bluuebunny/crossref_metadata_2025_split 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

AbstractThe 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

AbstractTopological 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

AbstractExisting 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

AbstractThe 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

AbstractPro-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

AbstractAberrant 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

AbstractThird-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

AbstractProtein 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.
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

AbstractInflammation 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

AbstractPolarization 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

AbstractTo 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

AbstractIn 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

AbstractInterfacial 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

AbstractPresent 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.