bluuebunny/crossref_metadata_2025 huggingface dataset:
Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification
Authors: Vasudevan Harish N. , Xu Peng , Servellita Venice , Miller Steve , Liu Leqian , Gopez Allan , Chiu Charles Y. , Abate Adam R.
Published: January 2021

The COVID-19 pandemic caused by the SARS-CoV-2 virus motivates diverse diagnostic approaches due to the novel causative pathogen, incompletely understood clinical sequelae, and limited availability of testing resources. Given the variability in viral load across and within patients, absolute viral load quantification directly from crude lysate is important for diagnosis and surveillance. Here, we investigate the use of digital droplet PCR (ddPCR) for SARS-CoV-2 viral load measurement directly from crude lysate without nucleic acid purification. We demonstrate ddPCR accurately quantifies SARS-CoV-2 standards from purified RNA and multiple sample matrices, including commonly utilized universal transport medium (UTM). In addition, we find ddPCR functions robustly at low input viral copy numbers on nasopharyngeal swab specimens stored in UTM without upfront RNA extraction. We also show ddPCR, but not qPCR, from crude lysate shows high concordance with viral load measurements from purified RNA. Our data suggest ddPCR offers advantages to qPCR for SARS-CoV-2 detection with higher sensitivity and robustness when using crude lysate rather than purified RNA as input. More broadly, digital droplet assays provide a potential method for nucleic acid measurement and infectious disease diagnosis with limited sample processing, underscoring the utility of such techniques in laboratory medicine.
High performing flexible optoelectronic devices using thin films of topological insulator
Authors: Pandey Animesh , Yadav Reena , Kaur Mandeep , Singh Preetam , Gupta Anurag , Husale Sudhir
Published: January 2021

Topological insulators (TIs) possess exciting nonlinear optical properties due to presence of metallic surface states with the Dirac fermions and are predicted as a promising material for broadspectral phodotection ranging from UV (ultraviolet) to deep IR (infrared) or terahertz range. The recent experimental reports demonstrating nonlinear optical properties are mostly carried out on non-flexible substrates and there is a huge demand for the fabrication of high performing flexible optoelectronic devices using new exotic materials due to their potential applications in wearable devices, communications, sensors, imaging etc. Here first time we integrate the thin films of TIs (Bi2Te3) with the flexible PET (polyethylene terephthalate) substrate and report the strong light absorption properties in these devices. Owing to small band gap material, evolving bulk and gapless surface state conduction, we observe high responsivity and detectivity at NIR (near infrared) wavelengths (39 A/W, 6.1 × 108 Jones for 1064 nm and 58 A/W, 6.1 × 108 Jones for 1550 nm). TIs based flexible devices show that photocurrent is linearly dependent on the incident laser power and applied bias voltage. Devices also show very fast response and decay times. Thus we believe that the superior optoelectronic properties reported here pave the way for making TIs based flexible optoelectronic devices.
Comparing objective cognitive impairments in patients with peripheral neuropathic pain or fibromyalgia
Authors: Jacobsen Henrik Børsting , Stiles Tore C. , Stubhaug Audun , Landrø Nils Inge , Hansson Per
Published: January 2021

Existing studies on cognitive impairments in chronic pain do not investigate peripheral neuropathic pain (PNP) or compare pain conditions in a satisfactory manner. Here we aimed to compare executive dysfunctions in PNP patients with fibromyalgia (FM) and healthy controls (HC). Patients who self-reported cognitive impairments were assessed according to criteria for PNP or FM. Seventy-three patients met criteria and completed testing on executive functioning and IQ measures. We also included twenty matched healthy controls. Regression models controlling for age, sex and IQ, tested associations between group category (PNP, FM or HC) and outcomes. If a substantial association was detected, we followed up with head-to-head comparisons between PNP and FM. Multivariate regression models then tested associations between executive functioning and pain type, controlling for significant confounders. Results from head-to-head comparison between pain conditions showed significant differences on years lived with pain (FM > PNP), the use of anticonvulsants (PNP > FM) and use of analgesics (PNP > FM). When controlled for all significant differences, PNP patients had significantly lower scores on an attention-demanding cued-recall task compared to FM. Poor performance on attention-demanding cued-recall task was associated with PNP, which translate into problems with retaining fast-pace or advanced information.
Gene expression and functional abnormalities in XX/Sry Leydig cells
Authors: Yanai Shogo , Baba Takashi , Inui Kai , Miyabayashi Kanako , Han Soyun , Inoue Miki , Takahashi Fumiya , Kanai Yoshiakira , Ohkawa Yasuyuki , Choi Man Ho , Morohashi Ken-ichirou
Published: January 2021

The SRY gene induces testis development even in XX individuals. However, XX/Sry testes fail to produce mature sperm, due to the absence of Y chromosome carrying genes essential for spermatogenesis. XX/Sry Sertoli cells show abnormalities in the production of lactate and cholesterol required for germ cell development. Leydig cells are essential for male functions through testosterone production. However, whether XX/Sry adult Leydig cells (XX/Sry ALCs) function normally remains unclear. In this study, the transcriptomes from XY and XX/Sry ALCs demonstrated that immediate early and cholesterogenic gene expressions differed between these cells. Interestingly, cholesterogenic genes were upregulated in XX/Sry ALCs, although downregulated in XX/Sry Sertoli cells. Among the steroidogenic enzymes, CYP17A1 mediates steroid 17α-hydroxylation and 17,20-lyase reaction, necessary for testosterone production. In XX/Sry ALCs, the latter reaction was selectively decreased. The defects in XX/Sry ALCs, together with those in the germ and Sertoli cells, might explain the infertility of XX/Sry testes.
Fucoxanthin from microalgae Phaeodactylum tricornutum inhibits pro-inflammatory cytokines by regulating both NF-κB and NLRP3 inflammasome activation
Authors: Lee A-Hyeon , Shin Hye-Yoon , Park Jong-Hwi , Koo Song Yi , Kim Sang Min , Yang Seung-Hoon
Published: January 2021

