bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reciprocal regulation of RIG-I and XRCC4 connects DNA repair with RIG-I immune signaling
Authors: Guo Guijie , Gao Ming , Gao Xiaochen , Zhu Bibo , Huang Jinzhou , Tu Xinyi , Kim Wootae , Zhao Fei , Zhou Qin , Zhu Shouhai , Wu Zheming , Yan Yuanliang , Zhang Yong , Zeng Xiangyu , Zhu Qian , Yin Ping , Luo Kuntian , Sun Jie , Deng Min , Lou Zhenkun 
Published: April 2021

AbstractThe RNA-sensing pathway contributes to type I interferon (IFN) production induced by DNA damaging agents. However, the potential involvement of RNA sensors in DNA repair is unknown. Here, we found that retinoic acid-inducible gene I (RIG-I), a key cytosolic RNA sensor that recognizes RNA virus and initiates the MAVS-IRF3-type I IFN signaling cascade, is recruited to double-stranded breaks (DSBs) and suppresses non-homologous end joining (NHEJ). Mechanistically, RIG-I interacts with XRCC4, and the RIG-I/XRCC4 interaction impedes the formation of XRCC4/LIG4/XLF complex at DSBs. High expression of RIG-I compromises DNA repair and sensitizes cancer cells to irradiation treatment. In contrast, depletion of RIG-I renders cells resistant to irradiation in vitro and in vivo. In addition, this mechanism suggests a protective role of RIG-I in hindering retrovirus integration into the host genome by suppressing the NHEJ pathway. Reciprocally, XRCC4, while suppressed for its DNA repair function, has a critical role in RIG-I immune signaling through RIG-I interaction. XRCC4 promotes RIG-I signaling by enhancing oligomerization and ubiquitination of RIG-I, thereby suppressing RNA virus replication in host cells. In vivo, silencing XRCC4 in mouse lung promotes influenza virus replication in mice and these mice display faster body weight loss, poorer survival, and a greater degree of lung injury caused by influenza virus infection. This reciprocal regulation of RIG-I and XRCC4 reveals a new function of RIG-I in suppressing DNA repair and virus integration into the host genome, and meanwhile endues XRCC4 with a crucial role in potentiating innate immune response, thereby helping host to prevail in the battle against virus.
Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis
Authors: Wang Michael F. Z. , Mantri Madhav , Chou Shao-Pei , Scuderi Gaetano J. , McKellar David W. , Butcher Jonathan T. , Danko Charles G. , De Vlaminck Iwijn 
Published: April 2021

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.
Defect-free potassium manganese hexacyanoferrate cathode material for high-performance potassium-ion batteries
Authors: Deng Leqing , Qu Jiale , Niu Xiaogang , Liu Juzhe , Zhang Juan , Hong Youran , Feng Meiying , Wang Jiangwei , Hu Miao , Zeng Liang , Zhang Qianfan , Guo Lin , Zhu Yujie 
Published: April 2021

AbstractPotassium-ion batteries (KIBs) are promising electrochemical energy storage systems because of their low cost and high energy density. However, practical exploitation of KIBs is hampered by the lack of high-performance cathode materials. Here we report a potassium manganese hexacyanoferrate (K2Mn[Fe(CN)6]) material, with a negligible content of defects and water, for efficient high-voltage K-ion storage. When tested in combination with a K metal anode, the K2Mn[Fe(CN)6]-based electrode enables a cell specific energy of 609.7 Wh kg−1 and 80% capacity retention after 7800 cycles. Moreover, a K-ion full-cell consisting of graphite and K2Mn[Fe(CN)6] as anode and cathode active materials, respectively, demonstrates a specific energy of 331.5 Wh kg−1, remarkable rate capability, and negligible capacity decay for 300 cycles. The remarkable electrochemical energy storage performances of the K2Mn[Fe(CN)6] material are attributed to its stable frameworks that benefit from the defect-free structure.
Short-wave infrared organic phototransistors with strong infrared-absorbing polytriarylamine by electron-transfer doping
Authors: Lee Chulyeon , Kim Hwajeong , Kim Youngkyoo 
Published: April 2021

