bluuebunny/crossref_metadata_2025_split huggingface dataset:
SSMFN: a fused spatial and sequential deep learning model for methylation site prediction
Authors: Lumbanraja Favorisen Rosyking , Mahesworo Bharuno , Cenggoro Tjeng Wawan , Sudigyo Digdo , Pardamean Bens 
Published: August 2021

Background
Conventional in vivo methods for post-translational modification site prediction such as spectrophotometry, Western blotting, and chromatin immune precipitation can be very expensive and time-consuming. Neural networks (NN) are one of the computational approaches that can predict effectively the post-translational modification site. We developed a neural network model, namely the Sequential and Spatial Methylation Fusion Network (SSMFN), to predict possible methylation sites on protein sequences.

Method
We designed our model to be able to extract spatial and sequential information from amino acid sequences. Convolutional neural networks (CNN) is applied to harness spatial information, while long short-term memory (LSTM) is applied for sequential data. The latent representation of the CNN and LSTM branch are then fused. Afterwards, we compared the performance of our proposed model to the state-of-the-art methylation site prediction models on the balanced and imbalanced dataset.

Results
Our model appeared to be better in almost all measurement when trained on the balanced training dataset. On the imbalanced training dataset, all of the models gave better performance since they are trained on more data. In several metrics, our model also surpasses the PRMePred model, which requires a laborious effort for feature extraction and selection.

Conclusion
Our models achieved the best performance across different environments in almost all measurements. Also, our result suggests that the NN model trained on a balanced training dataset and tested on an imbalanced dataset will offer high specificity and low sensitivity. Thus, the NN model for methylation site prediction should be trained on an imbalanced dataset. Since in the actual application, there are far more negative samples than positive samples.
Identifying transcript 5′ capped ends in Plasmodium falciparum
Authors: Shaw Philip J. , Piriyapongsa Jittima , Kaewprommal Pavita , Wongsombat Chayaphat , Chaosrikul Chadapohn , Teeravajanadet Krirkwit , Boonbangyang Manon , Uthaipibull Chairat , Kamchonwongpaisan Sumalee , Tongsima Sissades 
Published: August 2021

Background
The genome of the human malaria parasite Plasmodium falciparum is poorly annotated, in particular, the 5′ capped ends of its mRNA transcripts. New approaches are needed to fully catalog P. falciparum transcripts for understanding gene function and regulation in this organism.

Methods
We developed a transcriptomic method based on next-generation sequencing of complementary DNA (cDNA) enriched for full-length fragments using eIF4E, a 5′ cap-binding protein, and an unenriched control. DNA sequencing adapter was added after enrichment of full-length cDNA using two different ligation protocols. From the mapped sequence reads, enrichment scores were calculated for all transcribed nucleotides and used to calculate P-values of 5′ capped nucleotide enrichment. Sensitivity and accuracy were increased by combining P-values from replicate experiments. Data were obtained for P. falciparum ring, trophozoite and schizont stages of intra-erythrocytic development.

Results
5′ capped nucleotide signals were mapped to 17,961 non-overlapping P. falciparum genomic intervals. Analysis of the dominant 5′ capped nucleotide in these genomic intervals revealed the presence of two groups with distinctive epigenetic features and sequence patterns. A total of 4,512 transcripts were annotated as 5′ capped based on the correspondence of 5′ end with 5′ capped nucleotide annotated from full-length cDNA data.

Discussion
The presence of two groups of 5′ capped nucleotides suggests that alternative mechanisms may exist for producing 5′ capped transcript ends in P. falciparum. The 5′ capped transcripts that are antisense, outside of, or partially overlapping coding regions may be important regulators of gene function in P. falciparum.
A customizable aluminum compensator system for total body irradiation
Authors: Naessig Madison , Hernandez Soleil , Astorga Nestor Rodrigo , McCulloch James , Saenz Daniel , Myers Pamela , Rasmussen Karl , Stathakis Sotirios , Ha Chul S. , Papanikolaou Niko , Ford John , Kirby Neil 
Published: August 2021