Pro-inflammatory cytokines such as IL-1β, IL-6, and TNF-α are mediated by the activation of various kinds of signaling pathways in the innate immune system. Particularly, NF-κB and NLRP3 inflammasome signaling are involved in the production and secretion of these cytokines. Each signaling is participated in the two steps necessary for IL-1β, a representative pro-inflammatory cytokine, to be processed into a form secreted by cells. In the priming step stimulated by LPS, pro-IL-1β is synthesized through NF-κB activation. Pro-IL-1β cleavages into mature IL-1β by formed NLRP3 inflammasome in the activation step induced by ATP. The mature form of IL-1β is subsequently secreted out of the cell, causing inflammation. Moreover, IL-6 and TNF-α are known to increase in NLRP3 inflammasome-mediated conditions. Here, we found that fucoxanthin, one of the major components of Phaeodactylum tricornutum, has an inhibitory effect on NF-κB and NLRP3 inflammasome activation induced by the combination of LPS and ATP in bone marrow-derived immune cells as well as astrocytes. Fucoxanthin, which is abundant in the EtOH fraction of Phaeodactylum tricornutum extracts, has shown to have less cell toxicity and found to decrease the production of major pro-inflammatory cytokines such as IL-1β, IL-6, and TNF-α. Fucoxanthin has also shown to suppress the expression of cleaved caspase-1 and the oligomerization of ASC, which are the main components of the NLRP3 inflammasome. Furthermore, phosphorylated IκBα and pro-IL-1β expression decreased in the presence of fucoxanthin, suggesting that fucoxanthin can negatively regulate the priming step of inflammasome signaling. Thus, our results provide reliable evidence that fucoxanthin may serve as a key candidate in the development of potential therapeutic agents for inflammatory diseases as well as neurodegenerative diseases caused by NF-κB and NLRP3 inflammasome activation.
Aberrant spinal mechanical loading stress triggers intervertebral disc degeneration by inducing pyroptosis and nerve ingrowth
Authors: Fu Fangda , Bao Ronghua , Yao Sai , Zhou Chengcong , Luo Huan , Zhang Zhiguo , Zhang Huihao , Li Yan , Yan Shuxin , Yu Huan , Du Weibin , Yang Yanping , Jin Hongting , Tong Peijian , Sun Zhi-tao , Yue Ming , Chen Di , Wu Chengliang , Ruan Hongfeng
Published: January 2021

Aberrant mechanical factor is one of the etiologies of the intervertebral disc (IVD) degeneration (IVDD). However, the exact molecular mechanism of spinal mechanical loading stress-induced IVDD has yet to be elucidated due to a lack of an ideal and stable IVDD animal model. The present study aimed to establish a stable IVDD mouse model and evaluated the effect of aberrant spinal mechanical loading on the pathogenesis of IVDD. Eight-week-old male mice were treated with lumbar spine instability (LSI) surgery to induce IVDD. The progression of IVDD was evaluated by μCT and Safranin O/Fast green staining analysis. The metabolism of extracellular matrix, ingrowth of sensory nerves, pyroptosis in IVDs tissues were determined by immunohistological or real-time PCR analysis. The apoptosis of IVD cells was tested by TUNEL assay. IVDD modeling was successfully produced by LSI surgery, with substantial reductions in IVD height, BS/TV, Tb.N. and lower IVD score. LSI administration led to the histologic change of disc degeneration, disruption of the matrix metabolism, promotion of apoptosis of IVD cells and invasion of sensory nerves into annulus fibrosus, as well as induction of pyroptosis. Moreover, LSI surgery activated Wnt signaling in IVD tissues. Mechanical instability caused by LSI surgery accelerates the disc matrix degradation, nerve invasion, pyroptosis, and eventually lead to IVDD, which provided an alternative mouse IVDD model.
Scalable long read self-correction and assembly polishing with multiple sequence alignment
Authors: Morisse Pierre , Marchet Camille , Limasset Antoine , Lecroq Thierry , Lefebvre Arnaud
Published: January 2021

Third-generation sequencing technologies allow to sequence long reads of tens of kbp, that are expected to solve various problems. However, they display high error rates, currently capped around 10%. Self-correction is thus regularly used in long reads analysis projects. We introduce CONSENT, a new self-correction method that relies both on multiple sequence alignment and local de Bruijn graphs. To ensure scalability, multiple sequence alignment computation benefits from a new and efficient segmentation strategy, allowing a massive speedup. CONSENT compares well to the state-of-the-art, and performs better on real Oxford Nanopore data. Specifically, CONSENT is the only method that efficiently scales to ultra-long reads, and allows to process a full human dataset, containing reads reaching up to 1.5 Mbp, in 10 days. Moreover, our experiments show that error correction with CONSENT improves the quality of Flye assemblies. Additionally, CONSENT implements a polishing feature, allowing to correct raw assemblies. Our experiments show that CONSENT is 2-38x times faster than other polishing tools, while providing comparable results. Furthermore, we show that, on a human dataset, assembling the raw data and polishing the assembly is less resource consuming than correcting and then assembling the reads, while providing better results. CONSENT is available athttps://github.com/morispi/CONSENT.
Prediction of kinase inhibitors binding modes with machine learning and reduced descriptor sets
Authors: Abdelbaky Ibrahim , Tayara Hilal , Chong Kil To
Published: January 2021