AbstractShort-wavelength infrared (SWIR) sensors have attracted keen attention due to the increasing necessity in a variety of scientific and industrial applications, including biomedical and information technology fields. Because conventional SWIR sensors are made of inorganic materials with rigid and brittle characteristics, organic materials with a discrete SWIR absorption are required for flexible SWIR sensors in the flexible electronics era. Here, we demonstrate that a polytriarylamine, poly[N,N′-bis(4-butylphenyl)-N,N′-bis(phenyl)benzidine] (PolyTPD), can absorb almost full range of SWIR wavelength (λ = 1000–3200 nm) after 48 h doping with tris(pentafluorophenyl)borane (BCF). The spectroscopic characterization disclosed that an electron transfer from PolyTPD to BCF created a new low energy level (gap) state leading to the SWIR absorption in the BCF-doped PolyTPD complexes. Organic phototransistors (OPTRs) with the BCF-doped PolyTPD films as a gate-sensing layer could detect the SWIR light with a reasonable photoresponsivity of ~538 mA W−1 (λ = 1500 nm), ~541 mA W−1 (λ = 2000 nm), and ~222 mA W−1 (λ = 3000 nm). The present breakthrough SWIR-OPTR technology can pave a way for further advances in SWIR-absorbing organic materials and flexible SWIR sensors.
Initial atomic-scale oxidation pathways on a Ni–15Cr(100) alloy surface
Authors: Blades William H. , Barone Matthew R. , Reinke Petra 
Published: April 2021

AbstractTo understand the atomistic phenomenon behind initial oxidation processes, we have studied the nanoscale evolution of oxide growth prior to the formation of a complete layer on a Ni–15 wt%Cr(100) alloy surface using scanning tunneling microscopy/spectroscopy (STM/STS). At the onset of oxidation, a NiO superlattice forms oxide wedges across the step edges, eventually growing across the terraces. The completion of the NiO layer is followed by nucleation of the next layer, which always commences at the groove site of the superlattice. The Cr-oxide formation initiates as disk-shaped oxide particles early in the oxidation process, which Monte Carlo simulations reveal are likely caused by Cr clustering across the alloy surface. Upon further oxidation, a Cr(100)-p(2 × 2)O reconstructed surface is observed, indicating phase separation of Cr predicates the formation of the passive Cr-oxide film. The STS results vary across the oxide–alloy interface and between each oxide, providing greater insight into the origins of electronic heterogeneity and their effect on oxide growth. Using these data, we propose an oxidation model that highlights the growth of partial oxide layers on Ni–Cr(100) alloys within the pre-Cabrera–Mott regime.
Lower limb kinematic, kinetic, and EMG data from young healthy humans during walking at controlled speeds
Authors: Moreira Luís , Figueiredo Joana , Fonseca Pedro , Vilas-Boas João P. , Santos Cristina P. 
Published: April 2021

AbstractUnderstanding the lower limb kinematic, kinetic, and electromyography (EMG) data interrelation in controlled speeds is challenging for fully assessing human locomotion conditions. This paper provides a complete dataset with the above-mentioned raw and processed data simultaneously recorded for sixteen healthy participants walking on a 10 meter-flat surface at seven controlled speeds (1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4.0 km/h). The raw data include 3D joint trajectories of 24 retro-reflective markers, ground reaction forces (GRF), force plate moments, center of pressures, and EMG signals from Tibialis Anterior, Gastrocnemius Lateralis, Biceps Femoris, and Vastus Lateralis. The processed data present gait cycle-normalized data including filtered EMG signals and their envelope, 3D GRF, joint angles, and torques. This study details the experimental setup and presents a brief validation of the data quality. The presented dataset may contribute to (i) validate and enhance human biomechanical gait models, and (ii) serve as a reference trajectory for personalized control of robotic assistive devices, aiming an adequate assistance level adjusted to the gait speed and user’s anthropometry.
Central and mid-peripheral corneal astigmatism in an elderly population: a retrospective analysis of Scheimpflug topography results
Authors: Łabuz Grzegorz , Varadi Dorottya , Khoramnia Ramin , Auffarth Gerd U. 
Published: April 2021

