PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia
items: The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems
items: Turbidity interferes with foraging success of visual but not chemosensory predators
items: Attitudes towards suicide attempts broadcast on social media: an exploratory study of Chinese microblogs
items: A retrospective study on the outcomes of cataract surgery in an Eastern Regional Health Authority hospital of Trinidad and Tobago
items: Ecological and socio-demographic differences in maternal care services in Nepal
items: Transcriptional and posttranscriptional regulation of Bacillus sp. CDB3 arsenic-resistance operon ars1
items: An explanation of the relationship between mass, metabolic rate and characteristic length for placental mammals
items: Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of ‘river dolphins’ in the Americas
items: Assessing uncertainty in sighting records: an example of the Barbary lion

The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia
type: item
type: AcademicArticle
description: The influence of sea-cage aquaculture on wildfish assemblages has received little attention outside of Europe. Sea-cage aquaculture of finfish is a major focus in South Australia, and while the main species farmed is southern bluefin tuna (Thunnus maccoyii), there is also an important yellowtail kingfish (Seriola lalandi) industry. Yellowtail kingfish aquaculture did not appear to have any local or regional effects on demersal assemblages (primarily fish, but also some crustaceans) surveyed by baited remote underwater video (BRUV) in Fitzgerald Bay. We did, however, detect small scale spatial variations in assemblages within the bay. The type of bait used strongly influenced the assemblage recorded, with significantly greater numbers of fish attracted to deployments where sardines were used as the bait to compared to those with no bait. The pelleted feed used by the aquaculture industry was just as attractive as sardines at one site, and intermediate between sardines and no bait at the other. There was significant temporal variability in assemblages at both farm sites and one control site, while the second control site was temporally stable (over the 9 weeks of the study). Overall, the results suggested that aquaculture was having little if any impact on the abundance and assemblage structure of the demersal macrofauna in Fitzgerald Bay.
format: application/pdf
format: text/html
creator: Jason E. Tanner
creator: Kane Williams
subject: Aquaculture, Fisheries and Fish Science
subject: Biosphere Interactions
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.1238
publisher: PeerJ Inc.
rights: © 2015 Tanner and Williams
abstract: The influence of sea-cage aquaculture on wildfish assemblages has received little attention outside of Europe. Sea-cage aquaculture of finfish is a major focus in South Australia, and while the main species farmed is southern bluefin tuna (Thunnus maccoyii), there is also an important yellowtail kingfish (Seriola lalandi) industry. Yellowtail kingfish aquaculture did not appear to have any local or regional effects on demersal assemblages (primarily fish, but also some crustaceans) surveyed by baited remote underwater video (BRUV) in Fitzgerald Bay. We did, however, detect small scale spatial variations in assemblages within the bay. The type of bait used strongly influenced the assemblage recorded, with significantly greater numbers of fish attracted to deployments where sardines were used as the bait to compared to those with no bait. The pelleted feed used by the aquaculture industry was just as attractive as sardines at one site, and intermediate between sardines and no bait at the other. There was significant temporal variability in assemblages at both farm sites and one control site, while the second control site was temporally stable (over the 9 weeks of the study). Overall, the results suggested that aquaculture was having little if any impact on the abundance and assemblage structure of the demersal macrofauna in Fitzgerald Bay.
bibliographic citation: Tanner et al. (2015) The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia. PeerJ 3:e1238 https://doi.org/10.7717/peerj.1238
date submitted: 2015-04-27
date accepted: 2015-08-22
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanner
  given name: Jason E.
author list: Agent
  family name: Williams
  given name: Kane
doi: 10.7717/peerj.1238
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Tanner and Williams
attribution name: Tanner and Williams

The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems
type: item
type: AcademicArticle
description: The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
format: application/pdf
format: text/html
creator: Daniel J.G. Lahr
creator: Tanja Bosak
creator: Enrique Lara
creator: Edward A.D. Mitchell
subject: Biochemistry
subject: Biodiversity
subject: Evolutionary Studies
subject: Microbiology
subject: Paleontology
description: doi:10.7717/peerj.1234
publisher: PeerJ Inc.
rights: © 2015 Lahr et al.
abstract: The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
bibliographic citation: Lahr et al. (2015) The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems. PeerJ 3:e1234 https://doi.org/10.7717/peerj.1234
date submitted: 2015-05-29
date accepted: 2015-08-19
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lahr
  given name: Daniel J.G.
author list: Agent
  family name: Bosak
  given name: Tanja
author list: Agent
  family name: Lara
  given name: Enrique
author list: Agent
  family name: Mitchell
  given name: Edward A.D.
doi: 10.7717/peerj.1234
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Lahr et al.
attribution name: Lahr et al.