AbstractPurposeTo develop a simplified aluminum compensator system for total body irradiation (TBI) that is easy to assemble and modify in a short period of time for customized patient treatments.MethodsThe compensator is composed of a combination of 0.3 cm thick aluminum bars, two aluminum T‐tracks, spacers, and metal bolts. The system is mounted onto a plexiglass block tray. The design consists of 11 fixed sectors spanning from the patient's head to feet. The outermost sectors utilize 7.6 cm wide aluminum bars, while the remaining sectors use 2.5 cm wide aluminum bars. There is a magnification factor of 5 from the compensator to the patient treatment plane. Each bar of aluminum is interconnected at each adjacent sector with a tongue and groove arrangement and fastened to the T‐track using a metal washer, bolt, and nut. Inter‐bar leakage of the compensator was tested using a water tank and diode. End‐to‐end measurements were performed with an ion chamber in a solid water phantom and also with a RANDO phantom using internal and external optically stimulated luminescent detectors (OSLDs). In‐vivo patient measurements from the first 20 patients treated with this aluminum compensator were compared to those from 20 patients treated with our previously used lead compensator system.ResultsThe compensator assembly time was reduced to 20–30 min compared to the 2–4 h it would take with the previous lead design. All end‐to‐end measurements were within 10% of that expected. The median absolute in‐vivo error for the aluminum compensator was 3.7%, with 93.8% of measurements being within 10% of that expected. The median error for the lead compensator system was 5.3%, with 85.1% being within 10% of that expected.ConclusionThis design has become the standard compensator at our clinic. It allows for quick assembly and customization along with meeting the Task Group 29 recommendations for dose uniformity.
Iridium‐Catalyzed Enantioselective and Diastereoselective Hydrogenation of Racemic β’‐Keto‐β‐Amino Esters via Dynamic Kinetic Resolution
Authors: Ling Fei , Wang Yifan , Huang An , Wang Ze , Wang Shiliang , He Jiayin , Zhao Xianghua , Zhong Weihui 
Published: August 2021

AbstractAn iridium/f‐diaphos catalytic system for the enantioselective hydrogenation of α‐substituted β‐ketoesters via dynamic kinetic resolution is reported. The desired anti β’‐hydroxy‐β‐amino esters were obtained in moderate to good yields (60–95%) with 72–99% ees and 91:9 to 99:1 drs. This protocol tolerates various functional groups and could be easily conducted on gram scale with lower catalyst loading (TON up to 9100).magnified image
Visualizing the Active Paths in Morphologically Defective Organic Thin‐Film Transistors
Authors: Zhang Wen‐Shan , Matthiesen Maik , Günther Benjamin , Wensorra Jakob , Fischer Daniel , Gade Lutz H. , Zaumseil Jana , Schröder Rasmus R. 
Published: August 2021

AbstractThe charge‐carrier mobility of organic semiconductors extracted from thin‐film transistors is highly dependent on film morphology. Morphological defects can lead to the underestimation of charge transport properties, which may impede the rational design of novel materials. Herein, a novel analytical method is presented to functionally characterize entire active layers of solution‐processed thin‐film transistors. By correlating imaging and spectroscopy of secondary electrons, nano‐sized morphological defects are discovered and the effective current paths between source and drain electrodes are directly visualized. After image‐processing, the as‐measured mobility values of zone‐cast thin‐films of a tetraazaperopyrene derivative are corrected, obtaining charge–carrier mobilities of up to five times higher than the as‐measured values. The direct visualization of the electric functionality of the organic thin‐films facilitates a unique quantification of the impact of morphological defects and provides a solid benchmark to estimate the potential for further improvement of device performance.
Indoor Perovskite Photovoltaics for the Internet of Things—Challenges and Opportunities toward Market Uptake
Authors: Polyzoidis Christos , Rogdakis Konstantinos , Kymakis Emmanuel 
Published: August 2021

