PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Anthropogenic influences on the distribution of a threatened apex-predator around sustainable-use reserves following hydropower dam installation
items: Longer study length, standardized sampling techniques, and broader geographic scope leads to higher likelihood of detecting stable abundance patterns in long term black-legged tick studies
items: Description of the new species Sigambra nkossa (Annelida, Pilargidae), with an analysis of the distribution patterns of polychaetes associated with artificially hydrocarbon-enriched bottoms
items: Physical and chemical properties of the soils in selected communal property associations of South Africa
items: Xenobennettella coralliensis a new monoraphid diatom genus characterized by the alveolate sternum valve with cavum, observed from coral reef habitats
items: Learning about the meanings of ambiguous words: evidence from a word-meaning priming paradigm with short narratives
items: Radiomics combined with clinical features in distinguishing non-calcifying tuberculosis granuloma and lung adenocarcinoma in small pulmonary nodules
items: Evaluation of pulpal anesthesia and injection pain using IANB with pre-heated, buffered and conventional 2% lignocaine in teeth with symptomatic irreversible pulpitis—a randomized clinical study
items: Morphometric and meristic diversity of the species Androctonus crassicauda (Olivier, 1807) (Scorpiones: Buthidae) in Saudi Arabia
items: Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation

Anthropogenic influences on the distribution of a threatened apex-predator around sustainable-use reserves following hydropower dam installation
type: item
type: AcademicArticle
description: Although previous studies demonstrate declines in many large bodied species following hydropower dam installation, others suggest that some species, including the giant otter (Pteronura brasiliensis) may return to newly created reservoir habitats. Yet, there is a lack of evidence to support such theories. Here, we analyzed the effects of a hydropower dam on giant otters using a before-after control-impact study design in the eastern Brazilian Amazon. We collected data 3 years before (2011–2012 and 2015) and after (2017–2019) dam construction, totaling 6,459 km of surveys along rivers with 43 direct sightings of giant otters. Contrary to expectations, our results revealed that giant otters did not remain nor did they return to the dam reservoir. Beyond the zone directly impacted by the dam giant otter occurrence and relative abundance declined next to sustainable-use reserves where the river was more intensely used by people. Our study showed that in the absence of active management sustainable-use reserves and low human density were not sufficient to maintain this apex-predator. Our findings suggest a need to proactively create and maintain areas with low levels of anthropogenic disturbance to enable sustainable coexistence between energy demands and biodiversity across Amazonia.
format: application/pdf
format: text/html
creator: Deborah C. Dávila Raffo
creator: Darren Norris
creator: Sandra Maria Hartz
creator: Fernanda Michalski
subject: Conservation Biology
subject: Zoology
subject: Coupled Natural and Human Systems
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.14287
publisher: PeerJ Inc.
rights: © 2022 Raffo et al.
abstract: Although previous studies demonstrate declines in many large bodied species following hydropower dam installation, others suggest that some species, including the giant otter (Pteronura brasiliensis) may return to newly created reservoir habitats. Yet, there is a lack of evidence to support such theories. Here, we analyzed the effects of a hydropower dam on giant otters using a before-after control-impact study design in the eastern Brazilian Amazon. We collected data 3 years before (2011–2012 and 2015) and after (2017–2019) dam construction, totaling 6,459 km of surveys along rivers with 43 direct sightings of giant otters. Contrary to expectations, our results revealed that giant otters did not remain nor did they return to the dam reservoir. Beyond the zone directly impacted by the dam giant otter occurrence and relative abundance declined next to sustainable-use reserves where the river was more intensely used by people. Our study showed that in the absence of active management sustainable-use reserves and low human density were not sufficient to maintain this apex-predator. Our findings suggest a need to proactively create and maintain areas with low levels of anthropogenic disturbance to enable sustainable coexistence between energy demands and biodiversity across Amazonia.
bibliographic citation: Raffo et al. (2022) Anthropogenic influences on the distribution of a threatened apex-predator around sustainable-use reserves following hydropower dam installation. PeerJ 10:e14287 https://doi.org/10.7717/peerj.14287
date submitted: 2022-07-07
date accepted: 2022-10-02
issued: 2022-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raffo
  given name: Deborah C. Dávila
author list: Agent
  family name: Norris
  given name: Darren
author list: Agent
  family name: Hartz
  given name: Sandra Maria
author list: Agent
  family name: Michalski
  given name: Fernanda
doi: 10.7717/peerj.14287
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-20
copyright: © 2022 Raffo et al.
attribution name: Raffo et al.

