positive_augmented_dataset.csv

prpnt_basic_id,prpnt_basic_doi,prpnt_basic_title,prpnt_basic_display_name,prpnt_basic_publication_year,prpnt_basic_publication_date,prpnt_basic_language,prpnt_basic_type,prpnt_basic_type_crossref,prpnt_source_journal_name,prpnt_source_issn,prpnt_source_issn_l,prpnt_source_publisher,prpnt_source_type,prpnt_metrics_cited_by_count,prpnt_metrics_is_retracted,prpnt_metrics_fwci,prpnt_metrics_referenced_works_count,prpnt_classification_primary_topic_name,prpnt_classification_primary_topic_score,prpnt_classification_primary_topic_field,prpnt_classification_primary_topic_subfield,prpnt_access_is_oa,prpnt_access_oa_status,prpnt_access_oa_url,prpnt_access_pdf_url,prpnt_access_license,prpnt_abstract,prpnt_authors_position,prpnt_authors_name,prpnt_authors_id,prpnt_authors_orcid,prpnt_authors_is_corresponding,article_basic_id,article_basic_doi,article_basic_title,article_basic_display_name,article_basic_publication_year,article_basic_publication_date,article_basic_language,article_basic_type,article_basic_type_crossref,article_source_journal_name,article_source_issn,article_source_issn_l,article_source_publisher,article_source_type,article_metrics_cited_by_count,article_metrics_is_retracted,article_metrics_fwci,article_metrics_referenced_works_count,article_classification_primary_topic_name,article_classification_primary_topic_score,article_classification_primary_topic_field,article_classification_primary_topic_subfield,article_access_is_oa,article_access_oa_status,article_access_oa_url,article_access_pdf_url,article_access_license,article_abstract,article_authors_position,article_authors_name,article_authors_id,article_authors_orcid,article_authors_is_corresponding
https://openalex.org/W2020559395,https://doi.org/10.5194/acpd-11-3071-2011,A regional chemical transport modeling to identify the influences of biomass burning during 2006 BASE-ASIA,A regional chemical transport modeling to identify the influences of biomass burning during 2006 BASE-ASIA,2011,2011-01-28,en,article,posted-content,,,,,,9,False,1.02,86,Atmospheric Aerosols and their Impacts,1.0,Earth and Planetary Sciences,Atmospheric Science,True,green,https://doi.org/10.5194/acpd-11-3071-2011,,cc-by,"Abstract. To evaluate the impact of biomass burning from Southeast Asia to East Asia, this study conducted numerical simulations during NASA's 2006 Biomass-burning Aerosols in South-East Asia: Smoke Impact Assessment (BASE-ASIA). Two typical episode periods (27–28 March and 13–14 April) were examined. Two emission inventories, FLAMBE and GFED, were used in the simulations. The influences during two episodes in the source region (Southeast Asia) contributed to CO, O3 and PM2.5 concentrations as high as 400 ppbv, 20 ppbv and 80 μg/m3, respectively. The perturbations with and without biomass burning of the above three species were in the range of 10 to 60%, 10 to 20% and 30 to 70%, respectively. The impact due to long-range transport could spread over the southeastern parts of East Asia and could reach about 160 to 360 ppbv, 8 to 18 ppbv and 8 to 64 μg/m3 on CO, O3 and PM2.5, respectively; the percentage impact could reach 20 to 50% on CO, 10 to 30% on O3, and as high as 70% on PM2.5. An impact pattern can be found in April, while the impact becomes slightly broader and goes up to Yangtze River Delta. Two cross-sections at 15° N and 20° N were used to compare the vertical flux of biomass burning. In the source region (Southeast Asia), CO, O3 and PM2.5 concentrations had a strong upward tendency from surface to high altitudes. The eastward transport becomes strong from 2 to 8 km in the free troposphere. The subsidence contributed 60 to 70%, 20 to 50%, and 80% on CO, O3 and PM2.5, respectively to surface in the downwind area. The study reveals the significant impact of Southeastern Asia biomass burning on the air quality in both local and downwind areas, particularly during biomass burning episodes. This modeling study might provide constraints of lower limit. An additional study is underway for an active biomass burning year to obtain an upper limit and climate effects.",first,Joshua S. Fu,https://openalex.org/A5036365752,https://orcid.org/0000-0001-5464-9225,False,https://openalex.org/W2042738430,https://doi.org/10.5194/acp-12-3837-2012,Evaluating the influences of biomass burning during 2006 BASE-ASIA: a regional chemical transport modeling,Evaluating the influences of biomass burning during 2006 BASE-ASIA: a regional chemical transport modeling,2012,2012-05-02,en,article,journal-article,Atmospheric chemistry and physics,1680-7316$@$1680-7324,1680-7316,Copernicus Publications,journal,111,False,5.993,68,Atmospheric chemistry and aerosols,1.0,Earth and Planetary Sciences,Atmospheric Science,True,gold,https://acp.copernicus.org/articles/12/3837/2012/acp-12-3837-2012.pdf,https://acp.copernicus.org/articles/12/3837/2012/acp-12-3837-2012.pdf,cc-by,"Abstract. To evaluate the impact of biomass burning from Southeast Asia to East Asia, this study conducted numerical simulations during NASA's 2006 Biomass-burning Aerosols