bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of loop-mediated isothermal amplification (LAMP)-based assays for rapid detection of SARS-CoV-2 genes
Authors: Urrutia-Cabrera Daniel , Liou Roxanne Hsiang-Chi , Wang Jiang-Hui , Chan Jianxiong , Hung Sandy Shen-Chi , Hewitt Alex W. , Martin Keith R. , Edwards Thomas L. , Kwan Patrick , Wong Raymond Ching-Bong 
Published: November 2021

AbstractThe COVID-19 pandemic caused by SARS-CoV-2 has infected millions worldwide, therefore there is an urgent need to increase our diagnostic capacity to identify infected cases. Although RT-qPCR remains the gold standard for SARS-CoV-2 detection, this method requires specialised equipment in a diagnostic laboratory and has a long turn-around time to process the samples. To address this, several groups have recently reported the development of loop-mediated isothermal amplification (LAMP) as a simple, low cost and rapid method for SARS-CoV-2 detection. Herein we present a comparative analysis of three LAMP-based assays that target different regions of the SARS-CoV-2: ORF1ab RdRP, ORF1ab nsp3 and Gene N. We perform a detailed assessment of their sensitivity, kinetics and false positive rates for SARS-CoV-2 diagnostics in LAMP or RT-LAMP reactions, using colorimetric or fluorescent detection. Our results independently validate that all three assays can detect SARS-CoV-2 in 30 min, with robust accuracy at detecting as little as 1000 RNA copies and the results can be visualised simply by color changes. Incorporation of RT-LAMP with fluorescent detection further increases the detection sensitivity to as little as 100 RNA copies. We also note the shortcomings of some LAMP-based assays, including variable results with shorter reaction time or lower load of SARS-CoV-2, and false positive results in some experimental conditions and clinical saliva samples. Overall for RT-LAMP detection, the ORF1ab RdRP and ORF1ab nsp3 assays have faster kinetics for detection but varying degrees of false positives detection, whereas the Gene N assay exhibits no false positives in 30 min reaction time, which highlights the importance of optimal primer design to minimise false-positives in RT-LAMP. This study provides validation of the performance of LAMP-based assays as a rapid, highly sensitive detection method for SARS-CoV-2, which have important implications in development of point-of-care diagnostics for SARS-CoV-2.
Tumor volume and tumor crossing of the axial renal midline predict renal function after robotic partial nephrectomy
Authors: Ohsugi Haruyuki , Akiyama Kyojiro , Taniguchi Hisanori , Yanishi Masaaki , Sugi Motohiko , Matsuda Tadashi , Kinoshita Hidefumi 
Published: November 2021

AbstractThere are several nephrometry scoring systems for predicting surgical complexity and potential perioperative morbidity. The R.E.N.A.L. scoring system, one of the most well-known nephrometry scoring systems, emphasizes the features on which it is based (Radius, Exophytic/endophytic, Nearness to collecting system or sinus, Anterior/posterior, and Location relative to polar lines). The ability of these nephrometry scoring systems to predict loss of renal function after robotic partial nephrectomy (RPN) remains controversial. Therefore, we verified which combination of factors from nephrometry scoring systems, including tumor volume, was the most significant predictor of postoperative renal function. Patients who underwent RPN for cT1 renal tumors in our hospital were reviewed retrospectively (n = 163). The preoperative clinical data (estimated glomerular filtration rate [eGFR], comorbidities, and nephrometry scoring systems including R.E.N.A.L.) and perioperative outcomes were evaluated. We also calculated the tumor volume using the equation applied to an ellipsoid by three-dimensional computed tomography. The primary outcome was reduced eGFR, which was defined as an eGFR reduction of ≥ 20% from baseline to 6 months after RPN. Multivariable logistic regression analyses were used to evaluate the relationships between preoperative variables and reduced eGFR. Of 163 patients, 24 (14.7%) had reduced eGFR. Multivariable analyses indicated that tumor volume (cutoff value ≥ 14.11 cm3, indicating a sphere with a diameter ≥ approximately 3 cm) and tumor crossing of the axial renal midline were independent factors associated with a reduced eGFR (odds ratio [OR] 4.57; 95% confidence interval [CI] 1.69–12.30; P = 0.003 and OR 3.50; 95% CI 1.30–9.46; P = 0.034, respectively). Our classification system using these two factors showed a higher area under the receiver operating characteristic curve (AUC) than previous nephrometry scoring systems (AUC = 0.786 vs. 0.653–0.719), and it may provide preoperative information for counseling patients about renal function after RPN.
Mathematical models for thermionic emission current density of graphene emitter
Authors: Olawole Olukunle C. , De Dilip K. , Oyedepo Sunday O. , Ezema Fabian I. 
Published: November 2021

