bluuebunny/crossref_metadata_2025_split huggingface dataset:
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks
Authors: Oberti Mauricio , Vaisman Iosif I. 
Published: June 2020

AbstractIntrinsically disordered regions (IDR) play an important role in key biological processes and are closely related to human diseases. IDRs have great potential to serve as targets for drug discovery, most notably in disordered binding regions. Accurate prediction of IDRs is challenging because their genome wide occurrence and a low ratio of disordered residues make them difficult targets for traditional classification techniques. Existing computational methods mostly rely on sequence profiles to improve accuracy which is time consuming and computationally expensive. This article describes an ab initio sequence‐only prediction method—which tries to overcome the challenge of accurate prediction posed by IDRs—based on reduced amino acid alphabets and convolutional neural networks (CNNs). We experiment with six different 3‐letter reduced alphabets. We argue that the dimensional reduction in the input alphabet facilitates the detection of complex patterns within the sequence by the convolutional step. Experimental results show that our proposed IDR predictor performs at the same level or outperforms other state‐of‐the‐art methods in the same class, achieving accuracy levels of 0.76 and AUC of 0.85 on the publicly available Critical Assessment of protein Structure Prediction dataset (CASP10). Therefore, our method is suitable for proteome‐wide disorder prediction yielding similar or better accuracy than existing approaches at a faster speed.
Pink Fluorescent Carbon Dots Derived from the Phytomedicine for Breast Cancer Cell Imaging
Authors: Naik Gaurav Gopal , Alam Md Bayazeed , Pandey Vivek , Dubey Pawan Kumar , Parmar Avanish S. , Sahu Alakh N. 
Published: June 2020

AbstractPhytomedicines have been beneficial to humankind for the treatment of implacable ailments from time immemorial. In this report, we have synthesized a carbon dots as a photomedicine from traditional phytomedicine Andrographis paniculata which is widely spread across Southern and Southeastern Asia. Interestingly, these carbon dots exhibited unique pink fluorescence that is perceptibly distinctive from the previous reports. The inherent properties of carbon dots were characterised using Transmission Electron Microscopy, Fluorescence spectroscopy, Absorption spectroscopy, Fourier transform infrared spectroscopy, Selected area diffraction, X‐Ray Diffraction, and Energy Dispersive X‐ray Spectroscopy. Furthermore, thermal stability of carbon dots was determined using Thermo gravimetric analysis. The carbon dots are fabricated to possess breast cancer cell bioimaging applications apart from anti‐bacterial activities against clinically isolated strains of gram‐positive and gram‐negative bacteria and free radicals sensing and scavenging attributes. These findings establish carbon dots as a potential photomedicine with wide healthcare applications.
Convenient and Versatile Synthetic Protocol for Arylidene‐1H‐imidazol‐5(4H)‐ones
Authors: Sokolov Anatolii I. , Myasnyanko Ivan N. , Baleeva Nadezhda S. , Baranov Mikhail S. 
Published: June 2020

AbstractWe propose a new protocol for synthesis of the arylidene‐1H‐imidazol‐5(4H)‐ones which is based on O‐alkylation of amidoacetates using triethyloxonium tetrafluoroborate leading to carboximidates. These imidates have long been used in the synthesis of imidazolones by [2+3] cycloaddition reaction with Schiff bases. However, diversity of carboximidates prepared by the common techniques was limited. The protocol we proposed eliminated these limitations. Using this technique, a number of derivatives of the green fluorescent protein (GFP) and asFP chromophores were synthesized, and influence of the C2 residue on their optical properties was studied.
Atomic Thickness Catalysts: Synthesis and Applications
Authors: Han Ali , Zhang Zedong , Li Xinyuan , Wang Dingsheng , Li Yadong 
Published: June 2020

AbstractAtomic thickness catalysts (ATCs) have shown huge prospects in energy conversion applications due to the prominent advantages in large specific surface area and high density of exposed surface atoms over their bulk counterparts. The established ATCs, including metals (alloys), layered double hydroxides (LDHs), transition metal dichalcogenides (TMDs), transition metal oxides (TMOs), and carbon‐based materials, have exhibited higher efficiency and better catalytic stability than that of commercial noble metal‐based nanocrystals for energy conversion related reactions. In this review, important progress is exemplified from the aspects of synthetic methods (e.g., bottom‐up and top‐down methods) and energy conversion related reactions, for instance, oxygen reduction reaction (ORR), formic acid oxidation reaction (FAOR), methanol oxidation reaction (MOR), ethanol oxidation reaction (EOR), oxygen evolution reaction (OER), hydrogen evolution reaction (HER), and carbon dioxide (CO2) reduction reaction (CRR). Furthermore, a valuable insight into the remaining challenges and potential opportunities for ATCs is provided in the fields of energy conversion applications.
Mildly hydrophobic biobased mulch: A sustainable approach to controlling bare soil evaporation
Authors: Barnes Jesse Lee , Nicholl Michael John 
Published: June 2020