Turbidity interferes with foraging success of visual but not chemosensory predators
type: item
type: AcademicArticle
description: Predation can significantly affect prey populations and communities, but predator effects can be attenuated when abiotic conditions interfere with foraging activities. In estuarine communities, turbidity can affect species richness and abundance and is changing in many areas because of coastal development. Many fish species are less efficient foragers in turbid waters, and previous research revealed that in elevated turbidity, fish are less abundant whereas crabs and shrimp are more abundant. We hypothesized that turbidity altered predatory interactions in estuaries by interfering with visually-foraging predators and prey but not with organisms relying on chemoreception. We measured the effects of turbidity on the predation rates of two model predators: a visual predator (pinfish, Lagodon rhomboides) and a chemosensory predator (blue crabs, Callinectes sapidus) in clear and turbid water (0 and ∼100 nephelometric turbidity units). Feeding assays were conducted with two prey items, mud crabs (Panopeus spp.) that rely heavily on chemoreception to detect predators, and brown shrimp (Farfantepenaus aztecus) that use both chemical and visual cues for predator detection. Because turbidity reduced pinfish foraging on both mud crabs and shrimp, the changes in predation rates are likely driven by turbidity attenuating fish foraging ability and not by affecting prey vulnerability to fish consumers. Blue crab foraging was unaffected by turbidity, and blue crabs were able to successfully consume nearly all mud crab and shrimp prey. Turbidity can influence predator–prey interactions by reducing the feeding efficiency of visual predators, providing a competitive advantage to chemosensory predators, and altering top-down control in food webs.
format: application/pdf
format: text/html
creator: Jessica Lunt
creator: Delbert L. Smee
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.1212
publisher: PeerJ Inc.
rights: © 2015 Lunt and Smee
abstract: Predation can significantly affect prey populations and communities, but predator effects can be attenuated when abiotic conditions interfere with foraging activities. In estuarine communities, turbidity can affect species richness and abundance and is changing in many areas because of coastal development. Many fish species are less efficient foragers in turbid waters, and previous research revealed that in elevated turbidity, fish are less abundant whereas crabs and shrimp are more abundant. We hypothesized that turbidity altered predatory interactions in estuaries by interfering with visually-foraging predators and prey but not with organisms relying on chemoreception. We measured the effects of turbidity on the predation rates of two model predators: a visual predator (pinfish, Lagodon rhomboides) and a chemosensory predator (blue crabs, Callinectes sapidus) in clear and turbid water (0 and ∼100 nephelometric turbidity units). Feeding assays were conducted with two prey items, mud crabs (Panopeus spp.) that rely heavily on chemoreception to detect predators, and brown shrimp (Farfantepenaus aztecus) that use both chemical and visual cues for predator detection. Because turbidity reduced pinfish foraging on both mud crabs and shrimp, the changes in predation rates are likely driven by turbidity attenuating fish foraging ability and not by affecting prey vulnerability to fish consumers. Blue crab foraging was unaffected by turbidity, and blue crabs were able to successfully consume nearly all mud crab and shrimp prey. Turbidity can influence predator–prey interactions by reducing the feeding efficiency of visual predators, providing a competitive advantage to chemosensory predators, and altering top-down control in food webs.
bibliographic citation: Lunt et al. (2015) Turbidity interferes with foraging success of visual but not chemosensory predators. PeerJ 3:e1212 https://doi.org/10.7717/peerj.1212
date submitted: 2015-05-13
date accepted: 2015-08-05
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lunt
  given name: Jessica
author list: Agent
  family name: Smee
  given name: Delbert L.