Protein kinases are receiving wide research interest, from drug perspective, due to their important roles in human body. Available kinase-inhibitor data, including crystallized structures, revealed many details about the mechanism of inhibition and binding modes. The understanding and analysis of these binding modes are expected to support the discovery of kinase-targeting drugs. The huge amounts of data made it possible to utilize computational techniques, including machine learning, to help in the discovery of kinase-targeting drugs. Machine learning gave reasonable predictions when applied to differentiate between the binding modes of kinase inhibitors, promoting a wider application in that domain. In this study, we applied machine learning supported by feature selection techniques to classify kinase inhibitors according to their binding modes. We represented inhibitors as a large number of molecular descriptors, as features, and systematically reduced these features in a multi-step manner while trying to attain high classification accuracy. Our predictive models could satisfy both goals by achieving high accuracy while utilizing at most 5% of the modeling features. The models could differentiate between binding mode types with MCC values between 0.67 and 0.92, and balanced accuracy values between 0.78 and 0.97 for independent test sets.
Author Correction: Frequency-dependent drug screening using optogenetic stimulation of human iPSC-derived cardiomyocytes
Authors: Lapp Hendrik , Bruegmann Tobias , Malan Daniela , Friedrichs Stephanie , Kilgus Carsten , Heidsieck Alexandra , Sasse Philipp
Published: January 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Combining CRP and CA19-9 in a novel prognostic score in pancreatic ductal adenocarcinoma
Authors: Nurmi Anna M. , Mustonen Harri K. , Stenman Ulf-Håkan , Seppänen Hanna E. , Haglund Caj H.
Published: January 2021

Inflammation promotes tumor progression, induces invasion and metastatic spread. This retrospective study explored CRP, CA19-9, and routine laboratory values as preoperative prognostic factors in pancreatic cancer patients. Between 2000 and 2016, there were 212 surgically treated pancreatic cancer patients at Helsinki University Hospital, Finland. Out of these, 76 borderline resectable patients were treated with neoadjuvant therapy (NAT); 136 upfront resected patients were matched for age and sex at a 1:2 ratio. We analyzed preoperative CRP, CA19-9, CEA, leukocytes, albumin, bilirubin and platelets. CRP and CA19-9 were combined into a prognostic score: both CRP and CA19-9 below the cut-off values (3 mg/l and 37 kU/l, respectively), either CRP or CA19-9 above the cut-off value, and finally, both CRP and CA19-9 above the cut-off values. Among all patients, median disease-specific survival times were 54, 27 and 16 months, respectively (p < 0.001). At 5 years, among patients with CRP and CA19-9 levels below the cut-off values, 49% were alive and 45% were disease-free. Among NAT patients the corresponding survival rates were 52% and 45% and among those undergoing upfront surgery 45% and 40%, respectively. This novel prognostic score combining CRP and CA19-9 serves as a useful preoperative tool estimating survival.
Polarization control of THz emission using spin-reorientation transition in spintronic heterostructure
Authors: Khusyainov Dinar , Ovcharenko Sergei , Gaponov Mikhail , Buryakov Arseniy , Klimov Alexey , Tiercelin Nicolas , Pernod Philippe , Nozdrin Vadim , Mishina Elena , Sigov Alexander , Preobrazhensky Vladimir
Published: January 2021

Polarization of electromagnetic waves plays an extremely important role in interaction of radiation with matter. In particular, interaction of polarized waves with ordered matter strongly depends on orientation and symmetry of vibrations of chemical bonds in crystals. In quantum technologies, the polarization of photons is considered as a “degree of freedom”, which is one of the main parameters that ensure efficient quantum computing. However, even for visible light, polarization control is in most cases separated from light emission. In this paper, we report on a new type of polarization control, implemented directly in a spintronic terahertz emitter. The principle of control, realized by a weak magnetic field at room temperature, is based on a spin-reorientation transition (SRT) in an intermetallic heterostructure TbCo2/FeCo with uniaxial in-plane magnetic anisotropy. SRT is implemented under magnetic field of variable strength but of a fixed direction, orthogonal to the easy magnetization axis. Variation of the magnetic field strength in the angular (canted) phase of the SRT causes magnetization rotation without changing its magnitude. The charge current excited by the spin-to-charge conversion is orthogonal to the magnetization. As a result, THz polarization rotates synchronously with magnetization when magnetic field strength changes. Importantly, the radiation intensity does not change in this case. Control of polarization by SRT is applicable regardless of the spintronic mechanism of the THz emission, provided that the polarization direction is determined by the magnetic moment orientation. The results obtained open the prospect for the development of the SRT approach for THz emission control.
Automatic segmentation of ventricular volume by 3D ultrasonography in post haemorrhagic ventricular dilatation among preterm infants
Authors: Gontard Lionel C. , Pizarro Joaquín , Sanz-Peña Borja , Lubián López Simón P. , Benavente-Fernández Isabel
Published: January 2021