AbstractMulching with polyethylene film is the conventional approach to decrease evaporative water loss from agricultural soils, but it is not environmentally sustainable. In this study, a laboratory experiment was conducted to test the potential utility of partially polymerized soybean oil (PSO) coated sands as a surface treatment to reduce bare soil evaporation. Evaporation was tracked for 23.8 d from saturated sand columns treated with a surface layer (1 or 2 cm) of either coated medium sand (MS‐PSO) or coated coarse sand (CS‐PSO). The water drop penetration time (WDPT) was used to assess the hydrophobicity of fresh PSO‐coated sands; the saturated hydraulic conductivity (Ks) and particle density (ρs) were measured as well. The WDPT was also tested on MS‐PSO and CS‐PSO samples aged in four separate environmental conditions for 20–21 d. Both PSO‐coated sands were mildly hydrophobic, and the surface treatment layers reduced evaporative loss by 83–96% over bare soil, which is similar to previous work using extremely hydrophobic chemically treated sands. Freshly coated MS‐PSO had a higher WDPT score and lower Ks than CS‐PSO. After the environmental aging tests, the MS‐PSO and CS‐PSO samples remained mildly hydrophobic. Notably, CS‐PSO had a low initial WDPT (∼1.09 to ∼2.58 s) and a high Ks (2.66 × 10−1 cm s−1), suggesting coarse PSO‐coated sands will permit infiltration. Given these findings, PSO‐coated sand has the potential to be developed into a sustainable alternative to polyethylene film mulch.
Development of a simulation approach for laser powder bed fusion based on scanning strategy selection
Authors: Foteinopoulos Panagis , Papacharalampopoulos Alexios , Angelopoulos Konstantinos , Stavropoulos Panagiotis 
Published: June 2020

AbstractAn important quality-related aspect of metal-based additive manufacturing (AM) parts is the existence of thermal stresses and deformations. To address this issue, a 3D thermal simulation approach for powder bed fusion (PBF) processes has been developed, along with the definition of an index that encapsulates the intensity of the non-uniformity of the thermal field. The proposed approach delivers sufficient and computationally low-cost results regarding the intensity of the expected thermal stresses and deformations. A case study of eighteen parts is presented, in which eight different scanning strategies are tested to identify the optimum scanning strategy in terms of thermal stresses and deformations. Finally, the impact of different design elements on the importance of the scanning strategy selection in terms of thermal stresses and deformations is discussed. Both the developed model and the index have been benchmarked using experimental and computational data.
Experiences with image quality and radiation dose of cone beam computed tomography (CBCT) and multidetector computed tomography (MDCT) in pediatric extremity trauma
Authors: Tschauner Sebastian , Marterer Robert , Nagy Eszter , Singer Georg , Riccabona Michael , Sorantin Erich 
Published: June 2020

AbstractIntroductionNovel dedicated extremity cone beam computed tomography (CBCT) devices, recently introduced to the market, raised attention as a possible alternative in advanced diagnostic pediatric trauma imaging, today usually performed by multidetector computed tomography (MDCT). This work aimed to compare image quality and radiation dose of CBCT and MDCT.Materials and methodsFifty-four CBCT-MDCT examination pairs, containing nine MDCTs acquired in parallel prospectively and 45 MDCTs matched in retrospect, were included in this study. Image quality was analyzed semi-objectively by measuring noise, contrast-to-noise ratio (CNR), and signal-to-noise ratios (SNR) and subjectively by performing image impression ratings. CT dose records were readout.ResultsImage noise was significantly lower in CBCT compared with MDCT, both semi-objectively and subjectively (bothp < 0.001). CNR and SNRs were also in favor of CBCT, though CBCT examinations exhibited significantly more beam hardening artifacts that diminished the advantages of the superior semi-objective image quality. These artifacts were believed to occur more often in children due to numerous bone-cartilage transitions in open growth plates and may have led to a better subjective diagnostic certainty rating (p = 0.001). Motion artifacts were infrequently, but exclusively observed in CBCT. CT dose index (CTDIvol) was substantially lower in CBCT (p < 0.001).ConclusionDedicated extremity CBCT could be an alternative low-dose modality in the diagnostic pathway of pediatric fractures. At lower doses compared with MDCT and commonly affected by beam hardening artifacts, semi-objective CBCT image quality parameters were generally better than in MDCT.
Deep learning in interstitial lung disease—how long until daily practice
Authors: Trusculescu Ana Adriana , Manolescu Diana , Tudorache Emanuela , Oancea Cristian 
Published: June 2020

