bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the effect of variants on splicing using Convolutional Neural Networks
Authors: Thanapattheerakul Thanyathorn , Engchuan Worrawat , Chan Jonathan H. 
Published: July 2020

Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to diseases in humans. Various computational models have been developed to recognize the sequence pattern of the splice sites. In recent studies, Convolutional Neural Network (CNN) architectures were shown to outperform other existing models in predicting the splice sites. However, an insufficient effort has been put into extending the CNN model to predict the effect of the genomic variants on the splicing of mRNAs. This study proposes a framework to elaborate on the utility of CNNs to assess the effect of splice variants on the identification of potential disease-causing variants that disrupt the RNA splicing process. Five models, including three CNN-based and two non-CNN machine learning based, were trained and compared using two existing splice site datasets, Genome Wide Human splice sites (GWH) and a dataset provided at the Deep Learning and Artificial Intelligence winter school 2018 (DLAI). The donor sites were also used to test on the HSplice tool to evaluate the predictive models. To improve the effectiveness of predictive models, two datasets were combined. The CNN model with four convolutional layers showed the best splice site prediction performance with an AUPRC of 93.4% and 88.8% for donor and acceptor sites, respectively. The effects of variants on splicing were estimated by applying the best model on variant data from the ClinVar database. Based on the estimation, the framework could effectively differentiate pathogenic variants from the benign variants (p = 5.9 × 10−7). These promising results support that the proposed framework could be applied in future genetic studies to identify disease causing loci involving the splicing mechanism. The datasets and Python scripts used in this study are available on the GitHub repository at https://github.com/smiile8888/rna-splice-sites-recognition.
Evaluation of psychological stress in scientific researchers during the 2019–2020 COVID-19 outbreak in China
Authors: Zhang Xueyan , Li Xinyu , Liao Zhenxin , Zhao Mingyi , Zhuang Quan 
Published: July 2020

Background
Beginning in December 2019, coronavirus disease 2019 (COVID-19) caused an outbreak of infectious pneumonia. The Chinese government introduced a series of grounding measures to prevent the spread of COVID-19. The living and working patterns of many scientific researchers also underwent significant changes during this period.

Methods
An opportunity sample (n = 251) was obtained in China using a questionnaire with 42 questions on scientific research progress and psychological stress during the COVID-19 epidemic.

Results
Of the 251 participants, 76.9% indicated that their research was affected by the COVID-19 outbreak, and participants who were affected by the outbreak had higher stress levels than those who were not affected. Participants who conducted COVID-19 research and indicated concern that they would fail to finish the research on time were more likely to indicate high levels of stress. Respondents indicated that extending deadlines (64.1%), receiving support from superiors for research (51.8%), and increasing benefits for researchers (51.0%) would likely relieve outbreak-related stress.

Conclusion
The COVID-19 outbreak had a major impact on the experiments of researchers in the life sciences, especially in basic and clinical medicine. It has also caused high levels of psychological stress in these populations. Measures should be taken to relieve psychological pressure on basic medical researchers and students who will soon complete their degrees (e.g., Master’s and PhD candidates in graduation years).
Novel circulating protein biomarkers for thyroid cancer determined through data-independent acquisition mass spectrometry
Authors: Li Dandan , Wu Jie , Liu Zhongjuan , Qiu Ling , Zhang Yimin 
Published: July 2020

Background
Distinguishing between different types of thyroid cancers (TC) remains challenging in clinical laboratories. As different tumor types require different clinical interventions, it is necessary to establish new methods for accurate diagnosis of TC.

Methods
Proteomic analysis of the human serum was performed through data-independent acquisition mass spectrometry for 29 patients with TC (stages I–IV): 13 cases of papillary TC (PTC), 10 cases of medullary TC (MTC), and six cases follicular TC (FTC). In addition, 15 patients with benign thyroid nodules (TNs) and 10 healthy controls (HCs) were included in this study. Subsequently, 17 differentially expressed proteins were identified in 291 patients with TC, including 247 with PTC, 38 with MTC, and six with FTC, and 69 patients with benign TNs and 176 with HC, using enzyme-linked immunosorbent assays.