To train, evaluate, and validate the application of a deep learning framework in three-dimensional ultrasound (3D US) for the automatic segmentation of ventricular volume in preterm infants with post haemorrhagic ventricular dilatation (PHVD). We trained a 2D convolutional neural network (CNN) for automatic segmentation ventricular volume from 3D US of preterm infants with PHVD. The method was validated with the Dice similarity coefficient (DSC) and the intra-class coefficient (ICC) compared to manual segmentation. The mean birth weight of the included patients was 1233.1 g (SD 309.4) and mean gestational age was 28.1 weeks (SD 1.6). A total of 152 serial 3D US from 10 preterm infants with PHVD were analysed. 230 ventricles were manually segmented. Of these, 108 were used for training a 2D CNN and 122 for validating the methodology for automatic segmentation. The global agreement for manual versus automated measures in the validation data (n = 122) was excellent with an ICC of 0.944 (0.874–0.971). The Dice similarity coefficient was 0.8 (± 0.01). 3D US based ventricular volume estimation through an automatic segmentation software developed through deep learning improves the accuracy and reduces the processing time needed for manual segmentation using VOCAL. 3D US should be considered a promising tool to help deepen our current understanding of the complex evolution of PHVD.
Increasing the midsole bending stiffness of shoes alters gastrocnemius medialis muscle function during running
Authors: Cigoja Sasa , Fletcher Jared R. , Esposito Michael , Stefanyshyn Darren J. , Nigg Benno M.
Published: January 2021

In recent years, increasing the midsole bending stiffness (MBS) of running shoes by embedding carbon fibre plates in the midsole resulted in many world records set during long-distance running competitions. Although several theories were introduced to unravel the mechanisms behind these performance benefits, no definitive explanation was provided so far. This study aimed to investigate how the function of the gastrocnemius medialis (GM) muscle and Achilles tendon is altered when running in shoes with increased MBS. Here, we provide the first direct evidence that the amount and velocity of GM muscle fascicle shortening is reduced when running with increased MBS. Compared to control, running in the stiffest condition at 90% of speed at lactate threshold resulted in less muscle fascicle shortening (p = 0.006, d = 0.87), slower average shortening velocity (p = 0.002, d = 0.93) and greater estimated Achilles tendon energy return (p ≤ 0.001, d = 0.96), without a significant change in GM fascicle work (p = 0.335, d = 0.40) or GM energy cost (p = 0.569, d = 0.30). The findings of this study suggest that running in stiff shoes allows the ankle plantarflexor muscle–tendon unit to continue to operate on a more favourable position of the muscle’s force–length–velocity relationship by lowering muscle shortening velocity and increasing tendon energy return.
Descriptor selection for predicting interfacial thermal resistance by machine learning methods
Authors: Tian Xiaojuan , Chen Mingguang
Published: January 2021

Interfacial thermal resistance (ITR) is a critical property for the performance of nanostructured devices where phonon mean free paths are larger than the characteristic length scales. The affordable, accurate and reliable prediction of ITR is essential for material selection in thermal management. In this work, the state-of-the-art machine learning methods were employed to realize this. Descriptor selection was conducted to build robust models and provide guidelines on determining the most important characteristics for targets. Firstly, decision tree (DT) was adopted to calculate the descriptor importances. And descriptor subsets with topX highest importances were chosen (topX-DT, X = 20, 15, 10, 5) to build models. To verify the transferability of the descriptors picked by decision tree, models based on kernel ridge regression, Gaussian process regression and K-nearest neighbors were also evaluated. Afterwards, univariate selection (UV) was utilized to sort descriptors. Finally, the top5 common descriptors selected by DT and UV were used to build concise models. The performance of these refined models is comparable to models using all descriptors, which indicates the high accuracy and reliability of these selection methods. Our strategy results in concise machine learning models for a fast prediction of ITR for thermal management applications.
Vulnerability assessment of nearshore clam habitat subject to storm waves and surge
Authors: Zhang Yao , Wang Gang , Li Qingjie , Huang Wanru , Liu Xunan , Chen Chen , Shi Xiaoyong , Zheng Jinhai
Published: January 2021

Present work studied the lesion mechanism of coastal clam and its vulnerability assessment subject to the hydrodynamic disturbance of extreme storm events. A clam habitat at the northeast coast of China was chosen for the demonstration study. Relocation failure after passive transport due to excessive substrate erosion or suffocation in anoxic burial under overburdening sedimentation was identified the major cause of negative biomass responses during the storm. Based on the biological propensity and physiological sensitivity of the clam, a tunable loss probability function correlating the mortality with the shell length and the seabed change was proposed. A hydrodynamic model was then adopted to compute the sediment transport and net changes in the seafloor in response to the comprehensive process of storm waves and surge. The spatial distribution of the damage states was evaluated based on the numerical results incorporating the loss probability function. The estimated damage was mainly concentrated along the wave shoaling and breaking belts parallel to the shoreline. High surge levels pushed the “damage belt” shoreward, in which case large waves were able to propagate close to the shoreline before breaking. The scientific findings are helpful to better understand the vulnerability of the clam habitat to the storm disturbance. The study result as well provides a practical methodology of the storm risk assessment for benthic communities in broader ecological and geophysical scopes. The methodology are expected to be further validated and improved by more widespread sampling on coastal ecosystem or mariculture that will withstand future storms.
A latent highly activity energetic fuel: thermal stability and interfacial reaction kinetics of selected fluoropolymer encapsulated sub-micron sized Al particles
Authors: Wang Huixin , Ren Hui , Yan Tao , Li Yaru , Zhao Wanjun
Published: January 2021

