Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Virology
Title: Full-genome sequences of the first two SARS-CoV-2 viruses from India
Abstract: Background & objectives: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020. Methods: Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken. Results: Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population. Interpretation & conclusions: The two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.
Extracted statement — Has method: sequencing
Research field: Virology
Title: Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020
Abstract: The first case of coronavirus disease (COVID-19) in Finland was confirmed on 29 January 2020. No secondary cases were detected. We describe the clinical picture and laboratory findings 3–23 days since the first symptoms. The SARS-CoV-2/Finland/1/2020 virus strain was isolated, the genome showing a single nucleotide substitution to the reference strain from Wuhan. Neutralising antibody response appeared within 9 days along with specific IgM and IgG response, targeting particularly nucleocapsid and spike proteins.
Extracted statement — patient characteristics: symptoms
Research field: Virology
Title: Broad anti-coronaviral activity of FDA approved drugs against SARS-CoV-2 in vitro and SARS-CoV in vivo
Abstract: Abstract SARS-CoV-2 emerged in China at the end of 2019 and has rapidly become a pandemic with roughly 2.7 million recorded COVID-19 cases and greater than 189,000 recorded deaths by April 23rd, 2020 (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.WHO.org">www.WHO.org</jats:ext-link>). There are no FDA approved antivirals or vaccines for any coronavirus, including SARS-CoV-2. Current treatments for COVID-19 are limited to supportive therapies and off-label use of FDA approved drugs. Rapid development and human testing of potential antivirals is greatly needed. A quick way to test compounds with potential antiviral activity is through drug repurposing. Numerous drugs are already approved for human use and subsequently there is a good understanding of their safety profiles and potential side effects, making them easier to fast-track to clinical studies in COVID-19 patients. Here, we present data on the antiviral activity of 20 FDA approved drugs against SARS-CoV-2 that also inhibit SARS-CoV and MERS-CoV. We found that 17 of these inhibit SARS-CoV-2 at a range of IC50 values at non-cytotoxic concentrations. We directly follow up with seven of these to demonstrate all are capable of inhibiting infectious SARS-CoV-2 production. Moreover, we have evaluated two of these, chloroquine and chlorpromazine, in vivo using a mouse-adapted SARS-CoV model and found both drugs protect mice from clinical disease.
Extracted statement — Has participant: virus
Research field: Virology
Title: Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs
Abstract: Drug repositioning is the only feasible option to immediately address the COVID-19 global challenge. We screened a panel of 48 FDA-approved drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which were preselected by an assay of SARS-CoV. We identified 24 potential antiviral drug candidates against SARS-CoV-2 infection. Some drug candidates showed very low 50% inhibitory concentrations (IC 50 s), and in particular, two FDA-approved drugs—niclosamide and ciclesonide—were notable in some respects.
Extracted statement — Has participant: virus
Research field: Virology
Title: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication
Abstract: A novel coronavirus, named SARS-CoV-2, emerged in 2019 from Hubei region in China and rapidly spread worldwide. As no approved therapeutics exists to treat Covid-19, the disease associated to SARS-Cov-2, there is an urgent need to propose molecules that could quickly enter into clinics. Repurposing of approved drugs is a strategy that can bypass the time consuming stages of drug development. In this study, we screened the Prestwick Chemical Library® composed of 1,520 approved drugs in an infected cell-based assay. 90 compounds were identified. The robustness of the screen was assessed by the identification of drugs, such as Chloroquine derivatives and protease inhibitors, already in clinical trials. The hits were sorted according to their chemical composition and their known therapeutic effect, then EC50 and CC50 were determined for a subset of compounds. Several drugs, such as Azithromycine, Opipramol, Quinidine or Omeprazol present antiviral potency with 2<EC50<20µM. By providing new information on molecules inhibiting SARS-CoV-2 replication in vitro, this study could contribute to the short-term repurposing of drugs against Covid-19.
Extracted statement — Has participant: virus
Research field: Virology
Title: Human organ chip-enabled pipeline to rapidly repurpose therapeutics during viral pandemics
Abstract: The rising threat of pandemic viruses, such as SARS-CoV-2, requires development of new preclinical discovery platforms that can more rapidly identify therapeutics that are active in vitro and also translate in vivo. Here we show that human organ-on-a-chip (Organ Chip) microfluidic culture devices lined by highly differentiated human primary lung airway epithelium and endothelium can be used to model virus entry, replication, strain-dependent virulence, host cytokine production, and recruitment of circulating immune cells in response to infection by respiratory viruses with great pandemic potential. We provide a first demonstration of drug repurposing by using oseltamivir in influenza A virus-infected organ chip cultures and show that co-administration of the approved anticoagulant drug, nafamostat, can double oseltamivir’s therapeutic time window. With the emergence of the COVID-19 pandemic, the Airway Chips were used to assess the inhibitory activities of approved drugs that showed inhibition in traditional cell culture assays only to find that most failed when tested in the Organ Chip platform. When administered in human Airway Chips under flow at a clinically relevant dose, one drug – amodiaquine - significantly inhibited infection by a pseudotyped SARS-CoV-2 virus. Proof of concept was provided by showing that amodiaquine and its active metabolite (desethylamodiaquine) also significantly reduce viral load in both direct infection and animal-to-animal transmission models of native SARS-CoV-2 infection in hamsters. These data highlight the value of Organ Chip technology as a more stringent and physiologically relevant platform for drug repurposing, and suggest that amodiaquine should be considered for future clinical testing.