AbstractIn this study, five mathematical models were fitted in the absence of space charge with experimental data to find a more appropriate model and predict the emission current density of the graphene-based thermionic energy converter accurately. Modified Richardson Dushman model (MRDE) shows that TEC's electron emission depends on temperature, Fermi energy, work function, and coefficient of thermal expansion. Lowest Least square value of $$S=\sum {\left({J}_{th}-{J}_{exp}\right)}^{2}=0.0002 \,\text{A}^{2}/\text{m}^{4}$$

S
=
∑

J

th

-

J

exp

2

=
0.0002

A
2

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4

makes MRDE most suitable in modelling the emission current density of the graphene-based TEC over the other four tested models. The developed MRDE can be adopted in predicting the current emission density of two-dimensional materials and also future graphene-based TEC response.
Development of an orally delivered GLP-1 receptor agonist through peptide engineering and drug delivery to treat chronic disease
Authors: Pechenov Sergei , Revell Jefferson , Will Sarah , Naylor Jacqueline , Tyagi Puneet , Patel Chandresh , Liang Lihuan , Tseng Leo , Huang Yue , Rosenbaum Anton I. , Balic Kemal , Konkar Anish , Grimsby Joseph , Subramony J. Anand 
Published: November 2021

AbstractPeptide therapeutics are increasingly used in the treatment of disease, but their administration by injection reduces patient compliance and convenience, especially for chronic diseases. Thus, oral administration of a peptide therapeutic represents a significant advance in medicine, but is challenged by gastrointestinal instability and ineffective uptake into the circulation. Here, we have used glucagon-like peptide-1 (GLP-1) as a model peptide therapeutic for treating obesity-linked type 2 diabetes, a common chronic disease. We describe a comprehensive multidisciplinary approach leading to the development of MEDI7219, a GLP-1 receptor agonist (GLP-1RA) specifically engineered for oral delivery. Sites of protease/peptidase vulnerabilities in GLP-1 were removed by amino acid substitution and the peptide backbone was bis-lipidated to promote MEDI7219 reversible plasma protein binding without affecting potency. A combination of sodium chenodeoxycholate and propyl gallate was used to enhance bioavailability of MEDI7219 at the site of maximal gastrointestinal absorption, targeted by enteric-coated tablets. This synergistic approach resulted in MEDI7219 bioavailability of ~ 6% in dogs receiving oral tablets. In a dog model of obesity and insulin resistance, MEDI7219 oral tablets significantly decreased food intake, body weight and glucose excursions, validating the approach. This novel approach to the development of MEDI7219 provides a template for the development of other oral peptide therapeutics.
Health impacts of air pollution exposure from 1990 to 2019 in 43 European countries
Authors: Juginović Alen , Vuković Miro , Aranza Ivan , Biloš Valentina 
Published: November 2021