in South-East Asia: Smoke Impact Assessment (BASE-ASIA). Two typical episode periods (27–28 March and 13–14 April) were examined. Two emission inventories, FLAMBE and GFED, were used in the simulations. The influences during two episodes in the source region (Southeast Asia) contributed to the surface CO, O3 and PM2.5 concentrations as high as 400 ppbv, 20 ppbv and 80 μg m−3, respectively. The perturbations with and without biomass burning of the above three species during the intense episodes were in the range of 10 to 60%, 10 to 20% and 30 to 70%, respectively. The impact due to long-range transport could spread over the southeastern parts of East Asia and could reach about 160 to 360 ppbv, 8 to 18 ppbv and 8 to 64 μg m−3 on CO, O3 and PM2.5, respectively; the percentage impact could reach 20 to 50% on CO, 10 to 30% on O3, and as high as 70% on PM2.5. In March, the impact of biomass burning mainly concentrated in Southeast Asia and southern China, while in April the impact becomes slightly broader and even could go up to the Yangtze River Delta region. Two cross-sections at 15° N and 20° N were used to compare the vertical flux of biomass burning. In the source region (Southeast Asia), CO, O3 and PM2.5 concentrations had a strong upward transport from surface to high altitudes. The eastward transport becomes strong from 2 to 8 km in the free troposphere. The subsidence process during the long-range transport contributed 60 to 70%, 20 to 50%, and 80% on CO, O3 and PM2.5, respectively to surface in the downwind area. The study reveals the significant impact of Southeastern Asia biomass burning on the air quality in both local and downwind areas, particularly during biomass burning episodes. This modeling study might provide constraints of lower limit. An additional study is underway for an active biomass burning year to obtain an upper limit and climate effects.",first,Joshua S. Fu,https://openalex.org/A5036365752,https://orcid.org/0000-0001-5464-9225,False
https://openalex.org/W4213260597,https://doi.org/10.31234/osf.io/6fps2,Distance perception in virtual reality: A meta-analysis of the effect of head-mounted display characteristics,Distance perception in virtual reality: A meta-analysis of the effect of head-mounted display characteristics,2022,2022-02-12,en,preprint,posted-content,,,,,,6,False,,89,Virtual Reality Applications and Impacts,0.9982,Computer Science,Human-Computer Interaction,True,green,https://psyarxiv.com/6fps2/download,https://psyarxiv.com/6fps2/download,,"Distances are commonly underperceived in virtual reality (VR), and this finding has been documented repeatedly over more than two decades of research. Yet, there is evidence that perceived distance is more accurate in modern compared to older head-mounted displays (HMDs). This meta-analysis of 131 studies describes egocentric distance perception across 20 HMDs, and also examines the relationship between perceived distance and technical HMD characteristics. Judged distance was positively associated with HMD field of view (FOV), positively associated with HMD resolution, and negatively associated with HMD weight. The effects of FOV and resolution were more pronounced among heavier HMDs. These findings suggest that future improvements in these technical characteristics may be central to resolving the problem of distance underperception in VR.",first,Jonathan W. Kelly,https://openalex.org/A5011931977,https://orcid.org/0000-0002-4317-273X,True,https://openalex.org/W4289824348,https://doi.org/10.1109/tvcg.2022.3196606,Distance Perception in Virtual Reality: A Meta-Analysis of the Effect of Head-Mounted Display Characteristics,Distance Perception in Virtual Reality: A Meta-Analysis of the Effect of Head-Mounted Display Characteristics,2022,2022-08-04,en,review,journal-article,IEEE Transactions on Visualization and Computer Graphics,1077-2626$@$1941-0506$@$2160-9306,1077-2626,Institute of Electrical and Electronics Engineers,journal,40,False,2.128,96,Virtual Reality Applications and Impacts,0.9997,Computer Science,Human-Computer Interaction,True,green,https://osf.io/6fps2/download,,,"Distances are commonly underperceived in virtual reality (VR), and this finding has been documented repeatedly over more than two decades of research. Yet, there is evidence that perceived distance is more accurate in modern compared to older head-mounted displays (HMDs). This meta-analysis, based on 137 samples from 61 publications, describes egocentric distance perception across 20 HMDs and examines the relationship between perceived distance and technical HMD characteristics. Judged distance was positively associated with HMD field of view (FOV), positively associated with HMD resolution, and negatively associated with HMD weight. The effects of FOV and resolution were more pronounced among heavier HMDs. These findings suggest that future improvements in these technical characteristics may be central to resolving the problem of distance underperception in VR.",first,Jonathan W. Kelly,https://openalex.org/A5011931977,https://orcid.org/0000-0002-4317-273X,True