doi: 10.7717/peerj.1212
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Lunt and Smee
attribution name: Lunt and Smee

Attitudes towards suicide attempts broadcast on social media: an exploratory study of Chinese microblogs
type: item
type: AcademicArticle
description: Introduction. Broadcasting a suicide attempt on social media has become a public health concern in many countries, particularly in China. In these cases, social media users are likely to be the first to witness the suicide attempt, and their attitudes may determine their likelihood of joining rescue efforts. This paper examines Chinese social media (Weibo) users’ attitudes towards suicide attempts broadcast on Weibo. Methods. A total of 4,969 Weibo posts were selected from a customised Weibo User Pool which consisted of 1.06 million active users. The selected posts were then independently coded by two researchers using a coding framework that assessed: (a) Themes, (b) General attitudes, (c) Stigmatising attitudes, (d) Perceived motivations, and (e) Desired responses. Results and Discussion. More than one third of Weibo posts were coded as “stigmatising” (35%). Among these, 22%, 16%, and 15% of posts were coded as “deceitful,” “pathetic,” and “stupid,” respectively. Among the posts which reflected different types of perceived motivations, 57% of posts were coded as “seeking attention.” Among the posts which reflected desired responses, 37% were “not saving” and 28% were “encouraging suicide.” Furthermore, among the posts with negative desired responses (i.e., “not saving” and “encouraging suicide”), 57% and 17% of them were related to different types of stigmatising attitudes and perceived motivations, respectively. Specifically, 29% and 26% of posts reflecting both stigmatising attitudes and negative desired responses were coded as “deceitful” and “pathetic,” respectively, while 66% of posts reflecting both perceived motivations, and negative desired responses were coded as “seeking attention.” Very few posts “promoted literacy” (2%) or “provided resources” (8%). Gender differences existed in multiple categories. Conclusions. This paper confirms the need for stigma reduction campaigns for Chinese social media users to improve their attitudes towards those who broadc…
format: application/pdf
format: text/html
creator: Ang Li
creator: Xiaoxiao Huang
creator: Bibo Hao
creator: Bridianne O’Dea
creator: Helen Christensen
creator: Tingshao Zhu
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1209
publisher: PeerJ Inc.
rights: © 2015 Li et al.
abstract: Introduction. Broadcasting a suicide attempt on social media has become a public health concern in many countries, particularly in China. In these cases, social media users are likely to be the first to witness the suicide attempt, and their attitudes may determine their likelihood of joining rescue efforts. This paper examines Chinese social media (Weibo) users’ attitudes towards suicide attempts broadcast on Weibo. Methods. A total of 4,969 Weibo posts were selected from a customised Weibo User Pool which consisted of 1.06 million active users. The selected posts were then independently coded by two researchers using a coding framework that assessed: (a) Themes, (b) General attitudes, (c) Stigmatising attitudes, (d) Perceived motivations, and (e) Desired responses. Results and Discussion. More than one third of Weibo posts were coded as “stigmatising” (35%). Among these, 22%, 16%, and 15% of posts were coded as “deceitful,” “pathetic,” and “stupid,” respectively. Among the posts which reflected different types of perceived motivations, 57% of posts were coded as “seeking attention.” Among the posts which reflected desired responses, 37% were “not saving” and 28% were “encouraging suicide.” Furthermore, among the posts with negative desired responses (i.e., “not saving” and “encouraging suicide”), 57% and 17% of them were related to different types of stigmatising attitudes and perceived motivations, respectively. Specifically, 29% and 26% of posts reflecting both stigmatising attitudes and negative desired responses were coded as “deceitful” and “pathetic,” respectively, while 66% of posts reflecting both perceived motivations, and negative desired responses were coded as “seeking attention.” Very few posts “promoted literacy” (2%) or “provided resources” (8%). Gender differences existed in multiple categories. Conclusions. This paper confirms the need for stigma reduction campaigns for Chinese social media users to improve their attitudes towards those who broadc…
bibliographic citation: Li et al. (2015) Attitudes towards suicide attempts broadcast on social media: an exploratory study of Chinese microblogs. PeerJ 3:e1209 https://doi.org/10.7717/peerj.1209
date submitted: 2015-05-28
date accepted: 2015-08-03
issued: 2015-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ang
author list: Agent
  family name: Huang
  given name: Xiaoxiao
author list: Agent
  family name: Hao
  given name: Bibo
author list: Agent
  family name: O’Dea
  given name: Bridianne
author list: Agent
  family name: Christensen
  given name: Helen
author list: Agent
  family name: Zhu
  given name: Tingshao
doi: 10.7717/peerj.1209
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-08
copyright: © 2015 Li et al.
attribution name: Li et al.