Aluminum can enhance heat release of energetic composite in theory. However, the commonly used micron aluminum powder has several short comings like incomplete reaction and low reaction rate. Meanwhile, outer oxide shell of nano Al particle is thicker than micro Al, which leads to low active aluminum content and insufficient heat release. On the basis of previous research, reported fluoropolymers modified Al particles were compared and suitable F2311was chosen. Sub-micron scale Al (median particle size around 200 nm) was regarded as optimum coated object in consideration of activity content of aluminum powder changing with particle size. The super fine Al powder was prepared by electrical explosion method, and encapsulated in situ by selected fluorine rubber F2311. The experiments on thermal stability demonstrated F2311 coating thickness should be no less than 3.6 nm. These results were further confirmed by EXPLO5 thermo dynamic calculation. Calculated results showed that reaction characters of F2311 encapsulated Al exceeded conventional nano Al regardless of combustion and explosion. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), laser particle size analyzer and X-ray photoelectron spectroscopy (XPS) were used to characterize coated products’ morphology, particle size distribution and interfacial bonding information. The results showed that the coated samples were generally spherical shape, with median particle size of 217.7 nm and coating thickness of 3.6 nm. The coating shell contained a small amount of alumina and aluminum fluoride besides fluoropolymer. The non-isothermal dynamic equations of Al/F2311 and Al/Al2O3 were deduced by TG/DSC simultaneous thermal analysis. Compared with conventional nano-Al, the apparent activation energy of Al/F2311 decreased by 45 kJ/mol and the first exothermic peak temperature was about 10 °C earlier. Moreover, heat release was nearly twice as conventional nano-Al. TG-DSC-MS coupled measurements certified that active Al was enveloped by ‘fluorine atmosphere’ while F2311 decomposed in range of 200–400 °C. Alumina was replaced with aluminum fluoride inside coating layer during 400–550 °C, which broadened the diffusion path and then accelerated the permeation of oxidizing gas. In addition, the exothermic of Al-F was obviously larger than Al-O. Consequently, the oxidation reaction was activated rapidly, especially in initial exothermic period. Fluoropolymer encapsulated sub-micron sized Al was a latent highly activity energetic fuel and a potential candidate for aluminum powder.
Study on performance degradation and damage modes of thin-film photovoltaic cell subjected to particle impact
Authors: Xiao Kailu , Wu Xianqian , Song Xuan , Yuan Jianhua , Bai Wenyu , Wu Chenwu , Huang Chenguang
Published: January 2021

It has been a key issue for photovoltaic (PV) cells to survive under mechanical impacts by tiny dust. In this paper, the performance degradation and the damage behavior of PV cells subjected to massive dust impact are investigated using laser-shock driven particle impact experiments and mechanical modeling. The results show that the light-electricity conversion efficiency of the PV cells decreases with increasing the impact velocity and the particles’ number density. It drops from 26.7 to 3.9% with increasing the impact velocity from 40 to 185 m/s and the particles’ number densities from 35 to 150/mm2, showing a reduction up to 85.7% when being compared with the intact ones with the light-electricity conversion efficiency of 27.2%. A damage-induced conversion efficiency degradation (DCED) model is developed and validated by experiments, providing an effective method in predicting the performance degradation of PV cells under various dust impact conditions. Moreover, three damage modes, including damaged conducting grid lines, fractured PV cell surfaces, and the bending effects after impact are observed, and the corresponding strength of each mode is quantified by different mechanical theories.
Antiviral activity of lambda-carrageenan against influenza viruses and severe acute respiratory syndrome coronavirus 2
Authors: Jang Yejin , Shin Heegwon , Lee Myoung Kyu , Kwon Oh Seung , Shin Jin Soo , Kim Yong-il , Kim Chan Woo , Lee Hye-Ra , Kim Meehyein
Published: January 2021

Influenza virus and coronavirus, belonging to enveloped RNA viruses, are major causes of human respiratory diseases. The aim of this study was to investigate the broad spectrum antiviral activity of a naturally existing sulfated polysaccharide, lambda-carrageenan (λ-CGN), purified from marine red algae. Cell culture-based assays revealed that the macromolecule efficiently inhibited both influenza A and B viruses with EC50 values ranging from 0.3 to 1.4 μg/ml, as well as currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with an EC50 value of 0.9 ± 1.1 μg/ml. No toxicity to the host cells was observed at concentrations up to 300 μg/ml. Plaque titration and western blot analysis verified that λ-CGN reduced expression of viral proteins in cell lysates and suppressed progeny virus production in culture supernatants in a dose-dependent manner. This polyanionic compound exerts antiviral activity by targeting viral attachment to cell surface receptors and preventing virus entry. Moreover, its intranasal administration to mice during influenza A viral challenge not only alleviated infection-mediated reductions in body weight but also protected 60% of mice from virus-induced mortality. Thus, λ-CGN could be a promising antiviral agent for preventing infection with several respiratory viruses.
Apolipoprotein E4 effects on topological brain network organization in mild cognitive impairment
Authors: Sanabria-Diaz Gretel , Melie-Garcia Lester , Draganski Bogdan , Demonet Jean-Francois , Kherif Ferath
Published: January 2021