AbstractAir pollution is the fourth greatest overall risk factor for human health. Despite declining levels in Europe, air pollution still represents a major health and economic burden. We collected data from the Global Burden of Disease Study 2019 regarding overall, as well as ischemic heart disease (IHD), stroke, and tracheal, bronchus and lung cancer-specific disability adjusted life years (DALYs), years of life lost (YLL) and mortality attributable to air pollution for 43 European countries between 1990 and 2019. Concentrations of ambient particulate matter (aPM2.5), ozone, and household air pollution from solid fuels were obtained from State of Global Air 2020. We analysed changes in air pollution parameters, as well as DALYs, YLL, and mortality related to air pollution, also taking into account gross national income (GNI) and socio-demographic index (SDI). Using a novel calculation, aPM2.5 ratio (PMR) change and DALY rate ratio (DARR) change were used to assess each country’s ability to decrease its aPM2.5 pollution and DALYs to at least the extent of the European median decrease within the analysed period. Finally, we created a multiple regression model for reliably predicting YLL using aPM2.5 and household air pollution. The average annual population-weighted aPM2.5 exposure in Europe in 1990 was 20.8 μg/m3 (95% confidence interval (CI) 18.3–23.2), while in 2019 it was 33.7% lower at 13.8 μg/m3 (95% CI 12.0–15.6). There were in total 368 006 estimated deaths in Europe in 2019 attributable to air pollution, a 42.4% decrease compared to 639 052 in 1990. The majority (90.4%) of all deaths were associated with aPM2.5. IHD was the primary cause of death making up 44.6% of all deaths attributable to air pollution. The age-standardised DALY rate and YLL rate attributable to air pollution were more than 60% lower in 2019 compared to 1990. There was a strong positive correlation (r = 0.911) between YLL rate and aPM2.5 pollution in 2019 in Europe. Our multiple regression model predicts that for 10% increase in aPM2.5, YLL increases by 16.7%. Furthermore, 26 of 43 European countries had a positive DARR change. 31 of 43 European countries had a negative PMR change, thus not keeping up with the European median aPM2.5 concentration decrease. When categorising countries by SDI and GNI, countries in the higher brackets had significantly lower aPM2.5 concentration and DALY rate for IHD and stroke. Overall, air pollution levels, air pollution-related morbidity and mortality have decreased considerably in Europe in the last three decades. However, with the growing European population, air pollution remains an important public health and economic issue. Policies targeting air pollution reduction should continue to be strongly enforced to further reduce one of the greatest risk factors for human health.
MTAP-related increased erythroblast proliferation as a mechanism of polycythaemia vera
Authors: Tipgomut Chartsiam , Khuhapinant Archrob , Wilson Marieangela C. , Poldee Saiphon , Heesom Kate J. , Metheetrairut Chanatip , Sripichai Orapan , Mitrpant Chalermchai , Frayne Jan , Trakarnsanga Kongtana 
Published: November 2021

AbstractPolycythaemia vera (PV) is a haematological disorder caused by an overproduction of erythroid cells. To date, the molecular mechanisms involved in the disease pathogenesis are still ambiguous. This study aims to identify aberrantly expressed proteins in erythroblasts of PV patients by utilizing mass spectrometry-based proteomic analysis. Haematopoietic stem cells (HSCs) were isolated from newly-diagnosed PV patients, PV patients who have received cytoreductive therapy, and healthy subjects. In vitro erythroblast expansion confirmed that the isolated HSCs recapitulated the disease phenotype as the number of erythroblasts from newly-diagnosed PV patients was significantly higher than those from the other groups. Proteomic comparison revealed 17 proteins that were differentially expressed in the erythroblasts from the newly-diagnosed PV patients compared to those from healthy subjects, but which were restored to normal levels in the patients who had received cytoreductive therapy. One of these proteins was S-methyl-5′-thioadenosine phosphorylase (MTAP), which had reduced expression in PV patients’ erythroblasts. Furthermore, MTAP knockdown in normal erythroblasts was shown to enhance their proliferative capacity. Together, this study identifies differentially expressed proteins in erythroblasts of healthy subjects and those of PV patients, indicating that an alteration of protein expression in erythroblasts may be crucial to the pathology of PV.
Unidirectional Kondo scattering in layered NbS2
Authors: Martino Edoardo , Putzke Carsten , König Markus , Moll Philip J. W. , Berger Helmuth , LeBoeuf David , Leroux Maxime , Proust Cyril , Akrap Ana , Kirmse Holm , Koch Christoph , Zhang ShengNan , Wu QuanSheng , Yazyev Oleg V. , Forró László , Semeniuk Konstantin 
Published: November 2021