Longer study length, standardized sampling techniques, and broader geographic scope leads to higher likelihood of detecting stable abundance patterns in long term black-legged tick studies
type: item
type: AcademicArticle
description: Background Understanding how study design and monitoring strategies shape inference within, and synthesis across, studies is critical across biological disciplines. Many biological and field studies are short term and limited in scope. Monitoring studies are critical for informing public health about potential vectors of concern, such as Ixodes scapularis (black-legged ticks). Black-legged ticks are a taxon of ecological and human health concern due to their status as primary vectors of Borrelia burgdorferi, the bacteria that transmits Lyme disease. However, variation in black-legged tick monitoring, and gaps in data, are currently considered major barriers to understanding population trends and in turn, predicting Lyme disease risk. To understand how variable methodology in black-legged tick studies may influence which population patterns researchers find, we conducted a data synthesis experiment. Materials and Methods We searched for publicly available black-legged tick abundance dataset that had at least 9 years of data, using keywords about ticks in internet search engines, literature databases, data repositories and public health websites. Our analysis included 289 datasets from seven surveys from locations in the US, ranging in length from 9 to 24 years. We used a moving window analysis, a non-random resampling approach, to investigate the temporal stability of black-legged tick population trajectories across the US. We then used t-tests to assess differences in stability time across different study parameters. Results All of our sampled datasets required 4 or more years to reach stability. We also found several study factors can have an impact on the likelihood of a study reaching stability and of data leading to misleading results if the study does not reach stability. Specifically, datasets collected via dragging reached stability significantly faster than data collected via opportunistic sampling. Datasets that sampled larva reached stability significantly…
format: application/pdf
format: text/html
creator: Rowan Christie
creator: Kaitlin Stack Whitney
creator: Julia Perrone
creator: Christie A. Bahlai
subject: Bioinformatics
subject: Computational Biology
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.13916
publisher: PeerJ Inc.
rights: © 2022 Christie et al.
abstract: Background Understanding how study design and monitoring strategies shape inference within, and synthesis across, studies is critical across biological disciplines. Many biological and field studies are short term and limited in scope. Monitoring studies are critical for informing public health about potential vectors of concern, such as Ixodes scapularis (black-legged ticks). Black-legged ticks are a taxon of ecological and human health concern due to their status as primary vectors of Borrelia burgdorferi, the bacteria that transmits Lyme disease. However, variation in black-legged tick monitoring, and gaps in data, are currently considered major barriers to understanding population trends and in turn, predicting Lyme disease risk. To understand how variable methodology in black-legged tick studies may influence which population patterns researchers find, we conducted a data synthesis experiment. Materials and Methods We searched for publicly available black-legged tick abundance dataset that had at least 9 years of data, using keywords about ticks in internet search engines, literature databases, data repositories and public health websites. Our analysis included 289 datasets from seven surveys from locations in the US, ranging in length from 9 to 24 years. We used a moving window analysis, a non-random resampling approach, to investigate the temporal stability of black-legged tick population trajectories across the US. We then used t-tests to assess differences in stability time across different study parameters. Results All of our sampled datasets required 4 or more years to reach stability. We also found several study factors can have an impact on the likelihood of a study reaching stability and of data leading to misleading results if the study does not reach stability. Specifically, datasets collected via dragging reached stability significantly faster than data collected via opportunistic sampling. Datasets that sampled larva reached stability significantly…
bibliographic citation: Christie et al. (2022) Longer study length, standardized sampling techniques, and broader geographic scope leads to higher likelihood of detecting stable abundance patterns in long term black-legged tick studies. PeerJ 10:e13916 https://doi.org/10.7717/peerj.13916
date submitted: 2021-12-15
date accepted: 2022-07-28
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Christie
  given name: Rowan
author list: Agent
  family name: Stack Whitney
  given name: Kaitlin
author list: Agent
  family name: Perrone
  given name: Julia
author list: Agent
  family name: Bahlai
  given name: Christie A.
doi: 10.7717/peerj.13916
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Christie et al.
attribution name: Christie et al.

Description of the new species Sigambra nkossa (Annelida, Pilargidae), with an analysis of the distribution patterns of polychaetes associated with artificially hydrocarbon-enriched bottoms
type: item
type: AcademicArticle
description: The monitoring of the N’Kossa offshore oil and gas fields in the Republic of Congo allowed us to assess the ecological traits of two polychaete species belonging to Sigambra (Annelida, Pilargidae). Sigambra parva occur in very low densities in all bottoms, except the most impacted, where it is totally absent; it is an undescribed species that reached >4,000 ind/m2 in hydrocarbon-enriched sediments. Their distribution patterns are compared with those of other polychaetes, showing a range of affinities for hydrocarbon-enriched sediments in the N’Kossa region. Our results suggest that S. parva would be a representative of the original local fauna, while the species associated with artificial hydrocarbon-enriched sediments, including the other Sigambra, six more polychaetes and a bivalve, could be natively associated with natural hydrocarbon-enriched sediments, using the former as alternative habitats and as dispersal stepping stones. This ecological segregation, together with a careful morphological and morphometric analyses led us to describe the latter as a new species, namely Sigambra nkossa sp. nov. Moreover, morphometric analysis allowed us to discuss on the taxonomic robustness of the key morphological characters of S. nkossa sp. nov., as well as to emend the generic diagnosis of Sigambra to accommodate the new species.
format: application/pdf
format: text/html
creator: Daniel Martin
creator: João Gil
creator: Claude-Henri Chaineau
creator: Sébastien Thorin
creator: Romain Le Gall
creator: Eric Dutrieux
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13942
publisher: PeerJ Inc.
rights: © 2022 Martin et al.