A retrospective study on the outcomes of cataract surgery in an Eastern Regional Health Authority hospital of Trinidad and Tobago
type: item
type: AcademicArticle
description: Background. Worldwide, cataract is a major cause of blindness. The paper aims to evaluate factors associated with borderline and poor outcomes of cataract surgery at an Eastern Regional Health Authority (ERHA) hospital in Trinidad and Tobago. Materials and Methods. A hospital-based, retrospective study was done on 401 patients who had undergone cataract surgery (unilateral and bilateral) at an ERHA Hospital between March 2009 and September 2014. Data was collected on variables concerning demographic, medical history, surgical history, ocular findings and visual acuity (VA). The outcome variable of interest was Snellen’s post-operative (presenting) VA which was transformed into a dichotomous variable with borderline and poor outcomes as one and good outcomes as the other. Data were analysed using univariate and multivariate logistic regression analyses. Results. Good outcome (presenting VA 6/18 or better) was seen in 350 (67%) eyes. The fitted model consisted of ocular co-morbidity (OR =2.133; 95% CI [1.346–3.380]), hypertension (OR = 0.520; 95% CI [0.381–0.928]), surgical procedure (OR = 1.56; 95% CI [1.004–2.425]), good preoperative VA (OR = 0.388, 95% CI [0.211–0.714]), borderline preoperative VA (OR = 0.485; 95% CI = [0.278–0.843]) and year of first visit to clinic (OR = 2.243; 95% CI [1.215–4.141]). Conclusion. There is a need for community-based outreach to increase awareness of eye health and diseases. It is recommended that the general population is encouraged to take responsibility for personal management. The facilities at the Hospital should also be enhanced.
format: application/pdf
format: text/html
creator: Ebiakpo-aboere Sonron
creator: Vrijesh Tripathi
creator: Petra Bridgemohan
creator: Subash Sharma
subject: Epidemiology
subject: Ophthalmology
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1222
publisher: PeerJ Inc.
rights: © 2015 Sonron et al.
abstract: Background. Worldwide, cataract is a major cause of blindness. The paper aims to evaluate factors associated with borderline and poor outcomes of cataract surgery at an Eastern Regional Health Authority (ERHA) hospital in Trinidad and Tobago. Materials and Methods. A hospital-based, retrospective study was done on 401 patients who had undergone cataract surgery (unilateral and bilateral) at an ERHA Hospital between March 2009 and September 2014. Data was collected on variables concerning demographic, medical history, surgical history, ocular findings and visual acuity (VA). The outcome variable of interest was Snellen’s post-operative (presenting) VA which was transformed into a dichotomous variable with borderline and poor outcomes as one and good outcomes as the other. Data were analysed using univariate and multivariate logistic regression analyses. Results. Good outcome (presenting VA 6/18 or better) was seen in 350 (67%) eyes. The fitted model consisted of ocular co-morbidity (OR =2.133; 95% CI [1.346–3.380]), hypertension (OR = 0.520; 95% CI [0.381–0.928]), surgical procedure (OR = 1.56; 95% CI [1.004–2.425]), good preoperative VA (OR = 0.388, 95% CI [0.211–0.714]), borderline preoperative VA (OR = 0.485; 95% CI = [0.278–0.843]) and year of first visit to clinic (OR = 2.243; 95% CI [1.215–4.141]). Conclusion. There is a need for community-based outreach to increase awareness of eye health and diseases. It is recommended that the general population is encouraged to take responsibility for personal management. The facilities at the Hospital should also be enhanced.
bibliographic citation: Sonron et al. (2015) A retrospective study on the outcomes of cataract surgery in an Eastern Regional Health Authority hospital of Trinidad and Tobago. PeerJ 3:e1222 https://doi.org/10.7717/peerj.1222
date submitted: 2015-06-10
date accepted: 2015-08-09
issued: 2015-09-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sonron
  given name: Ebiakpo-aboere
author list: Agent
  family name: Tripathi
  given name: Vrijesh
author list: Agent
  family name: Bridgemohan
  given name: Petra
author list: Agent
  family name: Sharma
  given name: Subash
doi: 10.7717/peerj.1222
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-03
copyright: © 2015 Sonron et al.
attribution name: Sonron et al.

