytical approaches are therefore needed to efficiently monitor large areas. This study presents a novel, simple, fast, and inexpensive method to monitor heavy metal pollution that uses cation-exchange resin sachets and the micro-XRF core-scanning technique (XRF-CS). The resin passive samplers act as concentrators of cationic species and can be readily deployed spatially and temporally to record pollution signals. The large number of analytical tasks are then overcome by the fast and non-destructive XRF-CS to precisely assess elemental concentrations. Quantifying element loading involves direct comparison with a set of identically prepared and scanned resin reference standards containing Ca, Ti, Cr, Mn, Ni, Cu, Zn, Pb. The results show that within the test range (from 0–1000 s mg kg−1), the calibration lines have excellent regressions (R2 ≥ 0.97), even at the shortest exposure time (1 s). A pilot field survey of a suspected polluted area in central Taiwan, where 30 resin sachets had been deployed, identified a pollution hot spot in a rapid and economical manner. Therefore, this approach has the potential to become a valuable tool in environmental monitoring and forensics.
Transition metal trifluoroacetates (M = Fe, Co, Mn) as precursors for uniform colloidal metal difluoride and phosphide nanoparticles
Authors: Guntlin Christoph P. , Kravchyk Kostiantyn V. , Erni Rolf , Kovalenko Maksym V. 
Published: April 2019

AbstractWe report a simple one-pot synthesis of uniform transition metal difluoride MF2 (M = Fe, Mn, Co) nanorods based on transition metal trifluoroacetates (TMTFAs) as single-source precursors. The synthesis of metal fluorides is based on the thermolysis of TMTFAs at 250–320 °C in trioctylphosphine/trioctylphosphine oxide solvent mixtures. The FeF2 nanorods were converted into FeF3 nanorods by reaction with gaseous fluorine. The TMTFA precursors are also found to be suitable for the synthesis of colloidal transition metal phosphides. Specifically, we report that the thermolysis of a cobalt trifluoroacetate complex in trioctylphosphine as both the solvent and the phosphorus source can yield 20 nm long cobalt phosphide nanorods or, 3 nm large cobalt phosphide nanoparticles. We also assess electrochemical lithiation/de-lithiation of the obtained FeF2 and FeF3 nanomaterials.
Local stress and pressure in an inhomogeneous system of spherical active Brownian particles
Authors: Das Shibananda , Gompper Gerhard , Winkler Roland G. 
Published: April 2019

AbstractThe stress of a fluid on a confining wall is given by the mechanical wall forces, independent of the nature of the fluid being passive or active. At thermal equilibrium, an equation of state exists and stress is likewise obtained from intrinsic bulk properties; even more, stress can be calculated locally. Comparable local descriptions for active systems require a particular consideration of active forces. Here, we derive expressions for the stress exerted on a local volume of a systems of spherical active Brownian particles (ABPs). Using the virial theorem, we obtain two identical stress expressions, a stress due to momentum flux across a hypothetical plane, and a bulk stress inside of the local volume. In the first case, we obtain an active contribution to momentum transport in analogy to momentum transport in an underdamped passive system, and we introduce an active momentum. In the second case, a generally valid expression for the swim stress is derived. By simulations, we demonstrate that the local bulk stress is identical to the wall stress of a confined system for both, non-interacting ABPs as well as ABPs with excluded-volume interactions. This underlines the existence of an equation of state for a system of spherical ABPs. Most importantly, our calculations demonstrated that active stress is not a wall (boundary) effect, but is caused by momentum transport. We demonstrate that the derived stress expression permits the calculation of the local stress in inhomogeneous systems of ABPs.
A combined FSTRA-shotgun proteomics approach to identify molecular changes in zebrafish upon chemical exposure
Authors: Ayobahan Steve U. , Eilebrecht Elke , Kotthoff Matthias , Baumann Lisa , Eilebrecht Sebastian , Teigeler Matthias , Hollert Henner , Kalkhof Stefan , Schäfers Christoph 
Published: April 2019

AbstractThe fish short-term reproduction assay (FSTRA) is a common in vivo screening assay for assessing endocrine effects of chemicals on reproduction in fish. However, the current reliance on measures such as egg number, plasma vitellogenin concentration and morphological changes to determine endocrine effects can lead to false labelling of chemicals with non-endocrine modes- of-action. Here, we integrated quantitative liver and gonad shotgun proteomics into the FSTRA in order to investigate the causal link between an endocrine mode-of-action and adverse effects assigned to the endocrine axis. Therefore, we analyzed the molecular effects of fadrozole-induced aromatase inhibition in zebrafish (Danio rerio). We observed a concentration-dependent decrease in fecundity, a reduction in plasma vitellogenin concentrations and a mild oocyte atresia with oocyte membrane folding in females. Consistent with these apical measures, proteomics revealed a significant dysregulation of proteins involved in steroid hormone secretion and estrogen stimulus in the female liver. In the ovary, the deregulation of estrogen synthesis and binding of sperm to zona pellucida were among the most significantly perturbed pathways. A significant deregulation of proteins targeting the transcriptional activity of estrogen receptor (esr1) was observed in male liver and testis. Our results support that organ- and sex-specific quantitative proteomics represent a promising tool for identifying early gene expression changes preceding chemical-induced adverse outcomes. These data can help to establish consistency in chemical classification and labelling.
Enhanced output performance on LbL multilayer PVDF-TrFE piezoelectric films for charging supercapacitor
Authors: Chung Moon Hyun , Yoo Seunghwan , Kim Hyun-Jun , Yoo Jungjoon , Han Seol-Yee , Yoo Kyung-Hwa , Jeong Hakgeun 
Published: April 2019