abstract: The monitoring of the N’Kossa offshore oil and gas fields in the Republic of Congo allowed us to assess the ecological traits of two polychaete species belonging to Sigambra (Annelida, Pilargidae). Sigambra parva occur in very low densities in all bottoms, except the most impacted, where it is totally absent; it is an undescribed species that reached >4,000 ind/m2 in hydrocarbon-enriched sediments. Their distribution patterns are compared with those of other polychaetes, showing a range of affinities for hydrocarbon-enriched sediments in the N’Kossa region. Our results suggest that S. parva would be a representative of the original local fauna, while the species associated with artificial hydrocarbon-enriched sediments, including the other Sigambra, six more polychaetes and a bivalve, could be natively associated with natural hydrocarbon-enriched sediments, using the former as alternative habitats and as dispersal stepping stones. This ecological segregation, together with a careful morphological and morphometric analyses led us to describe the latter as a new species, namely Sigambra nkossa sp. nov. Moreover, morphometric analysis allowed us to discuss on the taxonomic robustness of the key morphological characters of S. nkossa sp. nov., as well as to emend the generic diagnosis of Sigambra to accommodate the new species.
bibliographic citation: Martin et al. (2022) Description of the new species Sigambra nkossa (Annelida, Pilargidae), with an analysis of the distribution patterns of polychaetes associated with artificially hydrocarbon-enriched bottoms. PeerJ 10:e13942 https://doi.org/10.7717/peerj.13942
date submitted: 2022-01-31
date accepted: 2022-08-03
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martin
  given name: Daniel
author list: Agent
  family name: Gil
  given name: João
author list: Agent
  family name: Chaineau
  given name: Claude-Henri
author list: Agent
  family name: Thorin
  given name: Sébastien
author list: Agent
  family name: Le Gall
  given name: Romain
author list: Agent
  family name: Dutrieux
  given name: Eric
doi: 10.7717/peerj.13942
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Martin et al.
attribution name: Martin et al.

Physical and chemical properties of the soils in selected communal property associations of South Africa
type: item
type: AcademicArticle
description: Communal Property Associations (CPAs) rangeland users need more knowledge on the state of their respective grazing lands and also the interaction of soil properties with grazing management implemented. This study aimed to investigate the effect grazing has on the physical and chemical properties of four different soil types found in selected CPAs of the Bela-Bela municipality, they are as follows: Mawela (Hutton-clay loam: HCL), Bela-Bela (Hutton-clay: HC), Moretele (Hutton-loamy sand: HLS) and Ramorula (Ecca sand-clay loam: ESCL).The macro and micro minerals, pH, nitrate-nitrogen, ammonium-nitrogen, organic carbon, soil particle size distribution, acidity and resistance were all measured. All data were subjected to two-way factorial analysis of variance (SAS, 2010). The topsoil was sampled at a depth of 300 mm at an interval of 100 m (100 and 200 m) from the same transect used for woody species data collection resulting in a total of 18 samples per CPA. In each CPA, three camps were selected. In each camp, three transects 200 m apart at the length of 200 m were set. In each transect, soils were drawn at 0, 100 and 200 m making a total of nine soil samples per each camp. The highest (P < 0.05) pH (7.14) recorded on the sub-soil was in HLS. Nitrate nitrogen (2.4 mg/kg) concentration on the topsoil was high (P < 0.05) in HC soil type. Soil organic carbon for both topsoil (0.66%) and subsoil (0.41%) was significantly lower (P < 0.05) in HLS soil type and ESCL soil type respectively. Phosphorus concentration was significantly high (P < 0.05) in ESCL soil type for both topsoil (12.86 mg/kg) and sub-soil (1.59 mg/kg). Iron concentration was high in both topsoil (11.8 mg/kg) and sub-soil (7.3 mg/kg) in ESCL soil type. Sub-soil manganese concentration was found to be higher (P < 0.05) in ESCL soil type (7.58 mg/kg). Soil resistance (2880 Ω ) measured in topsoil was high (P < 0.05) in HCL soil type compared to other soil types. Moreover, for the sub-soil the highest (P < 0.0…
format: application/pdf
format: text/html
creator: Malizo Ntalo
creator: Khuliso Emmanuel Ravhuhali
creator: Bethwell Moyo
creator: Ntuwiseni Emile Mmbi
creator: Kwena Hilda Mokoboki
subject: Agricultural Science
subject: Soil Science
description: doi:10.7717/peerj.13960
publisher: PeerJ Inc.
rights: © 2022 Ntalo et al.