https://openalex.org/W3048189011,https://doi.org/10.1101/2020.08.07.241687,Bioorthogonal red and far-red fluorogenic probes for wash-free live-cell and super-resolution microscopy,Bioorthogonal red and far-red fluorogenic probes for wash-free live-cell and super-resolution microscopy,2020,2020-08-07,en,preprint,posted-content,bioRxiv (Cold Spring Harbor Laboratory),,,Cold Spring Harbor Laboratory,repository,9,False,,46,Click Chemistry in Chemical Biology and Drug Development,0.9999,Chemistry,Organic Chemistry,True,green,https://doi.org/10.1101/2020.08.07.241687,,cc-by-nc-nd,"Abstract Small-molecule fluorophores enable the observation of biomolecules in their native context with fluorescence microscopy. Specific labelling via bioorthogonal tetrazine chemistry confers minimal label size and rapid labelling kinetics. At the same time, fluorogenic tetrazine-dye conjugates exhibit efficient quenching of dyes prior to target binding. However, live-cell compatible long-wavelength fluorophores with strong fluorogenicity have been difficult to realize. Here, we report close proximity tetrazine-dye conjugates with minimal distance between tetrazine and fluorophore. Two synthetic routes give access to a series of cell permeable and impermeable dyes including highly fluorogenic far-red emitting derivatives with electron exchange as dominant excited state quenching mechanism. We demonstrate their potential for live-cell imaging in combination with unnatural amino acids, wash-free multi-colour and super-resolution STED and SOFI imaging. These dyes pave the way for advanced fluorescence imaging of biomolecules with minimal label size.",first,Philipp Werther,https://openalex.org/A5087410446,https://orcid.org/0000-0003-1267-5614,False,https://openalex.org/W3193691807,https://doi.org/10.1021/acscentsci.1c00703,Bio-orthogonal Red and Far-Red Fluorogenic Probes for Wash-Free Live-Cell and Super-resolution Microscopy,Bio-orthogonal Red and Far-Red Fluorogenic Probes for Wash-Free Live-Cell and Super-resolution Microscopy,2021,2021-08-20,en,article,journal-article,ACS Central Science,2374-7943$@$2374-7951,2374-7943,American Chemical Society,journal,80,False,7.957,46,Click Chemistry and Applications,0.9999,Chemistry,Organic Chemistry,True,diamond,https://pubs.acs.org/doi/pdf/10.1021/acscentsci.1c00703,https://pubs.acs.org/doi/pdf/10.1021/acscentsci.1c00703,cc-by,"Small-molecule fluorophores enable the observation of biomolecules in their native context with fluorescence microscopy. Specific labeling via bio-orthogonal tetrazine chemistry combines minimal label size with rapid labeling kinetics. At the same time, fluorogenic tetrazine–dye conjugates exhibit efficient quenching of dyes prior to target binding. However, live-cell compatible long-wavelength fluorophores with strong fluorogenicity have been difficult to realize. Here, we report close proximity tetrazine–dye conjugates with minimal distance between tetrazine and the fluorophore. Two synthetic routes give access to a series of cell-permeable and -impermeable dyes including highly fluorogenic far-red emitting derivatives with electron exchange as the dominant excited-state quenching mechanism. We demonstrate their potential for live-cell imaging in combination with unnatural amino acids, wash-free multicolor and super-resolution STED, and SOFI imaging. These dyes pave the way for advanced fluorescence imaging of biomolecules with minimal label size.",first,Philipp Werther,https://openalex.org/A5087410446,https://orcid.org/0000-0003-1267-5614,False
https://openalex.org/W4244952185,https://doi.org/10.21203/rs.3.rs-62250/v1,Towards Understanding the Liver Fluke Transmission Dynamics on Farms: Detection of Liver Fluke Transmitting Snail and Liver Fluke-Specific Environmental DNA in Water Samples from an Irrigated Dairy Farm in Southeast Australia,Towards Understanding the Liver Fluke Transmission Dynamics on Farms: Detection of Liver Fluke Transmitting Snail and Liver Fluke-Specific Environmental DNA in Water Samples from an Irrigated Dairy Farm in Southeast Australia,2020,2020-08-24,en,preprint,posted-content,Research Square (Research Square),,,Research Square (United States),repository,0,False,,34,Helminth infection and control,0.9875,Veterinary,Small Animals,True,green,https://www.researchsquare.com/article/rs-62250/latest.pdf,https://www.researchsquare.com/article/rs-62250/latest.pdf,cc-by,"Abstract Background Livestock production around the world is impacted by liver fluke ( Fasciola spp.) infection resulting in serious economic losses to the beef, dairy and sheep industries with significant losses of about $90 million per annum in Australia. Liver fluke infection is predominantly controlled by anthelmintic treatment and Triclabendazole (TCBZ) is usually the drug of choice due its superior efficacy against early immature, immature and adult liver fluke stages; however, the widespread emergence of TCBZ resistance in livestock threatens liver fluke control. We are in the urgent need for alternative control measures to