AbstractInterstitial lung diseases are a diverse group of disorders that involve inflammation and fibrosis of interstitium, with clinical, radiological, and pathological overlapping features. These are an important cause of morbidity and mortality among lung diseases. This review describes computer-aided diagnosis systems centered on deep learning approaches that improve the diagnostic of interstitial lung diseases. We highlighted the challenges and the implementation of important daily practice, especially in the early diagnosis of idiopathic pulmonary fibrosis (IPF). Developing a convolutional neuronal network (CNN) that could be deployed on any computer station and be accessible to non-academic centers is the next frontier that needs to be crossed. In the future, early diagnosis of IPF should be possible. CNN might not only spare the human resources but also will reduce the costs spent on all the social and healthcare aspects of this deadly disease.Key Points• Deep learning algorithms are used in pattern recognition of different interstitial lung diseases.• High-resolution computed tomography plays a central role in the diagnosis and in the management of all interstitial lung diseases, especially fibrotic lung disease.• Developing an accessible algorithm that could be deployed on any computer station and be used in non-academic centers is the next frontier in the early diagnosis of idiopathic pulmonary fibrosis.
Additive effect of erythropoietin use on exercise-induced endothelial activation and hypercoagulability in athletes
Authors: Heuberger Jules A. A. C. , Posthuma Jelle J. , Ziagkos Dimitrios , Rotmans Joris I. , Daniels Johannes M. A. , Gal Pim , Stuurman Frederik E. , Spronk Henri M. H. , Ten Cate Hugo , Burggraaf Jacobus , Moerland Matthijs , Cohen Adam F. 
Published: June 2020

Abstract
Purpose
Recombinant human erythropoietin (rHuEPO) is known to increase thrombotic risk in patients and might have similar effects in athletes abusing the drug. rHuEPO is prohibited by anti-doping legislation, but this risk has not been investigated thoroughly. This analysis was designed to evaluate whether rHuEPO impacts hemostatic profile and endothelial and platelet activation markers in trained subjects, and whether the combination with exercise affects exercise induced alterations.

Methods
This double-blind, randomized, placebo-controlled trial enrolled healthy, trained male cyclists aged 18–50 years. Participants were randomly allocated (1:1) to receive subcutaneous injections of rHuEPO (epoetin-β; mean dose 6000 IU per week) or placebo (0.9% NaCl) for 8 weeks. Subjects performed five maximal exercise tests and a road race, coagulation and endothelial/platelet markers were measured at rest and directly after each exercise effort.

Results
rHuEPO increased P-selectin (+ 7.8% (1.5–14.5), p = 0.02) and E-selectin (+ 8.6% (2.0–15.7), p = 0.01) levels at rest. Maximal exercise tests significantly influenced all measured coagulation and endothelial/platelet markers, and in the rHuEPO group maximal exercise tests led to 15.3% ((7.0–24.3%), p = 0.0004) higher E-selectin and 32.1% ((4.6–66.8%), p = 0.0207) higher Platelet factor 4 (PF4) levels compared to the placebo group.

Conclusion
In conclusion, rHuEPO treatment resulted in elevated E- and P-selectin levels in trained cyclists, indicating enhanced endothelial activation and/or platelet reactivity. Exercise itself induces hypercoagulability, and the combination of rHuEPO and exercise increased E-selectin and PF4 levels more than either intervention alone. Based on this, exercise potentially increases thrombotic risk, a risk that might be enhanced in combination with rHuEPO use.
BDNF signaling during the lifetime of dendritic spines
Authors: Zagrebelsky Marta , Tacke Charlotte , Korte Martin 
Published: June 2020