abstract: Communal Property Associations (CPAs) rangeland users need more knowledge on the state of their respective grazing lands and also the interaction of soil properties with grazing management implemented. This study aimed to investigate the effect grazing has on the physical and chemical properties of four different soil types found in selected CPAs of the Bela-Bela municipality, they are as follows: Mawela (Hutton-clay loam: HCL), Bela-Bela (Hutton-clay: HC), Moretele (Hutton-loamy sand: HLS) and Ramorula (Ecca sand-clay loam: ESCL).The macro and micro minerals, pH, nitrate-nitrogen, ammonium-nitrogen, organic carbon, soil particle size distribution, acidity and resistance were all measured. All data were subjected to two-way factorial analysis of variance (SAS, 2010). The topsoil was sampled at a depth of 300 mm at an interval of 100 m (100 and 200 m) from the same transect used for woody species data collection resulting in a total of 18 samples per CPA. In each CPA, three camps were selected. In each camp, three transects 200 m apart at the length of 200 m were set. In each transect, soils were drawn at 0, 100 and 200 m making a total of nine soil samples per each camp. The highest (P < 0.05) pH (7.14) recorded on the sub-soil was in HLS. Nitrate nitrogen (2.4 mg/kg) concentration on the topsoil was high (P < 0.05) in HC soil type. Soil organic carbon for both topsoil (0.66%) and subsoil (0.41%) was significantly lower (P < 0.05) in HLS soil type and ESCL soil type respectively. Phosphorus concentration was significantly high (P < 0.05) in ESCL soil type for both topsoil (12.86 mg/kg) and sub-soil (1.59 mg/kg). Iron concentration was high in both topsoil (11.8 mg/kg) and sub-soil (7.3 mg/kg) in ESCL soil type. Sub-soil manganese concentration was found to be higher (P < 0.05) in ESCL soil type (7.58 mg/kg). Soil resistance (2880 Ω ) measured in topsoil was high (P < 0.05) in HCL soil type compared to other soil types. Moreover, for the sub-soil the highest (P < 0.0…
bibliographic citation: Ntalo et al. (2022) Physical and chemical properties of the soils in selected communal property associations of South Africa. PeerJ 10:e13960 https://doi.org/10.7717/peerj.13960
date submitted: 2022-04-01
date accepted: 2022-08-07
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ntalo
  given name: Malizo
author list: Agent
  family name: Ravhuhali
  given name: Khuliso Emmanuel
author list: Agent
  family name: Moyo
  given name: Bethwell
author list: Agent
  family name: Mmbi
  given name: Ntuwiseni Emile
author list: Agent
  family name: Mokoboki
  given name: Kwena Hilda
doi: 10.7717/peerj.13960
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Ntalo et al.
attribution name: Ntalo et al.

Xenobennettella coralliensis a new monoraphid diatom genus characterized by the alveolate sternum valve with cavum, observed from coral reef habitats
type: item
type: AcademicArticle
description: During a survey of benthic diatoms from the coral reefs of the Indian Ocean (Scattered Islands) and Pacific Ocean (Tuamotu Archipelago), an interesting monoraphid diatom was observed and examined by light microscopy and various electron microscopy methods including Focus Ion Beam milling. Our thorough analysis revealed the similarity of this diatom to Bennettella R.W.Holmes, which we reference in the name: Xenobennettella Witkowski & Riaux-Gobin gen. nov., with Xenobennettella coralliensis Witkowski & Riaux-Gobin sp. nov. as the generitype. The type habitat for this new species is the sublittoral coral reef of Juan de Nova in the Mozambique Channel. The sternum valve of the new genus is characterized by an alveolate ultrastructure with the rim of the alveola opening along the valve margin, resembling the sternum valve of Bennettella. Internally, Xenobennettella differs from the latter by possessing a cavum (horseshoe-shaped chamber) on one side of the valve, in a central axial position. The raphe valve of Xenobennettella has small, marginal, apically elongate chambers, which are internally delineated by transapical ribs that are very similar to Bennettella. However, the raphe in the new genus is different from the latter, resembling some Cocconeis and Planothidium with internal raphe endings bent in the opposite direction, while resembling some Planothidium taxa externally by ending on the apical part of the mantle. This contrasts to Bennettella, which has a unique raphe system, with external raphe endings below the apices, a prominent axial structure and a transapically expanded central area. Likewise, the external surface of Bennettella is different from that of the new genus with a complex mantle structure and biseriate striae. In Xenobennettella, the valve mantle of the raphe valve is simple and perforated by areola. The transapical striae occur in the valve margin and the axial area is ornamented along its course with a single row of densely packed areola on bo…
format: application/pdf
format: text/html
creator: Andrzej Witkowski
creator: Catherine Riaux-Gobin
creator: Adrian Kryk
creator: Tomasz Płociński
creator: Izabela Zgłobicka
creator: Krzysztof Kurzydłowski
subject: Biodiversity
subject: Marine Biology
subject: Plant Science
subject: Taxonomy
subject: Biological Oceanography
description: doi:10.7717/peerj.13977
publisher: PeerJ Inc.
rights: © 2022 Witkowski et al.