lower the exposure of livestock to liver fluke infection which would help to preserve the usefulness of current anthelmintic treatments. Our ability to understand the prevalence of intermediate snail hosts and infective liver fluke stages in the environment is crucial to implement alternative control measures for liver fluke control. However, identification of liver fluke and snails in the environment is hampered by lack of efficient diagnostic methods. Environmental DNA (eDNA) based identification of liver fluke and the intermediate snail host in the water bodies is a promising method to identify liver fluke and snail prevalence on farms. Our aim is to provide a proof of concept to use a molecular tool (quantitative PCR) to detect and quantify eDNA of liver fluke and snail in water bodies on Victorian farming properties for potential large-scale analysis of liver fluke and snail ecology in water bodies. Methods To demonstrate the identification of liver fluke and snail in water bodies, we used a multiplex quantitative PCR assay for the independent but simultaneous detection of eDNA released from snail ( Austropeplea tomentosa) a crucial intermediate snail host for liver fluke transmission in South-east Australia and free-living liver fluke stages ( Fasciola hepatica) . We have collected water samples from an irrigation channel over a period of 11 months in 2016 at a dairy farm located at Maffra, Victoria, South-east Australia and used water samples from selected months (February, March, May, September, October, November and December) for eDNA assay. Results The multiplex qPCR assay effectively allows for the detection and quantification of eDNA released from liver fluke life stages and snails and we observed differential levels of liver fluke and snail specific eDNA in water at the time points analysed in this study. This assay was able to detect 14 fg and 50 pg of liver fluke and snail DNA in the presence of potential inhibitors from field collected water samples. Conclusion The successful detection of eDNA specific to liver fluke and snails from the field collected water samples provides a proof of concept for the use of this method as a monitoring tool to determine the prevalence of liver fluke and liver fluke-transmitting snails in irrigation regions to allow for understanding the liver fluke transmission zones on farms to implement effective control strategies.",first,Vignesh Rathinasamy,https://openalex.org/A5065524774,https://orcid.org/0000-0002-4032-3424,False,https://openalex.org/W3126899836,https://doi.org/10.1016/j.vetpar.2021.109373,Towards understanding the liver fluke transmission dynamics on farms: Detection of liver fluke transmitting snail and liver fluke-specific environmental DNA in water samples from an irrigated dairy farm in Southeast Australia,Towards understanding the liver fluke transmission dynamics on farms: Detection of liver fluke transmitting snail and liver fluke-specific environmental DNA in water samples from an irrigated dairy farm in Southeast Australia,2021,2021-02-03,en,article,journal-article,Veterinary Parasitology,0304-4017$@$1873-2550,0304-4017,Elsevier BV,journal,16,False,1.892,36,Environmental DNA in Biodiversity Studies,0.997,Environmental Science,Ecology,True,green,https://www.researchsquare.com/article/rs-62250/latest.pdf,,,,first,Vignesh Rathinasamy,https://openalex.org/A5065524774,https://orcid.org/0000-0002-4032-3424,False
https://openalex.org/W4324046272,https://doi.org/10.21203/rs.3.rs-2640242/v1,Immunophysiology of tambaqui fed with different levels of dietary protein in a biofloc system and a clear water system,Immunophysiology of tambaqui fed with different levels of dietary protein in a biofloc system and a clear water system,2023,2023-03-13,en,preprint,posted-content,Research Square (Research Square),,,Research Square (United States),repository,0,False,,25,Aquaculture disease management and microbiota,0.9985,Immunology and Microbiology,Immunology,True,green,https://www.researchsquare.com/article/rs-2640242/latest.pdf,https://www.researchsquare.com/article/rs-2640242/latest.pdf,cc-by,"Abstract The present study evaluated the immunophysiological response in Colossoma macropomum fed with different levels of dietary protein in a biofloc system (BFS) and in clear water (CW) and under infection with Aeromonas jandaei . Juvenile tambaqui (9.20 ± 0.23 g) were fed isolipid feed with three levels of crude protein (CP) in the two production systems: BFS24, BFS28 and BFS32 and CW24, CW28 and CW32 with 24, 28 and 32% CP respectively, for 60 days. At the end of the experimental period, the physiological conditions (hematology, biochemistry, hormonal and oxidative stress) of the fish were analyzed. The results of erythrogram, cortisol, glycemia and serum biochemistry (p > 0.05) of the fish did not show significant differences between the breeding systems (BFS and CW) and the different protein levels. Tambaqui raised in the BFS showed monocytosis, thrombocytosis and higher respiratory activity of leukocytes, as well as higher glutathione (GSH) and