AbstractThe piezoelectric nanogenerator (PENG) has the potential to become a promising power supply for monitoring and sensors in Internet of Things (IoT) systems through wireless networks. In order to further increase the utilization of energy harvesters in an IoT system, we introduce a novel approach that greatly enhances the piezoelectric output performances by employing the layer-by-layer (LbL) method. Poly(vinylidenefluoride-co-trifluoroethylene) (PVDF-TrFE) polymer film, which has piezoelectric properties and mechanical flexibility, was used for the active layer in PENG. The maximum open-circuit voltage and closed-circuit current of the LbL multilayer PENG reached 34 V and 100 nA, respectively. In particular, the closed-circuit current of the LbL multilayer PENG was dramatically improved to be five times higher than that of the single-layer PENG. Furthermore, a supercapacitor was employed to investigate the energy storage capability of PENGs using different methods. The proposed LbL multilayer PENG is expected to be a candidate for a promising power supply for self-powered systems in the IoT system.
Long-term variations in PM2.5 concentrations under changing meteorological conditions in Taiwan
Authors: Cheng Fang-Yi , Hsu Chia-Hua 
Published: April 2019

AbstractWith emission control efforts, the PM2.5 concentrations and PM2.5 exceedance days (daily mean PM2.5 concentrations >35 µg m−3) show an apparent declining trend from 2006–2017. The PM2.5 concentrations increase from the northern to southern part of western Taiwan, and reductions in the PM2.5 concentration generally decrease from northern to southern part of western Taiwan. Thus, mitigation of the PM2.5 problem is less effective in southwestern Taiwan than in other regions in Taiwan. Analysis of a 39-year ERA-interim reanalysis dataset (1979–2017) reveals a weakening of the East Asian winter monsoon, a reduction in northeasterly (NE) monsoonal flow, and a tendency of enhanced stably stratified atmospheric structures in Taiwan and the surrounding area. The observed surface wind speed also presents a long-term decline. We can conclude that the long-term PM2.5 variations in Taiwan are mainly associated with changes in local anthropogenic emissions and modulated by short-term yearly variations due to strong haze events in China. In southwestern Taiwan, the long-term trend of PM2.5 reductions is possibly offset by worsening weather conditions, as this region is situated on the leeside of the mountains and often subject to stagnant wind when under the influence of NE monsoonal flow.
Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia
Authors: Stahlschmidt M. C. , Collin T. C. , Fernandes D. M. , Bar-Oz G. , Belfer-Cohen A. , Gao Z. , Jakeli N. , Matskevich Z. , Meshveliani T. , Pritchard J. K. , McDermott F. , Pinhasi R. 
Published: April 2019

AbstractMetagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.
The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability
Authors: Balasco Nicole , Smaldone Giovanni , Vigorita Marilisa , Del Vecchio Pompea , Graziano Giuseppe , Ruggiero Alessia , Vitagliano Luigi 
Published: April 2019

AbstractThe Ramachandran plot is a versatile and valuable tool that provides fundamental information for protein structure determination, prediction, and validation. The structural/thermodynamic effects produced by forcing a residue to adopt a conformation predicted to be forbidden were here explored using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model. Specifically, we mutated TmArgBP Gly52 that assumes a conformation believed to be strictly disallowed for non-Gly residues. Surprisingly, the crystallographic characterization of Gly52Ala TmArgBP indicates that the structural context forces the residue to adopt a non-canonical conformation never observed in any of the high-medium resolution PDB structures. Interestingly, the inspection of this high resolution structure demonstrates that only minor alterations occur. Nevertheless, experiments indicate that Gly52 replacements in TmArgBP produce destabilizations comparable to those observed upon protein truncation or dissection in domains. Notably, we show that force-fields commonly used in computational biology do not reproduce this non-canonical state. Using TmArgBP as model system we here demonstrate that the structural context may force residues to adopt conformations believed to be strictly forbidden and that barely detectable alterations produce major destabilizations. Present findings highlight the role of subtle strains in governing protein stability. A full understanding of these phenomena is essential for an exhaustive comprehension of the factors regulating protein structures.
Zooarchaeology of the social and economic upheavals in the Late Antique-Early Islamic sequence of the Negev Desert
Authors: Marom Nimrod , Meiri Meirav , Tepper Yotam , Erickson-Gini Tali , Reshef Hagar , Weissbrod Lior , Bar-Oz Guy 
Published: April 2019