abstract: During a survey of benthic diatoms from the coral reefs of the Indian Ocean (Scattered Islands) and Pacific Ocean (Tuamotu Archipelago), an interesting monoraphid diatom was observed and examined by light microscopy and various electron microscopy methods including Focus Ion Beam milling. Our thorough analysis revealed the similarity of this diatom to Bennettella R.W.Holmes, which we reference in the name: Xenobennettella Witkowski & Riaux-Gobin gen. nov., with Xenobennettella coralliensis Witkowski & Riaux-Gobin sp. nov. as the generitype. The type habitat for this new species is the sublittoral coral reef of Juan de Nova in the Mozambique Channel. The sternum valve of the new genus is characterized by an alveolate ultrastructure with the rim of the alveola opening along the valve margin, resembling the sternum valve of Bennettella. Internally, Xenobennettella differs from the latter by possessing a cavum (horseshoe-shaped chamber) on one side of the valve, in a central axial position. The raphe valve of Xenobennettella has small, marginal, apically elongate chambers, which are internally delineated by transapical ribs that are very similar to Bennettella. However, the raphe in the new genus is different from the latter, resembling some Cocconeis and Planothidium with internal raphe endings bent in the opposite direction, while resembling some Planothidium taxa externally by ending on the apical part of the mantle. This contrasts to Bennettella, which has a unique raphe system, with external raphe endings below the apices, a prominent axial structure and a transapically expanded central area. Likewise, the external surface of Bennettella is different from that of the new genus with a complex mantle structure and biseriate striae. In Xenobennettella, the valve mantle of the raphe valve is simple and perforated by areola. The transapical striae occur in the valve margin and the axial area is ornamented along its course with a single row of densely packed areola on bo…
bibliographic citation: Witkowski et al. (2022) Xenobennettella coralliensis a new monoraphid diatom genus characterized by the alveolate sternum valve with cavum, observed from coral reef habitats. PeerJ 10:e13977 https://doi.org/10.7717/peerj.13977
date submitted: 2022-05-04
date accepted: 2022-08-09
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Witkowski
  given name: Andrzej
author list: Agent
  family name: Riaux-Gobin
  given name: Catherine
author list: Agent
  family name: Kryk
  given name: Adrian
author list: Agent
  family name: Płociński
  given name: Tomasz
author list: Agent
  family name: Zgłobicka
  given name: Izabela
author list: Agent
  family name: Kurzydłowski
  given name: Krzysztof
doi: 10.7717/peerj.13977
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Witkowski et al.
attribution name: Witkowski et al.

Learning about the meanings of ambiguous words: evidence from a word-meaning priming paradigm with short narratives
type: item
type: AcademicArticle
description: Fluent language comprehension requires people to rapidly activate and integrate context-appropriate word meanings. This process is challenging for meanings of ambiguous words that are comparatively lower in frequency (e.g., the “bird” meaning of “crane”). Priming experiments have shown that recent experience makes such subordinate (less frequent) word meanings more readily available at the next encounter. These experiments used lists of unconnected sentences in which each ambiguity was disambiguated locally by neighbouring words. In natural language, however, disambiguation may occur via more distant contextual cues, embedded in longer, connected communicative contexts. In the present experiment, participants (N = 51) listened to 3-sentence narratives that ended in an ambiguous prime. Cues to disambiguation were relatively distant from the prime; the first sentence of each narrative established a situational context congruent with the subordinate meaning of the prime, but the remainder of the narrative did not provide disambiguating information. Following a short delay, primed subordinate meanings were more readily available (compared with an unprimed control), as assessed by responses in a word association task related to the primed meaning. This work confirms that listeners reliably disambiguate spoken ambiguous words on the basis of cues from wider narrative contexts, and that they retain information about the outcome of these disambiguation processes to inform subsequent encounters of the same word form.
format: application/pdf
format: text/html
creator: Lena M. Blott
creator: Oliver Hartopp
creator: Kate Nation
creator: Jennifer M. Rodd
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.14070
publisher: PeerJ Inc.
rights: © 2022 Blott et al.
abstract: Fluent language comprehension requires people to rapidly activate and integrate context-appropriate word meanings. This process is challenging for meanings of ambiguous words that are comparatively lower in frequency (e.g., the “bird” meaning of “crane”). Priming experiments have shown that recent experience makes such subordinate (less frequent) word meanings more readily available at the next encounter. These experiments used lists of unconnected sentences in which each ambiguity was disambiguated locally by neighbouring words. In natural language, however, disambiguation may occur via more distant contextual cues, embedded in longer, connected communicative contexts. In the present experiment, participants (N = 51) listened to 3-sentence narratives that ended in an ambiguous prime. Cues to disambiguation were relatively distant from the prime; the first sentence of each narrative established a situational context congruent with the subordinate meaning of the prime, but the remainder of the narrative did not provide disambiguating information. Following a short delay, primed subordinate meanings were more readily available (compared with an unprimed control), as assessed by responses in a word association task related to the primed meaning. This work confirms that listeners reliably disambiguate spoken ambiguous words on the basis of cues from wider narrative contexts, and that they retain information about the outcome of these disambiguation processes to inform subsequent encounters of the same word form.
bibliographic citation: Blott et al. (2022) Learning about the meanings of ambiguous words: evidence from a word-meaning priming paradigm with short narratives. PeerJ 10:e14070 https://doi.org/10.7717/peerj.14070
date submitted: 2022-06-26
date accepted: 2022-08-27
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blott
  given name: Lena M.
author list: Agent
  family name: Hartopp
  given name: Oliver
author list: Agent
  family name: Nation
  given name: Kate
author list: Agent
  family name: Rodd
  given name: Jennifer M.
doi: 10.7717/peerj.14070
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Blott et al.
attribution name: Blott et al.