Results
In total, 517 proteins were detected in the serum samples using an Orbitrap Q-Exactive-plus mass spectrometer. The amyloid beta A4 protein, apolipoprotein A-IV, gelsolin, contactin-1, gamma-glutamyl hydrolase, and complement factor H-related protein 1 (CFHR1) were selected for further analysis. The median serum CFHR1 levels were significantly higher in the MTC and FTC groups than in the PTC and control groups (P < 0.001). CFHR1 exhibited higher diagnostic performance in distinguishing patients with MTC from those with PTC (P < 0.001), with a sensitivity of 100.0%, specificity of 85.08%, area under the curve of 0.93, and detection cut-off of 0.92 ng/mL.

Conclusion
CFHR1 may serve as a novel biomarker to distinguish PTC from MTC with high sensitivity and specificity.
Hydroxicloroquine, What is the Role of the Drug in the Treatment of COVID-19? A Review
Authors: Ramos Eliza Miranda , Reis Francisco José Mendes dos , Facco Gilberto Gonçalves , Araújo Emerson Luiz Lima , Souza Igor Domingos de , Ramos Glícia Caroline Andrade , Fonseca Alessandro Carvalho da , Ramos Iara Barbosa , Ramos Hugo Vieira , Nascimento Valter Aragão do 
Published: July 2020

Introduction: Coronaviruses (COVID-19) is an emerging virus with severe respiratory infection. Despite several efforts, so far there is no medicine to fight it and use it as the ideal treatment. OBJECTIVES: This study aims to describe the role of hydroxychloroquine in the treatment of patients with COVID-19 and thus present its benefits in the respective doses.
Methodology: The methodology used was the systematic review with meta-analysis.
Results: From the reading of the 75 papers found, only three articles were excluded for not presenting a complete abstract, 65 were excluded for not presenting eligibility according to the inclusion criteria, 01 was excluded for reaching a methodological score below 20 points in Down and Black (1998) and ending the process of inclusion of the articles, only 06 articles were included and included 894 patients.
Conclusion: Despite the small number of published articles, this meta-analysis found that the use of hydroxychloroquine as an adjunct therapy in the follow-up of COVID-19 in patients with mild to severe clinical signs brings benefits and avoids hospitalization in intensive care.
Flexible and Semi‐Transparent Ultra‐Thin CIGSe Solar Cells Prepared on Ultra‐Thin Glass Substrate: A Key to Flexible Bifacial Photovoltaic Applications
Authors: Kim Dongryeol , Shin Sang Su , Lee Sang Min , Cho Jun‐Sik , Yun Jae Ho , Lee Ho Seong , Park Joo Hyung 
Published: July 2020

AbstractFor applications to semi‐transparent and/or bifacial solar cells in building‐integrated photovoltaics and building‐applied photovoltaics, studies are underway to reduce the processing cost and time by decreasing the thickness of Cu(In1−x,Gax)Se2 (CIGSe) absorber to the ultra‐thin scale (≤500 nm). To dynamically and affordably meet the growing demand for electric power, daylighting, and architectural aesthetics of buildings in urban area, flexible semi‐transparent ultra‐thin (F‐STUT) CIGSe solar cells are proposed on flexible ultra‐thin glass (UTG) and compared with rigid semi‐transparent ultra‐thin (STUT) CIGSe solar cells fabricated on soda‐lime glass (SLG). At all the tested deposition temperatures of CIGSe, the F‐STUT CIGSe solar cells exhibit superior performance compared to the rigid STUT CIGSe solar cells. Furthermore, through realistic measurement under ≈1.3‐sun illumination, maximum bifacial power conversion efficiency of 11.90% and 13.23% are obtained for SLG and UTG, respectively. The major advantages of using UTG instead of SLG are not only the intrinsic characteristics of UTG, such as flexibility and high transmittance, but also collateral benefits such as the larger CIGSe grain size at the deposition temperature, better CIGSe crystalline quality, more precise controllability of the alkali element, and reduced thickness of the interfacial GaOx layer, which enhance the photovoltaic parameters.
Phase Engineering of Transition Metal Dichalcogenides with Unprecedentedly High Phase Purity, Stability, and Scalability via Molten‐Metal‐Assisted Intercalation
Authors: Park Sanghyeon , Kim Changmin , Park Sung O. , Oh Nam Khen , Kim Ungsoo , Lee Junghyun , Seo Jihyung , Yang Yejin , Lim Hyeong Yong , Kwak Sang Kyu , Kim Guntae , Park Hyesung 
Published: July 2020