lower malondialdehyde (MDA) values (p < 0.05). In the bacterial challenge, after induction of aeromonosis, caused by Aeromonas jandaei , greater survival of fish raised in the BFS was observed. The results suggest that, even at lower protein levels, tambaqui maintain physiological homeostasis and, therefore, it may be possible to use up to 24% CP in the diet in the biofloc system. In addition, after the bacterial infection, this system promoted greater immunological resistance in the fish.",first,Michelle Midori Sena Fugimura,https://openalex.org/A5059890817,https://orcid.org/0000-0002-1354-2277,False,https://openalex.org/W4317396516,https://doi.org/10.1007/s10499-023-01047-1,Dietary protein requirement for tambaqui cultivated in biofloc and clear water systems,Dietary protein requirement for tambaqui cultivated in biofloc and clear water systems,2023,2023-01-18,en,article,journal-article,Aquaculture International,0967-6120$@$1573-143X,0967-6120,Springer Science+Business Media,journal,7,False,4.321,50,Metabolism and Nutrition in Aquaculture Feeds,0.9999,Agricultural and Biological Sciences,Aquatic Science,False,closed,,,,,first,Raphael Brito dos Santos,https://openalex.org/A5051287609,https://orcid.org/0000-0003-2168-8759,False
https://openalex.org/W2612690603,https://doi.org/10.1101/135053,Attention is required for knowledge-based sequential grouping of syllables into words,Attention is required for knowledge-based sequential grouping of syllables into words,2017,2017-05-08,en,preprint,posted-content,bioRxiv (Cold Spring Harbor Laboratory),,,Cold Spring Harbor Laboratory,repository,0,False,,72,Neural dynamics and brain function,0.9991,Neuroscience,Cognitive Neuroscience,True,green,https://www.biorxiv.org/content/biorxiv/early/2017/05/08/135053.full.pdf,https://www.biorxiv.org/content/biorxiv/early/2017/05/08/135053.full.pdf,cc-by,"Abstract How the brain sequentially groups sensory events into temporal chunks and how this process is modulated by attention are fundamental questions in cognitive neuroscience. Sequential grouping includes bottom-up primitive grouping and top-down knowledge-based grouping. In speech perception, grouping acoustic features into syllables can rely on bottom-up acoustic continuity cues but grouping syllables into words critically relies on the listener’s lexical knowledge. This study investigates whether top-down attention is required to apply lexical knowledge to group syllables into words, by concurrently monitoring neural entrainment to syllables and words using electroencephalography (EEG). When attention is directed to a competing speech stream or cross-modally to a silent movie, neural entrainment to syllables is weakened but neural entrainment to words largely diminishes. These results strongly suggest that knowledge-based grouping of syllables into words requires top-down attention and is a bottleneck for the neural processing of unattended speech.",first,Nai Ding,https://openalex.org/A5008847016,https://orcid.org/0000-0003-3428-2723,False,https://openalex.org/W2778438370,https://doi.org/10.1523/jneurosci.2606-17.2017,Attention Is Required for Knowledge-Based Sequential Grouping: Insights from the Integration of Syllables into Words,Attention Is Required for Knowledge-Based Sequential Grouping: Insights from the Integration of Syllables into Words,2017,2017-12-18,en,article,journal-article,Journal of Neuroscience,0270-6474$@$1529-2401,0270-6474,Society for Neuroscience,journal,80,False,3.31,86,EEG and Brain-Computer Interfaces,0.9986,Neuroscience,Cognitive Neuroscience,True,hybrid,https://www.jneurosci.org/content/jneuro/38/5/1178.full.pdf,https://www.jneurosci.org/content/jneuro/38/5/1178.full.pdf,cc-by-nc-sa,"How the brain groups sequential sensory events into chunks is a fundamental question in cognitive neuroscience. This study investigates whether top–down attention or specific tasks are required for the brain to apply lexical knowledge to group syllables into words. Neural responses tracking the syllabic and word rhythms of a rhythmic speech sequence were concurrently monitored using electroencephalography (EEG). The participants performed different tasks, attending to either the rhythmic speech sequence or a distractor, which was another speech stream or a nonlinguistic auditory/visual stimulus. Attention to speech, but not a lexical-meaning-related task, was required for reliable neural tracking of words, even when the distractor was a nonlinguistic stimulus presented cross-modally. Neural tracking of syllables, however, was reliably observed in all tested conditions. These results strongly suggest that neural encoding of individual auditory events (i.e., syllables) is automatic, while knowledge-based construction of temporal chunks (i.e., words) crucially relies on top–down attention. SIGNIFICANCE STATEMENT Why we cannot understand speech when not paying attention is an old question in psychology and cognitive neuroscience. Speech processing is a complex process that involves multiple stages, e.g., hearing and analyzing the speech sound, recognizing words, and combining words into phrases and sentences. The current study investigates which speech-processing stage is blocked when we do not listen carefully. We show that the brain can reliably encode syllables, basic units of speech sounds, even when we do not pay attention. Nevertheless, when distracted, the brain cannot group syllables into multisyllabic words, which are basic units for speech meaning. Therefore, the process of converting speech sound into meaning crucially relies on attention.",first,Nai Ding,https://openalex.org/A5008847016,https://orcid.org/0000-0003-3428-2723,False