Radiomics combined with clinical features in distinguishing non-calcifying tuberculosis granuloma and lung adenocarcinoma in small pulmonary nodules
type: item
type: AcademicArticle
description: Aim To evaluate the performance of radiomics models with the combination of clinical features in distinguishing non-calcified tuberculosis granuloma (TBG) and lung adenocarcinoma (LAC) in small pulmonary nodules. Methodology We conducted a retrospective analysis of 280 patients with pulmonary nodules confirmed by surgical biopsy from January 2017 to December 2020. Samples were divided into LAC group (n = 143) and TBG group (n = 137). We assigned them to a training dataset (n = 196) and a testing dataset (n = 84). Clinical features including gender, age, smoking, CT appearance (size, location, spiculated sign, lobulated shape, vessel convergence, and pleural indentation) were extracted and included in the radiomics models. 3D slicer and FAE software were used to delineate the Region of Interest (ROI) and extract clinical features. The performance of the model was evaluated by the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC). Results Based on the model selection, clinical features gender, and age in the LAC group and TBG group showed a significant difference in both datasets (P < 0.05). CT appearance lobulated shape was also significantly different in the LAC group and TBG group (Training dataset, P = 0.034; Testing dataset, P = 0.030). AUC were 0.8344 (95% CI [0.7712–0.8872]) and 0.751 (95% CI [0.6382–0.8531]) in training and testing dataset, respectively. Conclusion With the capacity to detect differences between TBG and LAC based on their clinical features, radiomics models with a combined of clinical features may function as the potential non-invasive tool for distinguishing TBG and LAC in small pulmonary nodules.
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format: text/html
creator: Qing Dong
creator: Qingqing Wen
creator: Nan Li
creator: Jinlong Tong
creator: Zhaofu Li
creator: Xin Bao
creator: Jinzhi Xu
creator: Dandan Li
subject: Biotechnology
subject: Oncology
subject: Surgery and Surgical Specialties
subject: Data Mining and Machine Learning
subject: Tuberculosis
description: doi:10.7717/peerj.14127
publisher: PeerJ Inc.
rights: © 2022 Dong et al.
abstract: Aim To evaluate the performance of radiomics models with the combination of clinical features in distinguishing non-calcified tuberculosis granuloma (TBG) and lung adenocarcinoma (LAC) in small pulmonary nodules. Methodology We conducted a retrospective analysis of 280 patients with pulmonary nodules confirmed by surgical biopsy from January 2017 to December 2020. Samples were divided into LAC group (n = 143) and TBG group (n = 137). We assigned them to a training dataset (n = 196) and a testing dataset (n = 84). Clinical features including gender, age, smoking, CT appearance (size, location, spiculated sign, lobulated shape, vessel convergence, and pleural indentation) were extracted and included in the radiomics models. 3D slicer and FAE software were used to delineate the Region of Interest (ROI) and extract clinical features. The performance of the model was evaluated by the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC). Results Based on the model selection, clinical features gender, and age in the LAC group and TBG group showed a significant difference in both datasets (P < 0.05). CT appearance lobulated shape was also significantly different in the LAC group and TBG group (Training dataset, P = 0.034; Testing dataset, P = 0.030). AUC were 0.8344 (95% CI [0.7712–0.8872]) and 0.751 (95% CI [0.6382–0.8531]) in training and testing dataset, respectively. Conclusion With the capacity to detect differences between TBG and LAC based on their clinical features, radiomics models with a combined of clinical features may function as the potential non-invasive tool for distinguishing TBG and LAC in small pulmonary nodules.
bibliographic citation: Dong et al. (2022) Radiomics combined with clinical features in distinguishing non-calcifying tuberculosis granuloma and lung adenocarcinoma in small pulmonary nodules. PeerJ 10:e14127 https://doi.org/10.7717/peerj.14127
date submitted: 2021-08-24
date accepted: 2022-09-06
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Qing
author list: Agent
  family name: Wen
  given name: Qingqing
author list: Agent
  family name: Li
  given name: Nan
author list: Agent
  family name: Tong
  given name: Jinlong
author list: Agent
  family name: Li
  given name: Zhaofu
author list: Agent
  family name: Bao
  given name: Xin
author list: Agent
  family name: Xu
  given name: Jinzhi
author list: Agent
  family name: Li
  given name: Dandan
doi: 10.7717/peerj.14127
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Dong et al.
attribution name: Dong et al.