AbstractThe high‐power conversion efficiency of flexible perovskite photovoltaics (PPV) at low light environment and their low‐cost manufacturing processes, render PPV superior to conventional rigid photovoltaics targeting indoor applications. However, various parameters related to materials, architecture, processing, and indoor characterization need to be optimized further toward improving indoor PPV (iPPV) efficiency, stability, and ecotoxicity. This work provides an overview of the recent progress, trends, and challenges in the field and suggests a holistic approach toward a viable design and integration of iPPVs into Internet of Things (IoT) platforms without any compromise on safety and cost effectiveness. The key impact of selecting proper materials and fabrication techniques, as well as optimizing the active area and architecture is described. Certain peculiarities of the indoor lighting conditions are discussed that can be addressed by proper simulation tools, including the understanding of the charge‐transfer mechanism, the diversification of the lamp types, as well as identifying the requirements for the production, standardization, and installation of iPPVs associated with IoT devices. A multidimensional engineering approach that considers aspects of architecture, light technology, load specifications, materials, processing, safety and cost, is proposed as a path toward accelerating iPPV market uptake for households, businesses, wearables and Industry 4.0 applications.
Machine‐Learning‐Assisted Selective Synthesis of a Semiconductive Silver Thiolate Coordination Polymer with Segregated Paths for Holes and Electrons
Authors: Wakiya Takuma , Kamakura Yoshinobu , Shibahara Hiroki , Ogasawara Kazuyoshi , Saeki Akinori , Nishikubo Ryosuke , Inokuchi Akihiro , Yoshikawa Hirofumi , Tanaka Daisuke 
Published: August 2021

AbstractCoordination polymers (CPs) with infinite metal–sulfur bond networks have unique electrical conductivities and optical properties. However, the development of new (‐M‐S‐)n‐structured CPs is hindered by difficulties with their crystallization. Herein, we describe the use of machine learning to optimize the synthesis of trithiocyanuric acid (H3ttc)‐based semiconductive CPs with infinite Ag−S bond networks, report three CP crystal structures, and reveal that isomer selectivity is mainly determined by proton concentration in the reaction medium. One of the CPs, [Ag2Httc]n, features a 3D‐extended infinite Ag−S bond network with 1D columns of stacked triazine rings, which, according to first‐principle calculations, provide separate paths for holes and electrons. Time‐resolved microwave conductivity experiments show that [Ag2Httc]n is highly photoconductive (φΣμmax=1.6×10−4 cm2 V−1 s−1). Thus, our method promotes the discovery of novel CPs with selective topologies that are difficult to crystallize.
New heterogeneous catalysts containing platinum group metals recovered from a spent catalytic converter
Authors: Racles Carmen , Zaltariov Mirela‐Fernanda , Coroaba Adina , Silion Mihaela , Diac Cornelia , Dascalu Andrei , Iacob Mihail , Cazacu Maria 
Published: August 2021

AbstractA spent catalytic converter was treated with concentrated HCl and hydrogen peroxide in very mild conditions to extract approximately half of its platinum group metals (PGMs) content, mainly as chlorides. The noble metals were subsequently charged into functionalized mesoporous silica by complexation with mercapto groups. A combination of methods was employed to prove the transfer of PGMs and to characterize the materials (inductively coupled plasma optical emission spectrometry [ICP‐OES], Fourier transform‐infrared [FT‐IR] spectroscopy, electrospray ionization mass spectrometry [ESI‐MS], thermogravimetric analysis [TGA], X‐ray photoelectron spectroscopy [XPS], X‐ray diffraction, and UV–Vis spectrophotometry). The resulted PGM‐loaded silica was successfully tested as a new heterogeneous catalyst for hydrosilylation and oxidation reactions. Information about the nature of the PGMs species extracted and loaded completes the existing literature data. The scrap cordierite may be valorized for retention of pollutants from water and also catalyzes the hydrosilylation reaction based on the remaining PGMs. Flexible composite materials can be obtained by incorporating scrap cordierite as filler and crosslinking catalyst into a silicone matrix, significantly enhancing the dielectric permittivity. Thus, complete re‐valorization of the main components of the catalytic converter as high‐added‐value materials was achieved at laboratory level, with very low energy demanding procedures.
Antidepressant effect of electroacupuncture on modulating the expression of c‐Fos/AP‐1 through the JNK signaling pathway
Authors: Li Xiang , Qi Si‐Min , Wang Yu , Jiang Hui‐Wu , Li Ya‐Huan , Zhao Bing‐Cong , Zhang Tao , Sun Yang , Gao Xing‐Zhou , Quan Song‐Xiao , Liu Peng‐Fei , Li Wen‐Shan , Wu Ji‐Hong , Bao Tu‐Ya , Jiang Hui‐Li 
Published: August 2021