AbstractThe crystalline phase of layered transition metal dichalcogenides (TMDs) directly determines their material property. The most thermodynamically stable phase structures in TMDs are the semiconducting 2H and metastable metallic 1T phases. To overcome the low phase purity and instability of 1T‐TMDs, which limits the utilization of their intrinsic properties, various synthesis strategies for 1T‐TMDs have been proposed in phase‐engineering studies. Herein, a facile and scalable synthesis of 1T‐phase molybdenum disulfide (MoS2) via the molten‐metal‐assisted intercalation (MMI) approach is introduced, which exploits the capillary action of molten potassium and the difference between the electron affinity of MoS2 and the ionization potential of potassium. Highly reactive molten potassium metal can readily intercalate into the MoS2 interlayers, inducing an efficient phase transition from the 2H to 1T crystal structure. The ionic bonding between the intercalated potassium and sulfur lowers the energy barrier of the 1T‐phase transition, enhancing the phase stability of the 1T crystals. Owing to the high purity and stability of the 1T phase, the electrocatalytic performance for the hydrogen evolution reaction is significantly higher in 1T‐MoS2 (MMI) than in 2H‐MoS2 and even in 1T‐MoS2 synthesized using n‐butyllithium.
Improved Mechanical Durability of High‐Performance OPVs Using Semi‐Interpenetrating Networks
Authors: Hu Zhiqi , Sun Changxu , Lin Allen , Jackson Joshua , Terlier Tanguy , Owolabi Damilola , Mei Hao , Li Yilin , Wang Yafei , Sidhik Siraj , Hao Fang , Yao Yan , Mohite Aditya D. , Verduzco Rafael 
Published: July 2020

AbstractOrganic photovoltaic (OPV) devices offer a number of unique advantages over conventional single crystal silicon solar cells, such as simple and low‐cost fabrication, significantly reduced weight, high flexibility, and semitransparency. However, OPV devices exhibit poor durability to mechanical deformations. Here, the use of an elastic semi‐interpenetrating network is studied to improve the mechanical durability of the active layer of OPV devices based on the high‐performance poly[(2,6‐(4,8‐bis(5‐(2‐ethylhexyl‐3‐fluoro)thiophen‐2‐yl)‐benzo[1,2‐b:4,5‐b′]dithiophene))‐alt‐(5,5‐(1′,3′‐di‐2‐thienyl‐5′,7′‐bis(2‐ethylhexyl)benzo[1′,2′‐c:4′,5′‐c′]dithiophene‐4,8‐dione)]:2,2′‐[[6,6,12,12‐tetrakis(4‐hexylphenyl)‐6,12‐dihydrodithieno[2,3‐d:2′,3′‐d′]‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene‐2,8‐diyl]bis[methylidyne(3‐oxo‐1H‐indene‐2,1(3H)‐diylidene)]]bis[propanedinitrile] donor:acceptor blend (PBDBT‐2F:ITIC). The elastic interpenetrating network is synthesized in situ through the UV photoinitiated crosslinking of thiol–ene additives in the active layer. The effects of strain as a function of bending on the network‐stabilized active layer structure are systematically investigated. The elastic interpenetrating network suppresses crack formation and improves durability to high‐curvature and repeated bending deformations. Performance measurements show that network‐stabilized devices outperform pristine devices above a critical bending strain and number of bending deformations. The photovoltaic performance in general decreases with the increase in the network content, and the best performing devices are obtained using network forming reagents that are most compatible with the donor:acceptor system. This work describes an effective route to flexible devices using semi‐interpenetrating polymer networks and provides insight into the design of the networks to maximize photovoltaic performance.
Flickering Polarons Extending over Ten Nanometres Mediate Charge Transport in High‐Mobility Organic Crystals
Authors: Giannini Samuele , Ziogos Orestis George , Carof Antoine , Ellis Matthew , Blumberger Jochen 
Published: July 2020