Extracted statement — Has participant: virus
Research field: Virology
Title: Discovery, Synthesis, And Structure-Based Optimization of a Series ofN-(tert-Butyl)-2-(N-arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CL Protease
Abstract: A high-throughput screen of the NIH molecular libraries sample collection and subsequent optimization of a lead dipeptide-like series of severe acute respiratory syndrome (SARS) main protease (3CLpro) inhibitors led to the identification of probe compound ML188 (16-(R), (R)-N-(4-(tert-butyl)phenyl)-N-(2-(tert-butylamino)-2-oxo-1-(pyridin-3-yl)ethyl)furan-2-carboxamide, Pubchem CID: 46897844). Unlike the majority of reported coronavirus 3CLpro inhibitors that act via covalent modification of the enzyme, 16-(R) is a noncovalent SARS-CoV 3CLpro inhibitor with moderate MW and good enzyme and antiviral inhibitory activity. A multicomponent Ugi reaction was utilized to rapidly explore structure-activity relationships within S(1'), S(1), and S(2) enzyme binding pockets. The X-ray structure of SARS-CoV 3CLpro bound with 16-(R) was instrumental in guiding subsequent rounds of chemistry optimization. 16-(R) provides an excellent starting point for the further design and refinement of 3CLpro inhibitors that act by a noncovalent mechanism of action.
Extracted statement — Has participant: virus
Research field: Virology
Title: Identification of potential treatments for COVID-19 through artificial intelligence-enabled phenomic analysis of human cells infected with SARS-CoV-2
Abstract: Abstract To identify potential therapeutic stop-gaps for SARS-CoV-2, we evaluated a library of 1,670 approved and reference compounds in an unbiased, cellular image-based screen for their ability to suppress the broad impacts of the SARS-CoV-2 virus on phenomic profiles of human renal cortical epithelial cells using deep learning. In our assay, remdesivir is the only antiviral tested with strong efficacy, neither chloroquine nor hydroxychloroquine have any beneficial effect in this human cell model, and a small number of compounds not currently being pursued clinically for SARS-CoV-2 have efficacy. We observed weak but beneficial class effects of β-blockers, mTOR/PI3K inhibitors and Vitamin D analogues and a mild amplification of the viral phenotype with β-agonists.
Extracted statement — Has participant: virus
Research field: Work, Economy and Organizations
Title: An investigation of skill requirements for business and data analytics positions: A content analysis of job advertisements
Abstract: Abstract Presently, analytics degree programs exhibit a growing trend to meet a strong market demand. To explore the skill sets required for analytics positions, the authors examined a sample of online job postings related to professions such as business analyst (BA), business intelligence analyst (BIA), data analyst (DA), and data scientist (DS) using content analysis. They present a ranked list of relevant skills belonging to specific skills categories for the studied positions. Also, they conducted a pairwise comparison between DA and DS as well as BA and BIA. Overall, the authors observed that decision making, organization, communication, and structured data management are key to all job categories. The analysis shows that technical skills like statistics and programming skills are in most demand for DAs. The analysis is useful for creating clear definitions with respect to required skills for job categories in the business and data analytics domain and for designing course curricula for this domain.
Extracted statement — method: comparison
Research field: Photonics
Title: Graphene Interdigital Electrodes for Improving Sensitivity in a Ga2O3:Zn Deep-Ultraviolet Photoconductive Detector
Abstract: Graphene (Gr) has been widely used as a transparent electrode material for photodetectors because of its high conductivity and high transmittance in recent years. However, the current low-efficiency manipulation of Gr has hindered the arraying and practical use of such detectors. We invented a multistep method of accurately tailoring graphene into interdigital electrodes for fabricating a sensitive, stable deep-ultraviolet photodetector based on Zn-doped Ga2O3 films. The fabricated photodetector exhibits a series of excellent performance, including extremely low dark current (∼10-11 A), an ultrahigh photo-to-dark ratio (>105), satisfactory responsivity (1.05 A/W), and excellent selectivity for the deep-ultraviolet band, compared to those with ordinary metal electrodes. The raise of photocurrent and responsivity is attributed to the increase of incident photons through Gr and separated carriers caused by the built-in electric field formed at the interface of Gr and Ga2O3:Zn films. The proposed ideas and methods of tailoring Gr can not only improve the performance of devices but more importantly contribute to the practical development of graphene.