Evaluation of pulpal anesthesia and injection pain using IANB with pre-heated, buffered and conventional 2% lignocaine in teeth with symptomatic irreversible pulpitis—a randomized clinical study
type: item
type: AcademicArticle
description: Background The efficacy of 2% lignocaine is reduced in a hot tooth. Local aesthetic agents can be preheated and buffered to increase their effectiveness. The present investigation was carried out due to limited information concerning adult patients with symptomatic irreversible pulpitis in mandibular teeth. Methods A total of 252 individuals were included in the clinical trial in accordance with the selection criteria only after clinical study was registered with the Clinical Trial Registry of India (CTRI/2020/09/027796). Scores on the visual analog scale (VAS) and electric pulp test (EPT) on a 1–10 scale were recorded prior to the commencement of therapy. In this double-blinded study, patients were randomly divided by a co-investigator using computer randomisation (www.randomizer.org) into three groups, group A: inferior alveolar nerve blocks (IANB) with 2% lignocaine preheated at 42 °C (injected at 37 °C) (N = 84), group B: IANB of 2% lignocaine buffered with 0.18 ml of 8.4% sodium bicarbonate (N = 80) and group C: 2% lignocaine (N = 88). Excluding the dropouts of individuals (n = 11), wherein the anaesthesia failed, a total of 241 people were finally assessed 15 minutes after profound anaesthesia, endodontic access, and intraoperative pain were quantified using VAS. Pain on injection for all three groups was recorded immediately after IANB with VAS. The analysis was performed using one way ANOVA with Tukey’s post hoc test and Paired T-Test using SPSS version 21. Results Preheated, Buffered, and conventional 2% lignocaine showed statistically significant reduction in intraoperative pain (P < 0.001) compared to pre-operative but on inter-group comparison preheated and buffered showed highly significant pain reduction compared with conventional 2% lignocaine (P < 0.001). Conclusions Warm and buffered local anaesthetic (LA) were effective in reducing intraoperative discomfort than conventional LA. Preheated local anesthetics caused the least pain, followed by buffere…
format: application/pdf
format: text/html
creator: Namita Gandhi
creator: Nimisha Shah
creator: Dian Agustin Wahjuningrum
creator: Sweetly Purnomo
creator: Riana Nooshian
creator: Suraj Arora
creator: Ajinkya M. Pawar
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Dentistry
subject: Drugs and Devices
description: doi:10.7717/peerj.14187
publisher: PeerJ Inc.
rights: © 2022 Gandhi et al.
abstract: Background The efficacy of 2% lignocaine is reduced in a hot tooth. Local aesthetic agents can be preheated and buffered to increase their effectiveness. The present investigation was carried out due to limited information concerning adult patients with symptomatic irreversible pulpitis in mandibular teeth. Methods A total of 252 individuals were included in the clinical trial in accordance with the selection criteria only after clinical study was registered with the Clinical Trial Registry of India (CTRI/2020/09/027796). Scores on the visual analog scale (VAS) and electric pulp test (EPT) on a 1–10 scale were recorded prior to the commencement of therapy. In this double-blinded study, patients were randomly divided by a co-investigator using computer randomisation (www.randomizer.org) into three groups, group A: inferior alveolar nerve blocks (IANB) with 2% lignocaine preheated at 42 °C (injected at 37 °C) (N = 84), group B: IANB of 2% lignocaine buffered with 0.18 ml of 8.4% sodium bicarbonate (N = 80) and group C: 2% lignocaine (N = 88). Excluding the dropouts of individuals (n = 11), wherein the anaesthesia failed, a total of 241 people were finally assessed 15 minutes after profound anaesthesia, endodontic access, and intraoperative pain were quantified using VAS. Pain on injection for all three groups was recorded immediately after IANB with VAS. The analysis was performed using one way ANOVA with Tukey’s post hoc test and Paired T-Test using SPSS version 21. Results Preheated, Buffered, and conventional 2% lignocaine showed statistically significant reduction in intraoperative pain (P < 0.001) compared to pre-operative but on inter-group comparison preheated and buffered showed highly significant pain reduction compared with conventional 2% lignocaine (P < 0.001). Conclusions Warm and buffered local anaesthetic (LA) were effective in reducing intraoperative discomfort than conventional LA. Preheated local anesthetics caused the least pain, followed by buffere…
bibliographic citation: Gandhi et al. (2022) Evaluation of pulpal anesthesia and injection pain using IANB with pre-heated, buffered and conventional 2% lignocaine in teeth with symptomatic irreversible pulpitis—a randomized clinical study. PeerJ 10:e14187 https://doi.org/10.7717/peerj.14187
date submitted: 2022-05-16
date accepted: 2022-09-14
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gandhi
  given name: Namita
author list: Agent
  family name: Shah
  given name: Nimisha
author list: Agent
  family name: Wahjuningrum
  given name: Dian Agustin
author list: Agent
  family name: Purnomo
  given name: Sweetly
author list: Agent
  family name: Nooshian
  given name: Riana
author list: Agent
  family name: Arora
  given name: Suraj
author list: Agent
  family name: Pawar
  given name: Ajinkya M.
doi: 10.7717/peerj.14187
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Gandhi et al.
attribution name: Gandhi et al.