The Apolipoprotein E isoform E4 (ApoE4) is consistently associated with an elevated risk of developing late-onset Alzheimer’s Disease (AD); however, less is known about the potential genetic modulation of the brain networks organization during prodromal stages like Mild Cognitive Impairment (MCI). To investigate this issue during this critical stage, we used a dataset with a cross-sectional sample of 253 MCI patients divided into ApoE4-positive (‛Carriers’) and ApoE4-negative (‘non-Carriers’). We estimated the cortical thickness (CT) from high-resolution T1-weighted structural magnetic images to calculate the correlation among anatomical regions across subjects and build the CT covariance networks (CT-Nets). The topological properties of CT-Nets were described through the graph theory approach. Specifically, our results showed a significant decrease in characteristic path length, clustering-index, local efficiency, global connectivity, modularity, and increased global efficiency for Carriers compared to non-Carriers. Overall, we found that ApoE4 in MCI shaped the topological organization of CT-Nets. Our results suggest that in the MCI stage, the ApoE4 disrupting the CT correlation between regions may be due to adaptive mechanisms to sustain the information transmission across distant brain regions to maintain the cognitive and behavioral abilities before the occurrence of the most severe symptoms.
How aging affects visuomotor adaptation and retention in a precision walking paradigm
Authors: Bakkum Amanda , Gunn Shaila M. , Marigold Daniel S.
Published: January 2021

Motor learning is a lifelong process. However, age-related changes to musculoskeletal and sensory systems alter the relationship (or mapping) between sensory input and motor output, and thus potentially affect motor learning. Here we asked whether age affects the ability to adapt to and retain a novel visuomotor mapping learned during overground walking. We divided participants into one of three groups (n = 12 each) based on chronological age: a younger-aged group (20–39 years old); a middle-aged group (40–59 years old); and an older-aged group (60–80 years old). Participants learned a new visuomotor mapping, induced by prism lenses, during a precision walking task. We assessed retention one-week later. We did not detect significant effects of age on measures of adaptation or savings (defined as faster relearning). However, we found that older adults demonstrated reduced initial recall of the mapping, reflected by greater foot-placement error during the first adaptation trial one-week later. Additionally, we found that increased age significantly associated with reduced initial recall. Overall, our results suggest that aging does not impair adaptation and that older adults can demonstrate visuomotor savings. However, older adults require some initial context during relearning to recall the appropriate mapping.
Pharmacological inactivation of the prion protein by targeting a folding intermediate
Authors: Spagnolli Giovanni , Massignan Tania , Astolfi Andrea , Biggi Silvia , Rigoli Marta , Brunelli Paolo , Libergoli Michela , Ianeselli Alan , Orioli Simone , Boldrini Alberto , Terruzzi Luca , Bonaldo Valerio , Maietta Giulia , Lorenzo Nuria L. , Fernandez Leticia C. , Codeseira Yaiza B. , Tosatto Laura , Linsenmeier Luise , Vignoli Beatrice , Petris Gianluca , Gasparotto Dino , Pennuto Maria , Guella Graziano , Canossa Marco , Altmeppen Hermann C. , Lolli Graziano , Biressi Stefano , Pastor Manuel M. , Requena Jesús R. , Mancini Ines , Barreca Maria L. , Faccioli Pietro , Biasini Emiliano
Published: January 2021

Recent computational advancements in the simulation of biochemical processes allow investigating the mechanisms involved in protein regulation with realistic physics-based models, at an atomistic level of resolution. These techniques allowed us to design a drug discovery approach, named Pharmacological Protein Inactivation by Folding Intermediate Targeting (PPI-FIT), based on the rationale of negatively regulating protein levels by targeting folding intermediates. Here, PPI-FIT was tested for the first time on the cellular prion protein (PrP), a cell surface glycoprotein playing a key role in fatal and transmissible neurodegenerative pathologies known as prion diseases. We predicted the all-atom structure of an intermediate appearing along the folding pathway of PrP and identified four different small molecule ligands for this conformer, all capable of selectively lowering the load of the protein by promoting its degradation. Our data support the notion that the level of target proteins could be modulated by acting on their folding pathways, implying a previously unappreciated role for folding intermediates in the biological regulation of protein expression.
A review of pharmaceutical occurrence and pathways in the aquatic environment in the context of a changing climate and the COVID-19 pandemic
Authors: O'Flynn Dylan , Lawler Jenny , Yusuf Azeez , Parle-McDermott Anne , Harold Denise , Mc Cloughlin Thomas , Holland Linda , Regan Fiona , White Blánaid
Published: January 2021

Active pharmaceutical ingredients (APIs) are increasingly being identified as contaminants of emerging concern (CECs).
Pressure effects on the structures and electronic properties of halide perovskite CsPbX3 (X = I, Br, Cl)
Authors: Wang Xinyu , Tian Hao , Li Xu , Sang Hai , Zhong Chonggui , Liu Jun-Ming , Yang Yurong
Published: January 2021

Two monoclinic C2/m phases and an insulator–metal transition were discovered in CsPbI3 at high pressure. Furthermore, the largest piezochromic effect in the perovskites occurs in the non-Pv-Pnma phase of CsPbI3 below 10 GPa.
Highly selective demethylation of anisole to phenol over H4Nb2O7 modified MoS2 catalyst
Authors: Ji Na , Wang Zhenjiao , Diao Xinyong , Jia Zhichao , Li Tingting , Zhao Yujun , Liu Qingling , Lu Xuebin , Ma Degang , Song Chunfeng
Published: January 2021

H4Nb2O7 modified MoS2 catalyst enables the highly selective demethylation of anisole to phenol which opens a window for the hydrogenolysis of lignin to value-added chemicals.
Treating octasilanol [Si8O12][OH]8 with tetramethoxysilane and trimethoxyvinylsilane: a halogen-free synthetic route to alkoxysilyl-substituted double-four-ring siloxanes
Authors: Nozawa Takeshi , Kobayashi Toshiaki , Matsumoto Tomohiro , Yagihashi Fujio , Sato Kazuhiko , Igarashi Masayasu
Published: January 2021