AbstractProgress in the design of high‐mobility organic semiconductors has been hampered by an incomplete fundamental understanding of the elusive charge carrier dynamics mediating electrical current in these materials. To address this problem, a novel fully atomistic non‐adiabatic molecular dynamics approach termed fragment orbital‐based surface hopping (FOB‐SH) that propagates the electron‐nuclear motion has been further improved and, for the first time, used to calculate the full 2D charge mobility tensor for the conductive planes of six structurally well characterized organic single crystals, in good agreement with available experimental data. The nature of the charge carrier in these materials is best described as a flickering polaron constantly changing shape and extensions under the influence of thermal disorder. Thermal intra‐band excitations from modestly delocalized band edge states (up to 5 nm or 10–20 molecules) to highly delocalized tail states (up to 10 nm or 40–60 molecules in the most conductive materials) give rise to short, ≈ 10 fs‐long bursts of the charge carrier wavefunction that drives the spatial displacement of the polaron, resulting in carrier diffusion and mobility. This study implies that key to the design of high‐mobility materials is a high density of strongly delocalized and thermally accessible tail states.
An Organic Borate Salt with Superior p‐Doping Capability for Organic Semiconductors
Authors: Wegner Berthold , Lungwitz Dominique , Mansour Ahmed E. , Tait Claudia E. , Tanaka Naoki , Zhai Tianshu , Duhm Steffen , Forster Michael , Behrends Jan , Shoji Yoshiaki , Opitz Andreas , Scherf Ullrich , List‐Kratochvil Emil J. W. , Fukushima Takanori , Koch Norbert 
Published: July 2020

AbstractMolecular doping allows enhancement and precise control of electrical properties of organic semiconductors, and is thus of central technological relevance for organic (opto‐) electronics. Beyond single‐component molecular electron acceptors and donors, organic salts have recently emerged as a promising class of dopants. However, the pertinent fundamental understanding of doping mechanisms and doping capabilities is limited. Here, the unique capabilities of the salt consisting of a borinium cation (Mes2B+; Mes: mesitylene) and the tetrakis(penta‐fluorophenyl)borate anion [B(C6F5)4]− is demonstrated as p‐type dopant for polymer semiconductors. With a range of experimental methods, the doping mechanism is identified to comprise electron transfer from the polymer to Mes2B+, and the positive charge on the polymer is stabilized by [B(C6F5)4]−. Notably, the former salt cation leaves during processing and is not present in films. The anion [B(C6F5)4]− even enables the stabilization of polarons and bipolarons in poly(3‐hexylthiophene), not yet achieved with other molecular dopants. From doping studies with high ionization energy polymer semiconductors, the effective electron affinity of Mes2B+[B(C6F5)4]− is estimated to be an impressive 5.9 eV. This significantly extends the parameter space for doping of polymer semiconductors.
Usefulness of microsurgical back‐table angioplasty for multiple hepatic arteries in living donor liver transplantation
Authors: Harada Noboru , Yoshizumi Tomoharu , Matsuura Toshiharu , Taguchi Tomoaki , Mori Masaki 
Published: July 2020