https://openalex.org/W2949817526,https://doi.org/10.1101/037101,Read-Based Phasing of Related Individuals,Read-Based Phasing of Related Individuals,2016,2016-01-18,en,preprint,posted-content,bioRxiv (Cold Spring Harbor Laboratory),,,Cold Spring Harbor Laboratory,repository,7,False,,26,Text Readability and Simplification,0.9512,Computer Science,Artificial Intelligence,True,green,https://www.biorxiv.org/content/biorxiv/early/2016/01/18/037101.full.pdf,https://www.biorxiv.org/content/biorxiv/early/2016/01/18/037101.full.pdf,,"Abstract Motivation Read-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information - reads and pedigree - has the potential to deliver results better than each individually. Results We provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2× for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15× coverage per individual. Availability https://bitbucket.org/whatshap/whatshap (branch pedmec) Contact [email protected]",first,Shilpa Garg,https://openalex.org/A5060605357,https://orcid.org/0000-0003-0200-4200,False,https://openalex.org/W2420821447,https://doi.org/10.1093/bioinformatics/btw276,Read-based phasing of related individuals,Read-based phasing of related individuals,2016,2016-06-11,en,article,journal-article,Bioinformatics,1367-4803$@$1367-4811,1367-4803,Oxford University Press,journal,44,False,7.736,28,Text Readability and Simplification,0.9452,Computer Science,Artificial Intelligence,True,hybrid,https://academic.oup.com/bioinformatics/article-pdf/32/12/i234/6695672/btw276.pdf,https://academic.oup.com/bioinformatics/article-pdf/32/12/i234/6695672/btw276.pdf,cc-by-nc,"Read-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information-reads and pedigree-has the potential to deliver results better than each individually.We provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2× for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15× coverage per individual.https://bitbucket.org/whatshap/[email protected].",first,Shilpa Garg,https://openalex.org/A5060605357,https://orcid.org/0000-0003-0200-4200,False
https://openalex.org/W3163880707,https://doi.org/10.1101/2020.08.10.231720,Cell-specific imputation of drug connectivity mapping with incomplete data,Cell-specific imputation of drug connectivity mapping with incomplete data,2020,2020-08-10,en,preprint,posted-content,bioRxiv (Cold Spring Harbor Laboratory),,,Cold Spring Harbor Laboratory,repository,4,False,,33,Cell Image Analysis Techniques,0.999,"Biochemistry, Genetics and Molecular Biology",Biophysics,True,green,https://doi.org/10.1101/2020.08.10.231720,,cc-by-nc,"ABSTRACT Motivation Drug repositioning allows expedited discovery of new applications for existing compounds, but re-screening vast compound libraries is often prohibitively expensive. “Connectivity mapping” is a process that links drugs to diseases by identifying compounds whose impact on expression in a collection of cells reverses the disease’s impact on expression in disease-relevant tissues. The high throughput LINCS project has expanded the universe of compounds and cell types for which data are available, but even with this effort, many potentially clinically useful combinations are missing. To evaluate the possibility of repurposing drugs this way despite missing data, we compared collaborative filtering with either neighborhood-based or SVD imputation methods to two naive approaches via cross-validation. Results Methods were evaluated for their ability to predict drug connectivity despite missing data. Predictions improved when cell type was taken into account. Neighborhood-based collaborative filtering was the most successful method, with the best improvements in non-immortalized primary cells. We also explored which classes of compounds are most and least reliant on cell type for accurate imputation, and we identified connections between related compounds even when many were not measured in the relevant cells. We conclude that even for cells in which drug responses have not been fully characterized, it is possible to identify unassayed drugs that reverse in those cells the expression signatures observed in disease. Contact [email protected]",first,Diana Sapashnik,https://openalex.org/A5041230053,,False,https://openalex.org/W4321003439,https://doi.org/10.1371/journal.pone.0278289,Cell-specific imputation of drug connectivity mapping with incomplete data,Cell-specific imputation of drug connectivity mapping with incomplete