A halogen-free synthesis of methoxysilyl-substituted double-four-ring (D4R) siloxanes [Si8O12][OSiR(OMe)2] (R = OMe or vinyl) was accomplished.
Defining silica–water interfacial chemistry under nanoconfinement using lanthanides
Authors: Ilgen Anastasia G. , Kabengi Nadine , Leung Kevin , Ilani-Kashkouli Poorandokht , Knight Andrew W. , Loera Lourdes
Published: January 2021

A quarter of Earth's land surface is covered by porous sedimentary silicate rocks, so silica–water interfaces are critical to the fate and transport of chemical species on a global-scale.
Emerging investigator series: 3D graphene anchored zerovalent Fe/Cu aerogel activating persulfate for efficiently 2,4 dichlorophenol degradation over a broad pH range
Authors: Liu Kai , Li Mengran , Zhu Zhenlong , Gao Baolin , Zeng Haicen , Ma Yibing , Fang Liping
Published: January 2021

3D graphene anchored zerovalent metal aerogel as an alternative route for the efficient removal of organic pollutants from wastewater.
Biochanin A alleviates oxidative damage caused by the urban particulate matter
Authors: Xue Zhaohui , Gao Xin , Yu Wancong , Zhang Qian , Song Weichen , Li Shihao , Zheng Xu , Kou Xiaohong
Published: January 2021

The mechanism of BCA against WS-UPM-induced oxidative damage.
Sequential capillarity-assisted particle assembly in a microfluidic channel
Authors: Pioli Roberto , Fernandez-Rodriguez Miguel Angel , Grillo Fabio , Alvarez Laura , Stocker Roman , Isa Lucio , Secchi Eleonora
Published: January 2021

Exploiting capillarity, a new microfluidic platform enables the placement of multiple colloidal particles into complex patterns within a microchannel, as required in a variety of applications, including electronics, sensing, and plasmonics.
The fabrication of phospholipid vesicle-based artificial cells and their functions
Authors: Zhang Xunan , Shao Xiaotong , Cai Zhenzhen , Yan Xinyu , Zong Wei
Published: January 2021

Phospholipid vesicles as artificial cells are used to simulate the cellular structure and function.
A direct Z-scheme mechanism for selective hydrogenation of aromatic nitro compounds over a hybrid photocatalyst composed of ZnIn2S4 and WO3 nanorods
Authors: Liang Zhi-Yu , Huang Ren-Kun , Liang Ruo-Wen , Xie Dan-Hua , Yan Gui-Yang
Published: January 2021

A direct Z-scheme mechanism photocatalyst constructed from ZnIn2S4 and WO3 is a versatile photoredox platform for selective hydrogenation and environmental remediation.
Mukaiyama aldol reaction catalyzed by (benz)imidazolium-based halogen bond donors
Authors: Sutar Revannath L. , Erochok Nikita , Huber Stefan M.
Published: January 2021

A Mukaiyama aldol reaction can be catalyzed by bidentate halogen bond donors with very high efficiency. The halogenated catalysts were stable over multiple consecutive runs, which supports the halogen-bond-based mode of catalysis.
CaCO3blowing agent mixing method for biomass composites improved buffer packaging performance
Authors: Sun Kai-qiang , Li Fang-yi , Li Jian-yong , Li Jian-feng , Zhang Chuan-wei , Ji Mao-cheng , Guo Zi-yu
Published: January 2021

Biodegradable composites with an open-cell structure were developed to replace petroleum-based buffer packaging materials.
Organic dots (O-dots) for theranostic applications: preparation and surface engineering
Authors: Shiralizadeh Dezfuli Amin , Kohan Elmira , Tehrani Fateh Sepand , Alimirzaei Neda , Arzaghi Hamidreza , Hamblin Michael R.
Published: January 2021

Organic dots is a term used to represent materials including graphene quantum dots and carbon quantum dots because they rely on the presence of other atoms (O, H, and N) for their photoluminescence or fluorescence properties. Cargo delivery, bio-imaging, photodynamic therapy and photothermal therapy are major biomedical applications of organic dots.
Hemin-doped metal–organic frameworks based nanozyme electrochemical sensor with high stability and sensitivity for dopamine detection
Authors: Kang Kai , Wang Beibei , Ji Xueping , Liu Yuheng , Zhao Wenrui , Du Yaqing , Guo Zhiyong , Ren Jujie
Published: January 2021

Hemin-doped-HKUST-1 nanozyme has been successfully synthesized and used for dopamine detection with excellent reproducibility, stability and anti-interference.
Red/green-light emission in continuous dielectric phase transition materials: [Me3NVinyl]2[MnX4] (X = Cl, Br)
Authors: Li Yanyan , Lin Liting , Yang Jie , Qian Kun , Jiang Tao , Li Hong
Published: January 2021

The luminescence of dielectric phase transition materials is one important property for technological applications, such as low-energy electron excitation.
A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation
Authors: Abboud Skander A. , Cisse El hadji , Doudeau Michel , Bénédetti Hélène , Aucagne Vincent
Published: January 2021