AbstractThe graft hepatic artery orifice is tiny in living donor liver transplantation, and therefore, it is more difficult to reconstruct the hepatic artery than in deceased donor liver transplantation. In situ, multi‐vessel hepatic artery reconstruction in living donor liver transplantation is time‐consuming, and reconstructions are often complicated if the hepatic graft has several stumps. We describe two living donor liver transplants using back‐table microsurgical angioplasty to combine two hepatic artery stumps to create a single orifice, and sequential single‐vessel hepatic artery reconstruction in the recipient. Briefly, we used double‐needle interrupted sutures for the two hepatic artery stumps with a biangular stay‐suture method in back‐table microsurgical angioplasty. Each suture was placed from the inner side of the arterial wall to the outer side, which allowed for safe and reliable suturing. After placing the interrupted sutures in the anterior wall, we turned over the vessels in the cold storage on the back table and placed interrupted sutures in the posterior wall. In the recipient, the single stump of the graft was anastomosed to the recipient's hepatic artery using an interrupted pattern and a surgical microscope. The postoperative courses of the donors and recipients were uneventful. Back‐table hepatic artery angioplasty is a feasible option to overcome the complexities of multi‐vessel arterial reconstruction in living donor liver transplantation. We recommend performing secure multi‐vessel hepatic arterial reconstruction adapted to the clinical scenario. Using simple appropriate anastomosis, back‐table microsurgical angiography may provide good results in living donor liver transplantation.
Venetoclax and hypomethylating agents in FLT3‐mutated acute myeloid leukemia
Authors: Aldoss Ibrahim , Zhang Jianying , Mei Matthew , Al Malki Monzr M , Arslan Shukaib , Ngo Dat , Aribi Ahmed , Ali Haris , Sandhu Karamjeet , Salhotra Amandeep , Koller Paul , Khaled Samer , Artz Andrew , Snyder David , Nakamura Ryotaro , Forman Stephen J , Stein Anthony S. , Marcucci Guido , Pullarkat Vinod 
Published: July 2020

AbstractFMS‐like tyrosine kinase 3 (FLT3) mutations are prevalent in acute myeloid leukemia (AML), and their presence confers adverse risk. FLT3‐mutated (FLT3m) AML is a challenging leukemia to manage, particularly in older and unfit patients as well as patients with relapsed/refractory (r/r) disease. We retrospectively analyzed the outcomes of 50 FLT3m AML patients (17 treatment‐naïve, 33 r/r) treated with venetoclax (VEN) and hypomethylating agents (HMA). The overall CR/CRi rate with VEN‐HMA was 60% (94% in treatment‐naïve AML and 42% in r/r AML). Early (60‐days) treatment related mortality was 2%. The r/r AML setting was an independent predictor of lower complete response (OR: 0.08; 95%CI: 0.00‐0.60, P = .03). Cytogenetics‐molecular risk, concurrent mutations, the type of FLT3 mutation (ITD vs TKD), the ITD allelic ratio, the type of HMA, age, prior exposure to HMA and receipt of prior allogeneic transplant did not independently impact response or leukemia‐free survival (LFS). Concurrent IDH mutations were associated with lower CR/CRi (P = .01), while ASXL1 or TET2 mutations showed a non‐significant association toward higher CR/CRi (P = .07, for both). However, none of the concurrent mutations were an independent predictor for response when adjusted to AML setting. In conclusion, VEN‐HMA is associated with encouraging efficacy in FLT3m AML among both newly diagnosed unfit and r/r patients.
World‐Wide FINGERS Network: A global approach to risk reduction and prevention of dementia
Authors: Kivipelto Miia , Mangialasche Francesca , Snyder Heather M. , Allegri Ricardo , Andrieu Sandrine , Arai Hidenori , Baker Laura , Belleville Sylvie , Brodaty Henry , Brucki Sonia M. , Calandri Ismael , Caramelli Paulo , Chen Christopher , Chertkow Howard , Chew Effie , Choi Seong H. , Chowdhary Neerja , Crivelli Lucía , Torre Rafael De La , Du Yifeng , Dua Tarun , Espeland Mark , Feldman Howard H. , Hartmanis Maris , Hartmann Tobias , Heffernan Megan , Henry Christiani J. , Hong Chang H. , Håkansson Krister , Iwatsubo Takeshi , Jeong Jee H. , Jimenez‐Maggiora Gustavo , Koo Edward H. , Launer Lenore J. , Lehtisalo Jenni , Lopera Francisco , Martínez‐Lage Pablo , Martins Ralph , Middleton Lefkos , Molinuevo José L. , Montero‐Odasso Manuel , Moon So Y. , Morales‐Pérez Kristal , Nitrini Ricardo , Nygaard Haakon B. , Park Yoo K. , Peltonen Markku , Qiu Chengxuan , Quiroz Yakeel T. , Raman Rema , Rao Naren , Ravindranath Vijayalakshmi , Rosenberg Anna , Sakurai Takashi , Salinas Rosa M. , Scheltens Philip , Sevlever Gustavo , Soininen Hilkka , Sosa Ana L. , Suemoto Claudia K. , Tainta‐Cuezva Mikel , Velilla Lina , Wang Yongxiang , Whitmer Rachel , Xu Xin , Bain Lisa J. , Solomon Alina , Ngandu Tiia , Carrillo Maria C. 
Published: July 2020