AbstractThe Byzantine – Islamic transition (7th–8thcenturies CE) in the desert-edge Palaestina Tertia is examined using faunal remains recovered from archaeological sites in the Negev. Archaeozoological analyses suggest sharp differences between Late Byzantine and Early Islamic animal economies, especially in herding patterns and the exploitation of wildlife resources. These differences are suggested to reflect both cultural and land ownership changes following the Arab conquest, against the backdrop of climatic change. The archaeozoological record thereby provides independent evidence to the rise and fall of societal complexity in this marginal region.
Nanoindentation behavior of high entropy alloys with transformation-induced plasticity
Authors: Sinha S. , Mirshams R. A. , Wang T. , Nene S. S. , Frank M. , Liu K. , Mishra R. S. 
Published: April 2019

AbstractNanoindentation of three metastable dual-phase high entropy alloys (HEAs) was performed to obtain their inherent elastoplastic deformation responses. Excellent combination of hardness and elastic modulus in as-cast condition confirmed that, their inherently higher strength compared to other HEAs reported in literature, can be attributed to alloy chemistry induced phase stability. Further, hardness of 8.28 GPa combined with modulus of 221.8 GPa was obtained in Fe-Mn-Co-Cr-Si-Cu HEA by annealing the as-cast material, which is the best hardness-modulus combination obtained to date in HEAs from nanoindentation. On the other hand, although Fe-Mn-Co-Cr-Si HEA showed lower hardness and modulus than Fe-Mn-Co-Cr-Si-Al and Fe-Mn-Co-Cr-Si-Cu HEAs, the former alloy exhibited the highest strain rate sensitivity, as determined from tests performed at five different strain rates. The three alloys also had subtle differences in incipient plasticity and elastoplastic behavior, while retaining similar levels of hardness; and nanoindentation response showed microstructural dependence in friction stir processed, annealed and tensile-deformed specimens. Thus, the study highlighted that while higher strength was achieved by designing a class of HEAs with similar composition, any of the individual alloys can be tuned to obtain enhanced properties.
Cryogenian magmatic activity and early life evolution
Authors: Long Jie , Zhang Shixi , Luo Kunli 
Published: April 2019

AbstractData from the Qinling Orogenic Belt in China indicate that a strong magmatic-volcanic event on the Snowball Earth during the Cryogenian age (approximately 720–635 million years ago) was followed by a dynamic period of accelerated evolution of early life through the Ediacaran period. The studied volcanics of the Cryogenian Yaolinghe group are mainly represented by andesite, dacite and rhyolite, with minor amounts of basalt, trachy andesite and trachyte towards the top, which formed in the environment of an active island arc related to a continental margin. Compared with average felsic volcanics, the studied Cryogenian marine volcanic strata are enriched (1.5–30.6 times) in Co, Cr, Bi, Ni, Se, Ga, As, Cu, Ba, V, and Zn. Elemental concentrations (P, Cd, Co, Ni, and Se) of the studied volcanics are more than 5–26.4 times those in the contemporaneous Liantuo tillite. We propose that Cryogenian magmatic and volcanic activity increased the flux of some trace nutritional elements into the oceans which possibly provided essential nutrients for the development of early life.
Deep learning predicts hip fracture using confounding patient and healthcare variables
Authors: Badgeley Marcus A. , Zech John R. , Oakden-Rayner Luke , Glicksberg Benjamin S. , Liu Manway , Gale William , McConnell Michael V. , Percha Bethany , Snyder Thomas M. , Dudley Joel T. 
Published: April 2019

AbstractHip fractures are a leading cause of death and disability among older adults. Hip fractures are also the most commonly missed diagnosis on pelvic radiographs, and delayed diagnosis leads to higher cost and worse outcomes. Computer-aided diagnosis (CAD) algorithms have shown promise for helping radiologists detect fractures, but the image features underpinning their predictions are notoriously difficult to understand. In this study, we trained deep-learning models on 17,587 radiographs to classify fracture, 5 patient traits, and 14 hospital process variables. All 20 variables could be individually predicted from a radiograph, with the best performances on scanner model (AUC = 1.00), scanner brand (AUC = 0.98), and whether the order was marked “priority” (AUC = 0.79). Fracture was predicted moderately well from the image (AUC = 0.78) and better when combining image features with patient data (AUC = 0.86, DeLong paired AUC comparison, p = 2e-9) or patient data plus hospital process features (AUC = 0.91, p = 1e-21). Fracture prediction on a test set that balanced fracture risk across patient variables was significantly lower than a random test set (AUC = 0.67, DeLong unpaired AUC comparison, p = 0.003); and on a test set with fracture risk balanced across patient and hospital process variables, the model performed randomly (AUC = 0.52, 95% CI 0.46–0.58), indicating that these variables were the main source of the model’s fracture predictions. A single model that directly combines image features, patient, and hospital process data outperforms a Naive Bayes ensemble of an image-only model prediction, patient, and hospital process data. If CAD algorithms are inexplicably leveraging patient and process variables in their predictions, it is unclear how radiologists should interpret their predictions in the context of other known patient data. Further research is needed to illuminate deep-learning decision processes so that computers and clinicians can effectively cooperate.