Extracted statement — keywords: Electrodes
Research field: Photonics
Title: High Performance of Solution-Processed Amorphous p-Channel Copper-Tin-Sulfur-Gallium Oxide Thin-Film Transistors by UV/O3 Photocuring
Abstract: The development of p-type metal-oxide semiconductors (MOSs) is of increasing interest for applications in next-generation optoelectronic devices, display backplane, and low-power-consumption complementary MOS circuits. Here, we report the high performance of solution-processed, p-channel copper-tin-sulfide-gallium oxide (CTSGO) thin-film transistors (TFTs) using UV/O3 exposure. Hall effect measurement confirmed the p-type conduction of CTSGO with Hall mobility of 6.02 ± 0.50 cm2 V-1 s-1. The p-channel CTSGO TFT using UV/O3 treatment exhibited the field-effect mobility (μFE) of 1.75 ± 0.15 cm2 V-1 s-1 and an on/off current ratio (ION/IOFF) of ∼104 at a low operating voltage of -5 V. The significant enhancement in the device performance is due to the good p-type CTSGO material, smooth surface morphology, and fewer interfacial traps between the semiconductor and the Al2O3 gate insulator. Therefore, the p-channel CTSGO TFT can be applied for CMOS MOS TFT circuits for next-generation display.
Extracted statement — keywords: Semiconductors
Research field: Photonics
Title: High Performance of Solution-Processed Amorphous p-Channel Copper-Tin-Sulfur-Gallium Oxide Thin-Film Transistors by UV/O3 Photocuring
Abstract: The development of p-type metal-oxide semiconductors (MOSs) is of increasing interest for applications in next-generation optoelectronic devices, display backplane, and low-power-consumption complementary MOS circuits. Here, we report the high performance of solution-processed, p-channel copper-tin-sulfide-gallium oxide (CTSGO) thin-film transistors (TFTs) using UV/O3 exposure. Hall effect measurement confirmed the p-type conduction of CTSGO with Hall mobility of 6.02 ± 0.50 cm2 V-1 s-1. The p-channel CTSGO TFT using UV/O3 treatment exhibited the field-effect mobility (μFE) of 1.75 ± 0.15 cm2 V-1 s-1 and an on/off current ratio (ION/IOFF) of ∼104 at a low operating voltage of -5 V. The significant enhancement in the device performance is due to the good p-type CTSGO material, smooth surface morphology, and fewer interfacial traps between the semiconductor and the Al2O3 gate insulator. Therefore, the p-channel CTSGO TFT can be applied for CMOS MOS TFT circuits for next-generation display.
Extracted statement — keywords: Transistors
Research field: electrical engineering
Title: Solution-processed high-performance p-channel copper tin sulfide thin-film transistors
Abstract: <p>We introduce a solution-processed copper tin sulfide (CTS) thin film to realize high-performance of thin-film transistors (TFT) by optimizing the CTS precursor solution concentration.</p>
Extracted statement — keywords: Transistors
Research field: chemical engineering
Title: Disorder–Order Transition—Improving the Moisture Sensitivity of Waterborne Nanocomposite Barriers
Abstract: Systematic studies on the influence of crystalline vs disordered nanocomposite structures on barrier properties and water vapor sensitivity are scarce as it is difficult to switch between the two morphologies without changing other critical parameters. By combining water-soluble poly(vinyl alcohol) (PVOH) and ultrahigh aspect ratio synthetic sodium fluorohectorite (Hec) as filler, we were able to fabricate nanocomposites from a single nematic aqueous suspension by slot die coating that, depending on the drying temperature, forms different desired morphologies. Increasing the drying temperature from 20 to 50 °C for the same formulation triggers phase segregation and disordered nanocomposites are obtained, while at room temperature, one-dimensional (1D) crystalline, intercalated hybrid Bragg Stacks form. The onset of swelling of the crystalline morphology is pushed to significantly higher relative humidity (RH). This disorder-order transition renders PVOH/Hec a promising barrier material at RH of up to 65%, which is relevant for food packaging. The oxygen permeability (OP) of the 1D crystalline PVOH/Hec is an order of magnitude lower compared to the OP of the disordered nanocomposite at this elevated RH (OP = 0.007 cm3 μm m-2 day-1 bar-1 cf. OP = 0.047 cm3 μm m-2 day-1 bar-1 at 23 °C and 65% RH).