AbstractReducing the risk of dementia can halt the worldwide increase of affected people. The multifactorial and heterogeneous nature of late‐onset dementia, including Alzheimer's disease (AD), indicates a potential impact of multidomain lifestyle interventions on risk reduction. The positive results of the landmark multidomain Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) support such an approach. The World‐Wide FINGERS (WW‐FINGERS), launched in 2017 and including over 25 countries, is the first global network of multidomain lifestyle intervention trials for dementia risk reduction and prevention. WW‐FINGERS aims to adapt, test, and optimize the FINGER model to reduce risk across the spectrum of cognitive decline—from at‐risk asymptomatic states to early symptomatic stages—in different geographical, cultural, and economic settings. WW‐FINGERS aims to harmonize and adapt multidomain interventions across various countries and settings, to facilitate data sharing and analysis across studies, and to promote international joint initiatives to identify globally implementable and effective preventive strategies.
Electrocatalytic CO2 Reduction on CuOx Nanocubes: Tracking the Evolution of Chemical State, Geometric Structure, and Catalytic Selectivity using Operando Spectroscopy
Authors: Möller Tim , Scholten Fabian , Thanh Trung Ngo , Sinev Ilya , Timoshenko Janis , Wang Xingli , Jovanov Zarko , Gliech Manuel , Roldan Cuenya Beatriz , Varela Ana Sofia , Strasser Peter 
Published: July 2020

AbstractThe direct electrochemical conversion of carbon dioxide (CO2) into multi‐carbon (C2+) products still faces fundamental and technological challenges. While facet‐controlled and oxide‐derived Cu materials have been touted as promising catalysts, their stability has remained problematic and poorly understood. Herein we uncover changes in the chemical and morphological state of supported and unsupported Cu2O nanocubes during operation in low‐current H‐Cells and in high‐current gas diffusion electrodes (GDEs) using neutral pH buffer conditions. While unsupported nanocubes achieved a sustained C2+ Faradaic efficiency of around 60 % for 40 h, the dispersion on a carbon support sharply shifted the selectivity pattern towards C1 products. Operando XAS and time‐resolved electron microscopy revealed the degradation of the cubic shape and, in the presence of a carbon support, the formation of small Cu‐seeds during the surprisingly slow reduction of bulk Cu2O. The initially (100)‐rich facet structure has presumably no controlling role on the catalytic selectivity, whereas the oxide‐derived generation of under‐coordinated lattice defects, can support the high C2+ product yields.