We herein describe a straightforward approach for the introduction of a solubilizing tag on N-terminal cysteinyl segments used in native chemical ligation-based protein chemical synthesis. Conveniently, the tag is removed during the ligation.
A resilient and lightweight bacterial cellulose-derived C/rGO aerogel-based electromagnetic wave absorber integrated with multiple functions
Authors: Bai Tiantian , Guo Yan , Wang Dedong , Liu Hu , Song Gang , Wang Yaming , Guo Zhanhu , Liu Chuntai , Shen Changyu
Published: January 2021

A resilient and lightweight bacterial cellulose-derived C/rGO aerogel-based electromagnetic wave absorber integrated with multiple functions such as piezoresistive sensing, infrared stealth, thermal insulation, and Joule heating.
Extraordinary magnetic field effects on the LC phases of homochiral and racemic 4-cyanoresorcinol-based diamagnetic bent-core mesogens
Authors: Ocak Hale , Bilgin Eran Belkız , Nuray Sevgi , Özkonstanyan Aykun , Poppe Silvio , Tschierske Carsten
Published: January 2021

A huge effect of a magnetic field on the layer spacing of smectic and polar smectic liquid crystalline phases of a diamagnetic bent-core mesogen is reported, which is opposite for the uniformly chiral compound and its racemic mixture.
S2D2: Small-scale Significant substructure DBSCAN Detection
Authors: González Marta , Joncour Isabelle , Buckner Anne S. M. , Khorrami Zeinhab , Moraux Estelle , Lumsden Stuart L. , Clark Paul , Oudmaijer René D. , Blanco José Manuel , de la Calle Ignacio , Herrera-Fernandez José María , Salgado Jesús J. , Valero-Martín Luis , Torres Zoe , Hacar Álvaro , Ulla Ana
Published: January 2021

Context.The spatial and dynamical structure of star-forming regions can offer insights into stellar formation patterns. The amount of data from current and upcoming surveys calls for robust and objective procedures for detecting structures in order to statistically analyse the various regions and compare them.

Aims.We aim to provide the community with a tool capable of detecting, above random expectations, the small-scale significant structure in star-forming regions that could serve as an imprint of the stellar formation process. The tool makes use of the one-point correlation function to determine an appropriate length scale forϵand uses nearest-neighbour statistics to determine a minimum number of pointsNminfor the DBSCAN algorithm in the neighbourhood ofϵ.

Methods.We implemented the procedure and applied it to synthetic star-forming regions of different nature and characteristics to obtain its applicability range. We also applied the method to observed star-forming regions to demonstrate its performance in realistic circumstances and to analyse its results.

Results.The procedure successfully detects significant small-scale substructures in heterogeneous regions, fulfilling the goals it was designed for and providing very reliable structures. The analysis of regions close to complete spatial randomness (Q ∈ [0.7, 0.87]) shows that even when some structure is present and recovered, it is hardly distinguishable from spurious detection in homogeneous regions due to projection effects. Thus, any interpretation should be done with care. For concentrated regions, we detect a main structure surrounded by smaller ones, corresponding to the core plus some Poisson fluctuations around it. We argue that these structures do not correspond to the small compact regions we are looking for. In some realistic cases, a more complete hierarchical, multi-scale analysis would be needed to capture the complexity of the region.

Conclusions.We carried out implementations of our procedure and devised a catalogue of the Nested Elementary STructures (NESTs) detected as a result in four star-forming regions (Taurus, IC 348, Upper Scorpius, and Carina). This catalogue is being made publicly available to the community. Implementations of the 3D versionsof the procedure, as well as up to 6D versions, including proper movements, are in progress and will be provided in a future work.
Analytic, dust-independent mass-loss rates for red supergiant winds initiated by turbulent pressure
Authors: Kee N. D. , Sundqvist J. O. , Decin L. , de Koter A. , Sana H.
Published: January 2021

Context.Red supergiants are observed to undergo vigorous mass loss. However, to date, no theoretical model has succeeded in explaining the origins of these objects’ winds. This strongly limits our understanding of red supergiant evolution and Type II-P and II-L supernova progenitor properties.

Aims.We examine the role that vigorous atmospheric turbulence may play in initiating and determining the mass-loss rates of red supergiant stars.

Methods.We analytically and numerically solve the equations of conservation of mass and momentum, which we later couple to an atmospheric temperature structure, to obtain theoretically motivated mass-loss rates. We then compare these to state-of-the-art empirical mass-loss rate scaling formulae as well as observationally inferred mass-loss rates of red supergiants.

Results.We find that the pressure due to the characteristic turbulent velocities inferred for red supergiants is sufficient to explain the mass-loss rates of these objects in the absence of the normally employed opacity from circumstellar dust. Motivated by this initial success, we provide a first theoretical and fully analytic mass-loss rate prescription for red supergiants. We conclude by highlighting some intriguing possible implications of these rates for future studies of stellar evolution, especially in light of the lack of a direct dependence on metallicity.
Nuclear de-excitation lines as a probe of low-energy cosmic rays
Authors: Liu Bing , Yang Rui-zhi , Aharonian Felix
Published: January 2021

Low-energy cosmic rays (LECRs) contribute substantially to the energy balance of the interstellar medium. They play also significant role in the heating and chemistry of gas, and, consequently, on the star formation process. Because of the slow propagation coupled with enhanced energy losses of subrelativistic particles, LECRs are concentrated around their acceleration sites. LECRs effectively interact with the ambient gas through nuclear reactions. Although these processes are energetically less effective compared to heating and ionization, they are extremely important from the point of view of nuclear de-excitation lines, which carry unique information about LECRs. We present results on production of de-excitation lines combining the numerical treatment of nuclear reactions using the code TALYS, with the propagation and energy losses of LECRs.