data,2023,2023-02-16,en,article,journal-article,PLoS ONE,1932-6203,1932-6203,Public Library of Science,journal,1,False,0.449,33,Computational Methods in Drug Discovery,0.9992,Computer Science,Computational Theory and Mathematics,True,gold,https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0278289&type=printable,https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0278289&type=printable,public-domain,"Drug repositioning allows expedited discovery of new applications for existing compounds, but re-screening vast compound libraries is often prohibitively expensive. “Connectivity mapping” is a process that links drugs to diseases by identifying compounds whose impact on expression in a collection of cells reverses the disease’s impact on expression in disease-relevant tissues. The LINCS project has expanded the universe of compounds and cells for which data are available, but even with this effort, many clinically useful combinations are missing. To evaluate the possibility of repurposing drugs despite missing data, we compared collaborative filtering using either neighborhood-based or SVD imputation methods to two naive approaches via cross-validation. Methods were evaluated for their ability to predict drug connectivity despite missing data. Predictions improved when cell type was taken into account. Neighborhood collaborative filtering was the most successful method, with the best improvements in non-immortalized primary cells. We also explored which classes of compounds are most and least reliant on cell type for accurate imputation. We conclude that even for cells in which drug responses have not been fully characterized, it is possible to identify unassayed drugs that reverse in those cells the expression signatures observed in disease.",first,Diana Sapashnik,https://openalex.org/A5041230053,,True
https://openalex.org/W4323306896,https://doi.org/10.36227/techrxiv.22184071.v1,Embedded Pressure Sensing Metamaterials using TPU-Graphene Composites and Additive Manufacturing,Embedded Pressure Sensing Metamaterials using TPU-Graphene Composites and Additive Manufacturing,2023,2023-03-06,en,preprint,posted-content,,,,,,0,False,,52,Advanced Sensor and Energy Harvesting Materials,0.9998,Engineering,Biomedical Engineering,True,green,https://www.techrxiv.org/doi/pdf/10.36227/techrxiv.22184071.v1,https://www.techrxiv.org/doi/pdf/10.36227/techrxiv.22184071.v1,cc-by,"<p>Nearly 15% of the global population is affected by disabilities impacting mobility. Monitoring foot pressure distribution during gait is a fundamental aspect of evaluating rehabilitation. Wearable systems provide a portable alternative to stationary equipment monitoring gait without laboratory space limitations. However, wearable sensors in some applications present challenges in the calibration, sensitivity, and human-sensor interface, requiring application-specific sensors. This study aimed to develop wearable sensors where the structural and material properties can characterise the sensitivity and range of measurement during the design phase. We developed wearable piezoresistive sensors using additive manufacturing to create mechanical metamaterials with embedded pressure-sensing capabilities. The sensors were fabricated in TPU using SLS and graphene ink infusion processes. Three structural designs were developed for different measuring ranges (0 – 50 N, 0 – 100 N, and 0 – 150 N) using body-centred cubic lattices constructed via pyramid unit cells. Two graphene infusion processes were evaluated. We tested the sensors' mechanical and piezoresistive behaviour, measuring the compressive force, strain, and electrical resistance across the sensor. We analysed the influence of structural dimensions and the infusion process on the piezoresistive behaviour. The measuring range was affected mainly by tuneable structural dimensions. The infusion process influenced the piezoresistive sensitivity and affected the linearity response. The results indicate the characterisation of the sensitivity of piezoresistive sensors based on structural parameters and material properties. Mechanical metamaterials could embed pressure sensing in wearables, allowing for customisation based on design parameters using additive manufacture and graphene inks. </p>",first,Inigo Sanz Pena,https://openalex.org/A5041979699,,True,https://openalex.org/W4380303556,https://doi.org/10.1109/jsen.2023.3283460,Embedded Pressure Sensing Metamaterials Using TPU-Graphene Composites and Additive Manufacturing,Embedded Pressure Sensing Metamaterials Using TPU-Graphene Composites and Additive Manufacturing,2023,2023-06-12,en,article,journal-article,IEEE Sensors Journal,1530-437X$@$1558-1748,1530-437X,IEEE Sensors Council,journal,4,False,1.025,54,Wearable Nanogenerator Technology,0.9999,Engineering,Biomedical Engineering,True,green,https://www.techrxiv.org/doi/pdf/10.36227/techrxiv.22184071.v1,,,"Disabilities impacting mobility are a global concern requiring gait rehabilitation, where monitoring foot pressure distribution is fundamental. Wearable systems provide an