AbstractImplantation of toric intraocular lenses (IOLs) has become standard in the correction of corneal astigmatism. The IOL selection is based on keratometric measurements of the central cornea. However, mid-peripheral corneal changes may yield suboptimal correction in patients with larger pupils. This study retrospectively analyzed corneal topography data collected using a Scheimpflug device during routine clinical examinations. Of 11,953 patients, 641 met the inclusion criteria. Total corneal astigmatism was compared between five concentric zones (2–6 mm) using vector analysis. The absolute difference between astigmatism at 2 mm and 6 mm was 0.30 D (− 0.36 to 0.64), which decreased to 0.10 D (0 to 0.20) between the 5- and 6-mm zone. With-the-rule astigmatism was the most prevalent (53%), 34% had against-the-rule (ATR), and 13% had oblique. The decrease of the cylinder power with the diameter differed significantly between the three types, with ATR and oblique astigmatism being associated with the steepest change. Patients with high corneal astigmatism tend to demonstrate larger differences between the center and mid-periphery than those with low and moderate astigmatism. In conclusion, we demonstrated that central corneal astigmatism differs from that measured at the mid-periphery and that a larger difference was found in patients with ATR, oblique and high astigmatism.
Complement C3 identified as a unique risk factor for disease severity among young COVID-19 patients in Wuhan, China
Authors: Cheng Weiting , Hornung Roman , Xu Kai , Yang Cai hong , Li Jian 
Published: April 2021

AbstractGiven that a substantial proportion of the subgroup of COVID-19 patients that face a severe disease course are younger than 60 years, it is critical to understand the disease-specific characteristics of young COVID-19 patients. Risk factors for a severe disease course for young COVID-19 patients and possible non-linear influences remain unknown. Data were analyzed from COVID-19 patients with clinical outcome in a single hospital in Wuhan, China, collected retrospectively from Jan 24th to Mar 27th. Clinical, demographic, treatment and laboratory data were collected from patients' medical records. Uni- and multivariable analysis using logistic regression and random forest, with the latter allowing the study of non-linear influences, were performed to investigate the clinical characteristics of a severe disease course. A total of 762 young patients (median age 47 years, interquartile range [IQR] 38–55, range 18–60; 55.9% female) were included, as well as 714 elderly patients as a comparison group. Among the young patients, 362 (47.5%) had a severe/critical disease course and the mean age was statistically significantly higher in the severe subgroup than in the mild subgroup (59.3 vs. 56.0, Student's t-test: p < 0.001). The uni- and multivariable analysis suggested that several covariates such as elevated levels of serum amyloid A (SAA), C-reactive protein (CRP) and lactate dehydrogenase (LDH), and decreased lymphocyte counts influence disease severity independently of age. Elevated levels of complement C3 (odds ratio [OR] 15.6, 95% CI 2.41–122.3; p = 0.039) are particularly associated with the risk of developing severe COVID-19 specifically in young patients, whereas no such influence seems to exist for elderly patients. Additional analysis suggests that the influence of complement C3 in young patients is independent of age, gender, and comorbidities. Variable importance values and partial dependence plots obtained using random forests delivered additional insights, in particular indicating non-linear influences of risk factors on disease severity. This study identified increased levels of complement C3 as a unique risk factor for adverse outcomes specific to young COVID-19 patients.
Design, synthesis and docking studies of novel thiazole derivatives incorporating pyridine moiety and assessment as antimicrobial agents
Authors: Khidre Rizk E. , Radini Ibrahim Ali M. 
Published: April 2021

AbstractA novel series of substituted 4,6-dimethyl-2-oxo-1-(thiazol-2-ylamino)-1,2-dihydropyridine-3-carbonitrile derivatives 6, 9, 13, 15, and 17 was synthesized in a good to excellent yield from the reaction of 1-(3-cyano-4,6-dimethyl-2-oxopyridin-1(2H)-yl)thiourea with 2-oxo-N'-arylpropanehydrazonoyl chloride, chloroacetone, α-bromoketones, ethyl chloroacetate, and 2,3-dichloroquinoxaline, respectively. The potential DNA gyrase inhibitory activity was examined using in silico molecular docking simulation. The novel thiazoles exhibit dock score values between − 6.4 and − 9.2 kcal/mol and they were screened for their antimicrobial activities. Compound 13a shown good antibacterial activities with MIC ranged from 93.7–46.9 μg/mL, in addition, it shown good antifungal activities with MIC ranged from 7.8 and 5.8 μg/mL.
Future behavior of wind wave extremes due to climate change
Authors: Lobeto Hector , Menendez Melisa , Losada Iñigo J. 
Published: April 2021