AbstractDendritic spines are tiny membrane specialization forming the postsynaptic part of most excitatory synapses. They have been suggested to play a crucial role in regulating synaptic transmission during development and in adult learning processes. Changes in their number, size, and shape are correlated with processes of structural synaptic plasticity and learning and memory and also with neurodegenerative diseases, when spines are lost. Thus, their alterations can correlate with neuronal homeostasis, but also with dysfunction in several neurological disorders characterized by cognitive impairment. Therefore, it is important to understand how different stages in the life of a dendritic spine, including formation, maturation, and plasticity, are strictly regulated. In this context, brain-derived neurotrophic factor (BDNF), belonging to the NGF-neurotrophin family, is among the most intensively investigated molecule. This review would like to report the current knowledge regarding the role of BDNF in regulating dendritic spine number, structure, and plasticity concentrating especially on its signaling via its two often functionally antagonistic receptors, TrkB and p75NTR. In addition, we point out a series of open points in which, while the role of BDNF signaling is extremely likely conclusive, evidence is still missing.
A cost-efficient approach for simultaneous scanning electrochemical microscopy and scanning ion conductance microscopy
Authors: Wert Stefan , Baluchová Simona , Schwarzová-Pecková Karolina , Sedláková Silvia , Taylor Andrew , Matysik Frank-Michael 
Published: June 2020

AbstractA novel and cost-efficient probe fabrication method yielding probes for performing simultaneous scanning electrochemical microscopy (SECM) and scanning ion conductance microscopy (SICM) is presented. Coupling both techniques allows distinguishing topographical and electrochemical activity information obtained by SECM. Probes were prepared by deposition of photoresist onto platinum-coated, pulled fused silica capillaries, which resulted in a pipette probe with an integrated ring ultramicroelectrode. The fabricated probes were characterized by means of cyclic voltammetry and scanning electron microscopy. The applicability of probes was demonstrated by measuring and distinguishing topography and electrochemical activity of a model substrate. In addition, porous boron-doped diamond samples were investigated via simultaneously performed SECM and SICM.
Graphic abstract
Lungentransplantation
Authors: Jaksch Peter , Hoetzenecker Konrad 
Published: June 2020

ZusammenfassungDie Lungentransplantation (LuTX) ist eine etablierte Option bei chronischen Lungenerkrankungen, wenn alle anderen therapeutischen Möglichkeiten ausgeschöpft sind. Die häufigsten Indikationen stellen weiterhin das Lungenemphysem (30 %), die idiopathische Lungenfibrose (26 %) sowie die zystische Fibrose (15 %) dar. Zurzeit erfolgt in den meisten Fällen eine doppelseitige Operation. Mögliche Kandidaten für eine LuTX werden sorgfältig voruntersucht, um Komorbiditäten zu erfassen, die eine absolute oder relative Kontraindikation darstellen würden. Die Überlebenszahlen verbesserten sich in den letzten Jahren weiter. In großen Zentren betragen das 1‑Jahres-Überleben >90 % und das 5‑Jahres-Überleben 75–80 %. Zu den Problemen im Langzeit-Follow-up gehört die Entwicklung einer sog. chronischen Abstoßung (CLAD [„chronic lung allograft dysfunction“]). Sie stellt die häufigste Todesursache ab dem 2. Jahr nach LuTX dar, und die Therapiemöglichkeiten sind, trotz intensiver Bemühungen, noch gering.
Drug-induced hepatic steatosis in absence of severe mitochondrial dysfunction in HepaRG cells: proof of multiple mechanism-based toxicity
Authors: Allard Julien , Bucher Simon , Massart Julie , Ferron Pierre-Jean , Le Guillou Dounia , Loyant Roxane , Daniel Yoann , Launay Youenn , Buron Nelly , Begriche Karima , Borgne-Sanchez Annie , Fromenty Bernard 
Published: June 2020