Morphometric and meristic diversity of the species Androctonus crassicauda (Olivier, 1807) (Scorpiones: Buthidae) in Saudi Arabia
type: item
type: AcademicArticle
description: Intraspecific molecular and morphological variations among geographically isolated populations are useful for understanding the evolutionary processes, which is considered early stage of allopatric speciation. Also, the knowledge of the regional variation of scorpion venom composition is needed to improve antivenom therapeutic management. Androctonus crassicauda (Olivier, 1807) is the most common and medically important species in Arabia and the Middle East. Therefore, this study aimed to investigate the geographic morphological variation among A.crassicaudapopulations, regarding its geographical distribution in unexplored arid regions in Saudi Arabia. Samples were collected and examined morphologically under a dissecting microscope from different four eco-geographical regions. The results of ANOVA and multivariate statistical analyses provide strong evidence of geographical variation. The two populations from OTU3 and OUT4 showed the greatest degree of morphological difference from populations of OUT1 and OUT2. Each OTU3 and OTU4 populations showed significant speciation without overlapping in the two groups, while the remaining overlapped groups comprised two other populations. Several body variables influenced male separation, including carapace posterior width, metasoma 3rd length, and metasoma 2nd length. For females, telson length, metasoma 1st width, and sternite 7th width were highly influential variables. Such variation may suggest the existence of cryptic taxa within A. crassicauda populations in Saudi Arabia. Moreover, metasoma ratios can be used as good indicators in intraspecific variation studies of Scorpions.
format: application/pdf
format: text/html
creator: Abdulaziz R. Alqahtani
creator: Ahmed Badry
creator: Fahd Mohammed Abd Al Galil
creator: Zuhair S. Amr
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.14198
publisher: PeerJ Inc.
rights: © 2022 Alqahtani et al.
abstract: Intraspecific molecular and morphological variations among geographically isolated populations are useful for understanding the evolutionary processes, which is considered early stage of allopatric speciation. Also, the knowledge of the regional variation of scorpion venom composition is needed to improve antivenom therapeutic management. Androctonus crassicauda (Olivier, 1807) is the most common and medically important species in Arabia and the Middle East. Therefore, this study aimed to investigate the geographic morphological variation among A.crassicaudapopulations, regarding its geographical distribution in unexplored arid regions in Saudi Arabia. Samples were collected and examined morphologically under a dissecting microscope from different four eco-geographical regions. The results of ANOVA and multivariate statistical analyses provide strong evidence of geographical variation. The two populations from OTU3 and OUT4 showed the greatest degree of morphological difference from populations of OUT1 and OUT2. Each OTU3 and OTU4 populations showed significant speciation without overlapping in the two groups, while the remaining overlapped groups comprised two other populations. Several body variables influenced male separation, including carapace posterior width, metasoma 3rd length, and metasoma 2nd length. For females, telson length, metasoma 1st width, and sternite 7th width were highly influential variables. Such variation may suggest the existence of cryptic taxa within A. crassicauda populations in Saudi Arabia. Moreover, metasoma ratios can be used as good indicators in intraspecific variation studies of Scorpions.
bibliographic citation: Alqahtani et al. (2022) Morphometric and meristic diversity of the species Androctonus crassicauda (Olivier, 1807) (Scorpiones: Buthidae) in Saudi Arabia. PeerJ 10:e14198 https://doi.org/10.7717/peerj.14198
date submitted: 2022-07-19
date accepted: 2022-09-16
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alqahtani
  given name: Abdulaziz R.
author list: Agent
  family name: Badry
  given name: Ahmed
author list: Agent
  family name: Abd Al Galil
  given name: Fahd Mohammed
author list: Agent
  family name: Amr
  given name: Zuhair S.
doi: 10.7717/peerj.14198
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Alqahtani et al.
attribution name: Alqahtani et al.

Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation
type: item
type: AcademicArticle
description: Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1T. Prior to characterization of strain NS-1T, an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae. Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1T. In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons (e.g., 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1T, strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, buty…
format: application/pdf
format: text/html
creator: Sobroney Heng
creator: Sawannee Sutheeworapong
creator: Verawat Champreda
creator: Ayaka Uke
creator: Akihiko Kosugi
creator: Patthra Pason
creator: Rattiya Waeonukul
creator: Ruben Michael Ceballos
creator: Khanok Ratanakhanokchai
creator: Chakrit Tachaapaikoon
subject: Biodiversity
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.14211
publisher: PeerJ Inc.
rights: © 2022 Heng et al.
abstract: Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1T. Prior to characterization of strain NS-1T, an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae. Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1T. In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons (e.g., 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1T, strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, buty…
bibliographic citation: Heng et al. (2022) Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation. PeerJ 10:e14211 https://doi.org/10.7717/peerj.14211
date submitted: 2022-04-13
date accepted: 2022-09-19
issued: 2022-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heng
  given name: Sobroney
author list: Agent
  family name: Sutheeworapong
  given name: Sawannee
author list: Agent
  family name: Champreda
  given name: Verawat
author list: Agent
  family name: Uke
  given name: Ayaka
author list: Agent
  family name: Kosugi
  given name: Akihiko
author list: Agent
  family name: Pason
  given name: Patthra
author list: Agent
  family name: Waeonukul
  given name: Rattiya
author list: Agent
  family name: Ceballos
  given name: Ruben Michael
author list: Agent
  family name: Ratanakhanokchai
  given name: Khanok
author list: Agent
  family name: Tachaapaikoon
  given name: Chakrit
doi: 10.7717/peerj.14211
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-19
copyright: ©2022 Heng et al.
attribution name: Heng et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359