Extracted statement — Solvent: water
Research field: Agricultural and Resource Economics
Title: Farm Households' Simultaneous Use of Sources to Access Information on Cotton Crop Production
Abstract: ABSTRACT This study has investigated farm households' simultaneous use of social networks, field extension, traditional media, and modern information and communication technologies (ICTs) to access information on cotton crop production. The study was based on a field survey, conducted in Punjab, Pakistan. Data were collected from 399 cotton farm households using the multistage sampling technique. Important combinations of information sources were found in terms of their simultaneous use to access information. The study also examined the factors influencing the use of various available information sources. A multivariate probit model was used considering the correlation among the use of social networks, field extension, traditional media, and modern ICTs. The findings indicated the importance of different socioeconomic and institutional factors affecting farm households' use of available information sources on cotton production. Important policy conclusions are drawn based on findings.
Extracted statement — data collection:  Field survey
Research field: Agricultural and Resource Economics
Title: Farm Households' Simultaneous Use of Sources to Access Information on Cotton Crop Production
Abstract: ABSTRACT This study has investigated farm households' simultaneous use of social networks, field extension, traditional media, and modern information and communication technologies (ICTs) to access information on cotton crop production. The study was based on a field survey, conducted in Punjab, Pakistan. Data were collected from 399 cotton farm households using the multistage sampling technique. Important combinations of information sources were found in terms of their simultaneous use to access information. The study also examined the factors influencing the use of various available information sources. A multivariate probit model was used considering the correlation among the use of social networks, field extension, traditional media, and modern ICTs. The findings indicated the importance of different socioeconomic and institutional factors affecting farm households' use of available information sources on cotton production. Important policy conclusions are drawn based on findings.
Extracted statement — Econometric model: Multivariate probit model
Research field: Agricultural and Resource Economics
Title: Socio-economic Factors Affecting Adoption of Modern Information and Communication Technology by Farmers in India: Analysis Using Multivariate Probit Model
Abstract: Abstract Purpose: The paper analyzes factors that affect the likelihood of adoption of different agriculture-related information sources by farmers. Design/Methodology/Approach: The paper links the theoretical understanding of the existing multiple sources of information that farmer use, with the empirical model to analyze the factors that affect the farmer's adoption of different agriculture-related information sources. The analysis is done using a multivariate probit model and primary survey data of 1,200 farmer households of five Indo-Gangetic states of India, covering 120 villages. Findings: The results of the study highlight that farmer's age, education level and farm size influence farmer's behaviour in selecting different sources of information. The results show that farmers use multiple information sources, that may be complementary or substitutes to each other and this also implies that any single source does not satisfy all information needs of the farmer. Practical implication: If we understand the likelihood of farmer's choice of source of information then direction can be provided and policies can be developed to provide information through those sources in targeted regions with the most effective impact. Originality/Value: Information plays a key role in a farmer's life by enhancing their knowledge and strengthening their decision-making ability. Farmers use multiple sources of information as no one source is sufficient in itself.
Extracted statement — Econometric model: Multivariate probit model
Research field: Agricultural and Resource Economics
Title: Factors Influencing the Selection of Precision Farming Information Sources by Cotton Producers
Abstract: <jats:p>Precision farming information demanded by cotton producers is provided by various suppliers, including consultants, farm input dealerships, University Extension systems, and media sources. Factors associated with the decisions to select among information sources to search for precision farming information are analyzed using a multivariate probit regression accounting for correlation among the different selection decisions. Factors influencing these decisions are age, education, and income. These findings should be valuable to precision farming information providers who may be able to better meet their target clientele needs.</jats:p>
Extracted statement — Econometric model: Multivariate probit regression
Research field: Analytical Chemistry
Title: Exfoliated black phosphorus gas sensing properties at room temperature
Abstract: Room temperature gas sensing properties of chemically exfoliated black phosphorus (BP) to oxidizing (NO2, CO2) and reducing (NH3, H2, CO) gases in a dry air carrier have been reported. To study the gas sensing properties of BP, chemically exfoliated BP flakes have been drop casted on Si3N4 substrates provided with Pt comb-type interdigitated electrodes in N2 atmosphere. Scanning electron microscopy and x-ray photoelectron spectroscopy characterizations show respectively the occurrence of a mixed structure, composed of BP coarse aggregates dispersed on BP exfoliated few layer flakes bridging the electrodes, and a clear 2p doublet belonging to BP, which excludes the occurrence of surface oxidation. Room temperature electrical tests in dry air show a p-type response of multilayer BP with measured detection limits of 20 ppb and 10 ppm to NO2 and NH3 respectively. No response to CO and CO2 has been detected, while a slight but steady sensitivity to H2 has been recorded. The reported results confirm, on an experimental basis, what was previously theoretically predicted, demonstrating the promising sensing properties of exfoliated BP.
Extracted statement — Sensing material: Black phosphorus