AbstractSteatosis is a liver lesion reported with numerous pharmaceuticals. Prior studies showed that severe impairment of mitochondrial fatty acid oxidation (mtFAO) constantly leads to lipid accretion in liver. However, much less is known about the mechanism(s) of drug-induced steatosis in the absence of severe mitochondrial dysfunction, although previous studies suggested the involvement of mild-to-moderate inhibition of mtFAO, increased de novo lipogenesis (DNL), and impairment of very low-density lipoprotein (VLDL) secretion. The objective of our study, mainly carried out in human hepatoma HepaRG cells, was to investigate these 3 mechanisms with 12 drugs able to induce steatosis in human: amiodarone (AMIO, used as positive control), allopurinol (ALLO),d-penicillamine (DPEN), 5-fluorouracil (5FU), indinavir (INDI), indomethacin (INDO), methimazole (METHI), methotrexate (METHO), nifedipine (NIF), rifampicin (RIF), sulindac (SUL), and troglitazone (TRO). Hepatic cells were exposed to drugs for 4 days with concentrations decreasing ATP level by less than 30% as compared to control and not exceeding 100 × Cmax. Among the 12 drugs, AMIO, ALLO, 5FU, INDI, INDO, METHO, RIF, SUL, and TRO induced steatosis in HepaRG cells. AMIO, INDO, and RIF decreased mtFAO. AMIO, INDO, and SUL enhanced DNL. ALLO, 5FU, INDI, INDO, SUL, RIF, and TRO impaired VLDL secretion. These seven drugs reduced the mRNA level of genes playing a major role in VLDL assembly and also induced endoplasmic reticulum (ER) stress. Thus, in the absence of severe mitochondrial dysfunction, drug-induced steatosis can be triggered by different mechanisms, although impairment of VLDL secretion seems more frequently involved, possibly as a consequence of ER stress.
Governance of climate adaptation, which mode? An exploration of stakeholder viewpoints on how to organize adaptation
Authors: Molenveld Astrid , van Buuren Arwin , Ellen Gerald-Jan 
Published: June 2020

AbstractThere are many normative answers on the question how to realize climate adaptation, ranging from pleas for the government to play a decisive role, to calls for refraining from action and relying upon spontaneous adaptation of both government and non-governmental actors. In this article, we present a Q methodological study, aimed at investigating the governance preferences among non-governmental actors in the Netherlands and the “narratives” they use to motivate these preferences. Our empirical results underline the fact that the question “how to organize adaptation”, is a controversial one. The results resemble the various positions in the current academic debate about the governance of adaptation, and add important insights and nuances to it. Many respondents feel that the current climate adaptation policy is too non-committal. The dominant viewpoint underscores a need for more rules and norms and the possibility to sanction organizations that do not adapt. Minority viewpoints show an urge to stimulate and support self-organization of partners, as well as a need for more action. However, financial and regulatory preconditions are needed to stimulate actors in order to see to the necessary investments. Policy-makers have to invest in mixing their policy instruments. Clearly, most nongovernmental actors are in favor of the government setting a framework with rules and norms for climate adaption. However, the viewpoints show that this is not sufficient. The government should facilitate networks, joint efforts and create the financial and regulatory preconditions to remove current barriers blocking adaptation measures.
Iterative schemes for surfactant transport in porous media
Authors: Illiano Davide , Pop Iuliu Sorin , Radu Florin Adrian 
Published: June 2020

AbstractIn this work, we consider the transport of a surfactant in variably saturated porous media. The water flow is modelled by the Richards equations and it is fully coupled with the transport equation for the surfactant. Three linearization techniques are discussed: the Newton method, the modified Picard, and the L-scheme. Based on these, monolithic and splitting schemes are proposed and their convergence is analyzed. The performance of these schemes is illustrated on five numerical examples. For these examples, the number of iterations and the condition numbers of the linear systems emerging in each iteration are presented.
Exploring the diversity and distribution of crop wild relatives of cacao (Theobroma cacao L.) in Colombia
Authors: González-Orozco Carlos E. , Galán Angela A. Sánchez , Ramos Pablo E. , Yockteng Roxana 
Published: June 2020

AbstractCrop wild relatives are important for agriculture because they contain high levels of genetic diversity and grow in a wide range of habitats and environments. Colombia has the largest number of cacao crop wild relatives in the world, including different species of the genusTheobromaand its sister genusHerrania. This paper investigates diversity and distribution of cacao crop wild relatives in Colombia using species occurrences extracted from museum and herbarium archives, fieldwork collections gathered on recently conducted expeditions and species distribution modelling. A total of 211 botanical collections comprising 174 samples ofTheobromaspecies, and 37 samples ofHerraniaspecies were collected on expeditions to Caguán–Caquetá in the upper Amazon basin and La Victoria, in the Pacific region of central Choco. These collections represent 22 taxa of cacao crop wild relatives. On the Chocó expedition, we reported the highest richness and endemism, where seven taxa of Theobroma and three of Herrania were found within a radius of 10 km, which has never been recorded before. On the Amazon expedition, we found an abundance of wild populations ofTheobroma cacaoon the river banks. We estimated that 95% of the most suitable environments for wild cacao in Colombia are in unprotected areas. Our study reveals that species diversity and endemism of cacao crop wild relatives in Colombia is under sampled and distributional patterns are incomplete. Based on the findings of our study, we propose a conservation strategy that consists of further expeditions to collect herbarium and germplasm samples, and habitat protection of cacao crop wild relatives in Colombia.