AbstractThe effectiveness and safety of electroacupuncture (EA) for depression have been identified by abundant clinical trials and experimental findings. The c‐Jun‐NH(2)‐terminal kinase (JNK) signaling pathway is considered to be involved in the antidepressant mechanism of EA. However, the antidepressant effect of EA via modulating the expression of c‐Fos/activator protein‐1 (AP‐1) under the condition of JNK inhibition remains unexplored. In this study, we investigated the antidepressant effect and possible mechanism of EA in regulating the expression of c‐Fos/AP‐1 under the condition of JNK inhibition by SP600125 in rats exposed to chronic unpredictable mild stress (CUMS). The depression‐like behaviors were evaluated by the body weight, sucrose preference test (SPT), and open field test (OFT). The expression levels of c‐Jun in the hypothalamus, c‐Fos in the pituitary gland, and c‐Fos and AP‐1 in the serum of CUMS induced rat model of depression were detected by ELISA. The results indicated that treatment with EA and fluoxetine can reverse the CUMS‐induced depression‐like behaviors in rats and can up‐regulate the expression levels of c‐Jun in the hypothalamus, c‐Fos in the pituitary gland, and c‐Fos and AP‐1 in the serum. Of note, the data demonstrated that SP600125, the inhibitor of JNK signaling pathway, can exert synergistic effect with EA in regulating CUMS‐induced abnormal activation of the JNK signaling pathway. The antidepressant effect of EA might be mediated by modulating the expression of c‐Fos/AP‐1.
Sensitivity to changes in the surface‐layer turbulence parameterization for stable conditions in winter: A case study with a regional climate model over the Arctic
Authors: Schneider Thea , Lüpkes Christof , Dorn Wolfgang , Chechin Dmitry , Handorf Dörthe , Khosravi Sara , Gryanik Vladimir M. , Makhotina Irina , Rinke Annette 
Published: August 2021

AbstractThe modeling of the atmospheric boundary layer over sea ice is still challenging because of the complex interaction between clouds, radiation and turbulence over the often inhomogeneous sea ice cover. There is still much uncertainty concerning sea ice roughness, near‐surface thermal stability and related processes, and their accurate parameterization. Here, a regional Arctic climate model forced by ERA‐Interim data was used to test the sensitivity of climate simulations to a modified surface flux parameterization for wintertime conditions over the Arctic. The reference parameterization as well as the modified one is based on Monin–Obukhov similarity theory, but different roughness lengths were prescribed and the stability dependence of the transfer coefficients for momentum, heat and moisture differed from each other. The modified parameterization accounts for the most comprehensive observations that are presently available over sea ice in the inner Arctic. Independent of the parameterization used, the model was able to reproduce the two observed dominant winter states with respect to cloud cover and longwave radiation. A stepwise use of the different parameterization assumptions showed that modifications of both surface roughness and stability dependence had a considerable impact on quantities such as air pressure, wind and near‐surface turbulent fluxes. However, the reduction of surface roughness to values agreeing with those observed during the Surface Heat Budget of the Arctic Ocean campaign led to an improvement in the western Arctic, while the modified stability parameterization had only a minor impact. The latter could be traced back to the model's underestimation of the strength of stability over sea ice. Future work should concentrate on possible reasons for this underestimation and on the question of generality of the results for other climate models.
Functional characterization of a novel CYP119 variant to explore its biocatalytic potential
Authors: Sakalli Tugce , Surmeli Nur Basak 
Published: August 2021

AbstractBiocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild‐type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non‐natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry.
3D‐printed scaffold composites for the stimuli‐induced local delivery of bioactive adjuncts
Authors: Bandiera Antonella , Catanzano Ovidio , Bertoncin Paolo , Bergonzi Carlo , Bettini Ruggero , Elviri Lisa 
Published: August 2021