AbstractCrystalline defects can modify quantum interactions in solids, causing unintuitive, even favourable, properties such as quantum Hall effect or superconducting vortex pinning. Here we present another example of this notion—an unexpected unidirectional Kondo scattering in single crystals of 2H-NbS2. This manifests as a pronounced low-temperature enhancement in the out-of-plane resistivity and thermopower below 40 K, hidden for the in-plane charge transport. The anomaly can be suppressed by the c-axis-oriented magnetic field, but is unaffected by field applied along the planes. The magnetic moments originate from layers of 1T-NbS2, which inevitably form during the growth, undergoing a charge-density-wave reconstruction with each superlattice cell (David-star-shaped cluster of Nb atoms) hosting a localised spin. Our results demonstrate the unique and highly anisotropic response of a spontaneously formed Kondo-lattice heterostructure, intercalated in a layered conductor.
Mapping the irrecoverable carbon in Earth’s ecosystems
Authors: Noon Monica L. , Goldstein Allie , Ledezma Juan Carlos , Roehrdanz Patrick R. , Cook-Patton Susan C. , Spawn-Lee Seth A. , Wright Timothy Maxwell , Gonzalez-Roglich Mariano , Hole David G. , Rockström Johan , Turner Will R. 
Published: November 2021

AbstractAvoiding catastrophic climate change requires rapid decarbonization and improved ecosystem stewardship at a planetary scale. The carbon released through the burning of fossil fuels would take millennia to regenerate on Earth. Though the timeframe of carbon recovery for ecosystems such as peatlands, mangroves and old-growth forests is shorter (centuries), this timeframe still exceeds the time we have remaining to avoid the worst impacts of global warming. There are some natural places that we cannot afford to lose due to their irreplaceable carbon reserves. Here we map ‘irrecoverable carbon’ globally to identify ecosystem carbon that remains within human purview to manage and, if lost, could not be recovered by mid-century, by when we need to reach net-zero emissions to avoid the worst climate impacts. Since 2010, agriculture, logging and wildfire have caused emissions of at least 4.0 Gt of irrecoverable carbon. The world’s remaining 139.1 ± 443.6 Gt of irrecoverable carbon faces risks from land-use conversion and climate change. These risks can be reduced through proactive protection and adaptive management. Currently, 23.0% of irrecoverable carbon is within protected areas and 33.6% is managed by Indigenous peoples and local communities. Half of Earth’s irrecoverable carbon is concentrated on just 3.3% of its land, highlighting opportunities for targeted efforts to increase global climate security.
Role of sleep deprivation in immune-related disease risk and outcomes
Authors: Garbarino Sergio , Lanteri Paola , Bragazzi Nicola Luigi , Magnavita Nicola , Scoditti Egeria 
Published: November 2021

AbstractModern societies are experiencing an increasing trend of reduced sleep duration, with nocturnal sleeping time below the recommended ranges for health. Epidemiological and laboratory studies have demonstrated detrimental effects of sleep deprivation on health. Sleep exerts an immune-supportive function, promoting host defense against infection and inflammatory insults. Sleep deprivation has been associated with alterations of innate and adaptive immune parameters, leading to a chronic inflammatory state and an increased risk for infectious/inflammatory pathologies, including cardiometabolic, neoplastic, autoimmune and neurodegenerative diseases. Here, we review recent advancements on the immune responses to sleep deprivation as evidenced by experimental and epidemiological studies, the pathophysiology, and the role for the sleep deprivation-induced immune changes in increasing the risk for chronic diseases. Gaps in knowledge and methodological pitfalls still remain. Further understanding of the causal relationship between sleep deprivation and immune deregulation would help to identify individuals at risk for disease and to prevent adverse health outcomes.
Construction of poly-N-heterocyclic scaffolds via the controlled reactivity of Cu-allenylidene intermediates
Authors: Gannarapu Malla Reddy , Imai Takanori , Iwaki Kentaro , Tsuzuki Seiji , Shibata Norio 
Published: November 2021