alternative to stationary equipment eliminating space limitations. However, wearable sensors present challenges in the calibration, sensitivity, and human–sensor interface, requiring application-specific sensors. This study aimed to develop wearable sensors, where the structural and material properties can characterize the sensitivity and range of measurement during the design phase. We developed wearable piezoresistive sensors using additive manufacturing (AM) to create mechanical metamaterials with embedded pressure-sensing capabilities. Three structural designs were developed for different measuring ranges (0–50 N, 0–100 N, and 0–150 N) using body-centered cubic (BCC) lattices constructed via pyramid unit cells. In addition, two graphene infusion processes were evaluated. We analyzed the influence of structural dimensions and the graphene infusion process on the piezoresistive response of the sensors. The measuring range was affected mainly by tunable structural dimensions, while the infusion process influenced the piezoresistive sensitivity and the linear response. The outcomes in characterizing the piezoresistive sensors based on structural and material properties could allow the development of wearables with embedded pressure sensing with a predictive response solely based on design parameters using AM and graphene inks.",first,Inigo Sanz-Pena,https://openalex.org/A5027816754,https://orcid.org/0000-0002-8282-0648,False
https://openalex.org/W3212535440,https://doi.org/10.1101/2021.11.16.468842,Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization,Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization,2021,2021-11-18,en,preprint,posted-content,bioRxiv (Cold Spring Harbor Laboratory),,,Cold Spring Harbor Laboratory,repository,0,False,,28,Mitochondrial Function and Pathology,1.0,"Biochemistry, Genetics and Molecular Biology",Molecular Biology,True,green,https://www.biorxiv.org/content/biorxiv/early/2022/02/03/2021.11.16.468842.full.pdf,https://www.biorxiv.org/content/biorxiv/early/2022/02/03/2021.11.16.468842.full.pdf,cc-by,"Abstract A sudden increase in permeability of the mitochondrial inner membrane, mitochondrial permeability transition (PT), is the central event responsible for cell death and tissue damage in conditions such as stroke and heart attack. PT is caused by the opening of the Cyclosporin A (CSA) dependent calcium-induced pore, the Permeability Transition Pore (PTP). The molecular details of PTP are incompletely understood. We utilized a combination of holographic and fluorescent microscopy to assess the contribution of the ATP synthase and Adenine Nucleotide Translocator (ANT) towards PTP. In cells lacking either ATP synthase or ANT, we observed CSA-sensitive membrane depolarization, but not high-conductance PTP. Further, we found that in wild-type cells calcium induced CSA-sensitive depolarization precedes opening of the PTP, which occurred until after nearly complete mitochondrial membrane depolarization. We propose that both ATP synthase and ANT are required for high conductance PTP but not depolarization, which presumably occurs through activation of the low conductance PT, which has a molecular nature that is different from both complexes.",first,Maria Neginskaya,https://openalex.org/A5011920727,https://orcid.org/0000-0001-8490-5218,True,https://openalex.org/W4307726921,https://doi.org/10.1016/j.isci.2022.105447,Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization,Both ANT and ATPase are essential for mitochondrial permeability transition but not depolarization,2022,2022-10-28,en,article,journal-article,iScience,2589-0042,2589-0042,Cell Press,journal,24,False,3.22,47,ATP Synthase and ATPases Research,1.0,"Biochemistry, Genetics and Molecular Biology",Molecular Biology,True,gold,https://www.cell.com/article/S2589004222017199/pdf,https://www.cell.com/article/S2589004222017199/pdf,cc-by,"An increase in permeability of the mitochondrial inner membrane, mitochondrial permeability transition (PT), is the central event responsible for cell death and tissue damage in conditions such as stroke and heart attack. PT is caused by the cyclosporin A (CSA)-dependent calcium-induced pore, the permeability transition pore (PTP). The molecular details of PTP are incompletely understood. We utilized holographic and fluorescent microscopy to assess the contribution of ATP synthase and adenine nucleotide translocator (ANT) toward PTP. In cells lacking either ATP synthase or ANT, we observed CSA-sensitive membrane depolarization, but not high-conductance PTP. In wild-type cells, calcium-induced CSA-sensitive depolarization preceded opening of PTP, which occurred only after nearly complete mitochondrial membrane depolarization. We propose that both ATP synthase and ANT are required for high-conductance PTP but not depolarization, which presumably occurs through activation of the low-conductance PT, which has a molecular nature that is different from both complexes.",first,Maria Neginskaya,https://openalex.org/A5011920727,https://orcid.org/0000-0001-8490-5218,True