AbstractPolysaccharide scaffolds have been successfully employed to reconstruct environments that sustain skin tissue regeneration after injuries. Three‐dimensional (3D) advanced additive manufacturing technologies allow creating scaffolds with controlled and reproducible macro‐ and micro‐structure that improve the quality of the restored tissue to favor spontaneous repair. However, when persistent inflammation occurs, the physiological tissue healing capacity is reduced, like in the presence of pathologies like diabetes, vascular diseases, chronic infection, and others. In these circumstances, the bioavailability of therapeutic adjuncts like the growth factors in addition to the standard treatments represents undoubtedly a promising strategy to accelerate the healing of skin lesions. Precisely designed polysaccharide scaffolds obtained by 3D printing represent a robust platform that can be further implemented with the controlled delivery of bioactive adjuncts. Human elastin‐like polypeptides (HELPs) are stimuli‐responsive biopolymers. Their structure allows the integration of domains endowed with biological functionality, making them attractive compounds to prepare composites with smart properties. In the present study, 3D‐printed alginate and chitosan scaffolds were combined with the HELP components. The HELP biopolymer was fused to the epidermal growth factor (EGF) as the bioactive domain. Different constructs were prepared and the stimuli‐responsive behavior as well as the biological activity were evaluated, suggesting that these smart bioactive composites are suitable to realize multifunctional dressings that sustain the local release of therapeutic adjuncts.
Pseudogene HSPB1P1 contributes to renal cell carcinoma proliferation and metastasis by targeting miR‐296‐5p to regulate HMGA1 expression
Authors: Chen Zerong , Wang Ziming , Chen Zhuangfei , Fu Fangxiang , Huang Xiaomin , Huang Zehai 
Published: August 2021

AbstractWith the aid of next‐generation sequencing technology, pseudogenes have been widely recognized as functional regulators in the development and progression of certain diseases, especially cancer. Our present study aimed to investigate the functions and molecular mechanisms of HSPB1‐associated protein 1 pseudogene 1 (HSPB1P1) in renal cell carcinoma (RCC). HSPB1P1 expression at the mRNA levels was determined by quantitative real‐time polymerase chain reaction, and its clinical significance was assessed. Cell viability was detected by Cell Counting Kit‐8 assay. Cell migration and invasion were detected by transwell assays. The location of HSPB1P1 in RCC cells was detected by subcellular distribution analysis. The direct relationship between HSPB1P1 and miR‐296‐5p/HMGA1 axis was verified by dual‐luciferase reporter assay and RNA immunoprecipitation assay. Our results identify the elevated expression of HSPB1P1 in RCC tissues and cell lines, which predicted advanced progression and poor prognosis in patients with RCC. Knockdown of HSPB1P1 suppressed cell proliferation, migration, and invasion, and reversed epithelial–mesenchymal transition process in RCC. HSPB1P1 was mostly enriched in the cytoplasm and functioned as a miRNA sponge for miR‐296‐5p and then regulated high‐mobility group A1 expression. In conclusion, our study indicated that HSPB1P1 contributed to RCC progression by targeting the miR‐296‐5p/HMGA1 axis, and should be considered as a promising biomarker and therapeutic target for clinical applications.
Utilizing Design of Experiments Approach to Assess Kinetic Parameters for a Mn Homogeneous Hydrogenation Catalyst
Authors: van Schendel Robin K. A. , Yang Wenjun , Uslamin Evgeny A. , Pidko Evgeny A. 
Published: August 2021

AbstractHomogeneous hydrogenation catalysts based on metal complexes provide a diverse and highly tunable tool for the fine chemical industry. To fully unleash their potential, fast and effective methods for the evaluation of catalytic properties are needed. In turn, this requires changes in the experimental approaches to test and evaluate the performance of the catalytic processes. Design of experiment combined with statistical analysis can enable time‐ and resource‐efficient experimentation. In this work, we employ a set of different statistical models to obtain the detailed kinetic description of a highly active homogeneous Mn (I) ketone hydrogenation catalyst as a representative model system. The reaction kinetics were analyzed using a full second order polynomial regression model, two models with eliminated parameters and finally a model which implements “chemical logic”. The coefficients obtained are compared with the corresponding high‐quality kinetic parameters acquired using conventional kinetic experiments. We demonstrate that various kinetic effects can be well captured using different statistical models, providing important insights into the reaction kinetics and mechanism of a complex catalytic reaction.