AbstractExtreme waves will undergo changes in the future when exposed to different climate change scenarios. These changes are evaluated through the analysis of significant wave height (Hs) return values and are also compared with annual mean Hs projections. Hourly time series are analyzed through a seven-member ensemble of wave climate simulations and changes are estimated in Hs for return periods from 5 to 100 years by the end of the century under RCP4.5 and RCP8.5 scenarios. Despite the underlying uncertainty that characterizes extremes, we obtain robust changes in extreme Hs over more than approximately 25% of the ocean surface. The results obtained conclude that increases cover wider areas and are larger in magnitude than decreases for higher return periods. The Southern Ocean is the region where the most robust increase in extreme Hs is projected, showing local increases of over 2 m regardless the analyzed return period under RCP8.5 scenario. On the contrary, the tropical north Pacific shows the most robust decrease in extreme Hs, with local decreases of over 1.5 m. Relevant divergences are found in several ocean regions between the projected behavior of mean and extreme wave conditions. For example, an increase in Hs return values and a decrease in annual mean Hs is found in the SE Indian, NW Atlantic and NE Pacific. Therefore, an extrapolation of the expected change in mean wave conditions to extremes in regions presenting such divergences should be adopted with caution, since it may lead to misinterpretation when used for the design of marine structures or in the evaluation of coastal flooding and erosion.
Acoustically induced transparency for synchrotron hard x-ray photons
Authors: Khairulin I. R. , Radeonychev Y. V. , Antonov V. A. , Kocharovskaya Olga 
Published: April 2021

AbstractThe induced transparency of opaque medium for resonant electromagnetic radiation is a powerful tool for manipulating the field-matter interaction. Various techniques to make different physical systems transparent for radiation from microwaves to x-rays were implemented. Most of them are based on the modification of the quantum-optical properties of the medium under the action of an external coherent electromagnetic field. Recently, an observation of acoustically induced transparency (AIT) of the 57Fe absorber for resonant 14.4-keV photons from the radioactive 57Co source was reported. About 150-fold suppression of the resonant absorption of photons due to collective acoustic oscillations of the nuclei was demonstrated. In this paper, we extend the AIT phenomenon to a novel phase-locked regime, when the transmitted photons are synchronized with the absorber vibration. We show that the advantages of synchrotron Mössbauer sources such as the deterministic periodic emission of radiation and controlled spectral-temporal characteristics of the emitted photons along with high-intensity photon flux in a tightly focused beam, make it possible to efficiently implement this regime, paving the way for the development of the acoustically controlled interface between hard x-ray photons and nuclear ensembles.
Characterizing bulk rigidity of rigid red blood cell populations in sickle-cell disease patients
Authors: Gutierrez Mario , Shamoun Mark , Seu Katie Giger , Tanski Tyler , Kalfa Theodosia A. , Eniola-Adefeso Omolola 
Published: April 2021

AbstractIn this work, we utilized a parameterization model of ektacytometry to quantify the bulk rigidity of the rigid red blood cell (RBC) population in sickle cell disease (SCD) patients. Current ektacytometry techniques implement laser diffraction viscometry to estimate the RBC deformability in a whole blood sample. However, the diffraction measurement is an average of all cells present in the measured sample. By coupling an existing parameterization model of ektacytometry to an artificially rigid RBC model, we formulated an innovative system for estimating the average rigidity of the rigid RBC population in SCD blood. We demonstrated that this method could more accurately determine the bulk stiffness of the rigid RBC populations. This information could potentially help develop the ektacytometry technique as a tool for assessing disease severity in SCD patients, offering novel insights into the disease pathology and treatment.
The long noncoding RNA of RMRP is downregulated by PERK, which induces apoptosis in hepatocellular carcinoma cells
Authors: Yukimoto Atsushi , Watanabe Takao , Sunago Kotaro , Nakamura Yoshiko , Tanaka Takaaki , Koizumi Yohei , Yoshida Osamu , Tokumoto Yoshio , Hirooka Masashi , Abe Masanori , Hiasa Yoichi 
Published: April 2021