AbstractControlling the sequence of the three consecutive reactive carbon centres of Cu-allenylidene remains a challenge. One of the impressive achievements in this area is the Cu-catalyzed annulation of 4-ethynyl benzoxazinanones, which are transformed into zwitterionic Cu-stabilized allenylidenes that are trapped by interceptors to provide the annulation products. In principle, the reaction proceeds via a preferential γ-attack, while annulation reactions via an α- or β-attack are infrequent. Herein, we describe a method for controlling the annulation mode, by the manipulation of a CF3 or CH3 substituent, to make it proceed via either a γ-attack or an α- or β-attack. The annulation of CF3-substituted substrates with sulfamate-imines furnished densely functionalized N-heterocycles with excellent enantioselectivity via a cascade of an internal β-attack and an external α-attack. CH3-variants were transformed into different heterocycles that possess a spiral skeleton, via a cascade of an internal β-attack and a hydride α-migration followed by a Diels−Alder reaction.
Contact spacing controls the on-current for all-carbon field effect transistors
Authors: Özdemir Ali Deniz , Barua Pramit , Pyatkov Felix , Hennrich Frank , Chen Yuan , Wenzel Wolfgang , Krupke Ralph , Fediai Artem 
Published: November 2021

AbstractAll-carbon field-effect transistors, which combine carbon nanotubes and graphene hold great promise for many applications such as digital logic devices and single-photon emitters. However, the understanding of the physical properties of carbon nanotube (CNT)/graphene hybrid systems in such devices remained limited. In this combined experimental and theoretical study, we use a quantum transport model for field-effect transistors based on graphene electrodes and CNT channels to explain the experimentally observed low on currents. We find that large graphene/CNT spacing and short contact lengths limit the device performance. We have also elucidated in this work the experimentally observed ambipolar transport behavior caused by the flat conduction- and valence-bands and describe non-ideal gate-control of the contacts and channel region by the quantum capacitance of graphene and the carbon nanotube. We hope that our insights will accelerate the design of efficient all-carbon field-effect transistors.
Predicting synthesizability of crystalline materials via deep learning
Authors: Davariashtiyani Ali , Kadkhodaie Zahra , Kadkhodaei Sara 
Published: November 2021

AbstractPredicting the synthesizability of hypothetical crystals is challenging because of the wide range of parameters that govern materials synthesis. Yet, exploring the exponentially large space of novel crystals for any future application demands an accurate predictive capability for synthesis likelihood to avoid a haphazard trial-and-error. Typically, benchmarks of synthesizability are defined based on the energy of crystal structures. Here, we take an alternative approach to select features of synthesizability from the latent information embedded in crystalline materials. We represent the atomic structure of crystalline materials by three-dimensional pixel-wise images that are color-coded by their chemical attributes. The image representation of crystals enables the use of a convolutional encoder to learn the features of synthesizability hidden in structural and chemical arrangements of crystalline materials. Based on the presented model, we can accurately classify materials into synthesizable crystals versus crystal anomalies across a broad range of crystal structure types and chemical compositions. We illustrate the usefulness of the model by predicting the synthesizability of hypothetical crystals for battery electrode and thermoelectric applications.
Drivers of the evolution and amplitude of African Humid Periods
Authors: Menviel Laurie , Govin Aline , Avenas Arthur , Meissner Katrin J. , Grant Katharine M. , Tzedakis Polychronis C. 
Published: November 2021

AbstractDuring orbital precession minima, the Sahara was humid and more vegetated, providing potential corridors for Hominins migration. Uncertainties remain over the climatic processes controlling the initiation, demise and amplitude of these African Humid Periods. Here we study these processes using a series of transient simulations of the penultimate deglaciation and Last Interglacial period, and compare the results with a transient simulation of the last deglaciation and Holocene. We find that the strengthening of the Atlantic Meridional Overturning Circulation at the end of deglacial millennial-scale events exerts a dominant control on the abrupt initiation of African Humid Periods as the Atlantic Meridional Overturning Circulation modulates the position of the Intertropical Convergence Zone. In addition, residual Northern Hemispheric ice-sheets can delay the peak of the African Humid Period. Through its impact on Northern Hemispheric ice-sheets disintegration and thus Atlantic Meridional Overturning Circulation, the larger rate of insolation increase during the penultimate compared to the last deglaciation can explain the earlier and more abrupt onset of the African Humid Period during the Last Interglacial period. Finally, we show that the mean climate state modulates precipitation variability, with higher variability under wetter background conditions.