AbstractEndoplasmic reticulum (ER) stress plays an important role in hepatocyte degeneration, especially in patients with chronic liver injury. Protein kinase R-like endoplasmic reticulum kinase (PERK) is a key molecule in ER stress. PERK may contribute to apoptotic cell death in HCC, however the details of the mechanism are not clear. In this study, we identified PERK-associated molecules using transcriptome analysis. We modulated PERK expression using a plasmid, tunicamycin and siRNA against PERK, and then confirmed the target gene expression with real-time PCR and Northern blotting. We further analyzed the apoptotic function. Transcriptome analysis revealed that expression of the RNA component of mitochondrial RNA processing endoribonuclease (RMRP), which is a long noncoding RNA, was strongly correlated with the function of PERK. The expression of RMRP was correlated with the expression of PERK in experiments with the siRNA and PERK plasmid in both HCC cell lines and human HCC tissue. Furthermore, RMRP downregulation induced apoptotic cell death. RMRP is downregulated by PERK, which induces apoptosis in HCC. RMRP could be a new therapeutic target to regulate HCC in patients with chronic liver diseases associated with ER stress.
Dyskinesia estimation during activities of daily living using wearable motion sensors and deep recurrent networks
Authors: Hssayeni Murtadha D. , Jimenez-Shahed Joohi , Burack Michelle A. , Ghoraani Behnaz 
Published: April 2021

AbstractLevodopa-induced dyskinesias are abnormal involuntary movements experienced by the majority of persons with Parkinson’s disease (PwP) at some point over the course of the disease. Choreiform as the most common phenomenology of levodopa-induced dyskinesias can be managed by adjusting the dose/frequency of PD medication(s) based on a PwP’s motor fluctuations over a typical day. We developed a sensor-based assessment system to provide such information. We used movement data collected from the upper and lower extremities of 15 PwPs along with a deep recurrent model to estimate dyskinesia severity as they perform different activities of daily living (ADL). Subjects performed a variety of ADLs during a 4-h period while their dyskinesia severity was rated by the movement disorder experts. The estimated dyskinesia severity scores from our model correlated highly with the expert-rated scores (r= 0.87 (p< 0.001)), which was higher than the performance of linear regression that is commonly used for dyskinesia estimation (r= 0.81 (p< 0.001)). Our model provided consistent performance at different ADLs with minimumr= 0.70 (during walking) to maximumr= 0.84 (drinking) in comparison to linear regression withr= 0.00 (walking) tor= 0.76 (cutting food). These findings suggest that when our model is applied to at-home sensor data, it can provide an accurate picture of changes of dyskinesia severity facilitating effective medication adjustments.
Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
Authors: Bayega Anthony , Oikonomopoulos Spyros , Gregoriou Maria-Eleni , Tsoumani Konstantina T. , Giakountis Antonis , Wang Yu Chang , Mathiopoulos Kostas D. , Ragoussis Jiannis 
Published: April 2021

AbstractThe olive fruit fly, Bactrocera oleae, is the most important pest for the olive fruit but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development for the first time in this organism. Sequencing on the MinION platform generated over 31 million reads. Over 50% of the expressed genes had at least one read covering its entire length validating our full-length approach. We generated a de novo transcriptome assembly and identified 1768 new genes and a total of 79,810 isoforms; a fourfold increase in transcriptome diversity compared to the current NCBI predicted transcriptome. Absolute transcript quantification per embryo allowed an insight into the dramatic re-organization of maternal transcripts. We further identified Zelda as a possible regulator of early zygotic genome activation in B. oleae and provide further insights into the maternal-to-zygotic transition. These data show the utility of long-read RNA in improving characterization of non-model organisms that lack a fully annotated genome, provide potential targets for sterile insect technic approaches, and provide the first insight into the transcriptome landscape of the developing olive fruit fly embryo.