Ecological and socio-demographic differences in maternal care services in Nepal
type: item
type: AcademicArticle
description: Background. Nepal is set to achieve MDG-5 goals by end of 2015. However, maternal health parameters will remain way below those of developed countries. This study was conducted to assess the factors contributing to utilization of ANC and safe delivery services with the aim of furthering overall maternal health parameters in Nepal. Material and Methods. Using survey data from the Nepal Demographic and Health Survey 2011, socio-economic and demographic factors associated with the utilization of ANC and safe delivery services among women aged 15–49 years who gave births during the last three years preceding the survey are examined. Data was segregated into three ecological zones: Mountain, Hill and Terai zones for univariate analyses. Data from all three zones was then pooled for univariate and multivariate logistic regression analyses of Antenatal Care and Safe Delivery services in Nepal. Results and Conclusion. The analyses show that rural place of residence is at a disadvantage in receiving ANC (OR, 0.8; 95% CI [0.7–0.9]) and ensuring safe delivery (OR, 0.6; 95% CI [0.5–0.7]). Woman’s education, husband’s education and wealth quintile are significant factors in ensuring ANC and safe delivery services. Further, the analyses show that Budh/Muslim/Kirat/Christians are at a significant disadvantage in ensuring safe delivery (OR, 0.8; 95% CI [0.7–0.9]) as compared with Hindus. Though ecological zones lost their significance in receiving ANC, women in the Terai region are at a significant advantage in ensuring safe delivery (OR, 1.7; 95% CI [1.2–2.1]). Recommendation. Segregated targets should be set for the different ecological zones for further improvement in maternal mortality rates in Nepal.
format: application/pdf
format: text/html
creator: Vrijesh Tripathi
creator: Rajvir Singh
subject: Global Health
subject: Public Health
subject: Women's Health
description: doi:10.7717/peerj.1215
publisher: PeerJ Inc.
rights: © 2015 Tripathi and Singh
abstract: Background. Nepal is set to achieve MDG-5 goals by end of 2015. However, maternal health parameters will remain way below those of developed countries. This study was conducted to assess the factors contributing to utilization of ANC and safe delivery services with the aim of furthering overall maternal health parameters in Nepal. Material and Methods. Using survey data from the Nepal Demographic and Health Survey 2011, socio-economic and demographic factors associated with the utilization of ANC and safe delivery services among women aged 15–49 years who gave births during the last three years preceding the survey are examined. Data was segregated into three ecological zones: Mountain, Hill and Terai zones for univariate analyses. Data from all three zones was then pooled for univariate and multivariate logistic regression analyses of Antenatal Care and Safe Delivery services in Nepal. Results and Conclusion. The analyses show that rural place of residence is at a disadvantage in receiving ANC (OR, 0.8; 95% CI [0.7–0.9]) and ensuring safe delivery (OR, 0.6; 95% CI [0.5–0.7]). Woman’s education, husband’s education and wealth quintile are significant factors in ensuring ANC and safe delivery services. Further, the analyses show that Budh/Muslim/Kirat/Christians are at a significant disadvantage in ensuring safe delivery (OR, 0.8; 95% CI [0.7–0.9]) as compared with Hindus. Though ecological zones lost their significance in receiving ANC, women in the Terai region are at a significant advantage in ensuring safe delivery (OR, 1.7; 95% CI [1.2–2.1]). Recommendation. Segregated targets should be set for the different ecological zones for further improvement in maternal mortality rates in Nepal.
bibliographic citation: Tripathi et al. (2015) Ecological and socio-demographic differences in maternal care services in Nepal. PeerJ 3:e1215 https://doi.org/10.7717/peerj.1215
date submitted: 2015-02-07
date accepted: 2015-08-05
issued: 2015-09-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tripathi
  given name: Vrijesh
author list: Agent
  family name: Singh
  given name: Rajvir
doi: 10.7717/peerj.1215
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-03
copyright: © 2015 Tripathi and Singh
attribution name: Tripathi and Singh

Transcriptional and posttranscriptional regulation of Bacillus sp. CDB3 arsenic-resistance operon ars1
type: item
type: AcademicArticle
description: Bacillus sp. CDB3 possesses a novel eight-gene ars cluster (ars1, arsRYCDATorf7orf8) with some unusual features in regard to expression regulation. This study demonstrated that the cluster is a single operon but can also produce a short three-gene arsRYC transcript. A hairpin structure formed by internal inverted repeats between arsC and arsD was shown to diminish the expression of the full operon, thereby probably acting as a transcription attenuator. A degradation product of the arsRYC transcript was also identified. Electrophoretic mobility shift analysis demonstrated that ArsR interacts with the ars1 promoter forming a protein-DNA complex that could be impaired by arsenite. However, no interaction was detected between ArsD and the ars1 promoter, suggesting that the CDB3 ArsD protein may not play a regulatory role. Compared to other ars gene clusters, regulation of the Bacillus sp. CDB3 ars1 operon is more complex. It represents another example of specific mRNA degradation in the transporter gene region and possibly the first case of attenuator-mediated regulation of ars operons.
format: application/pdf
format: text/html
creator: Xuefei Yu
creator: Wei Zheng
creator: Somanath Bhat
creator: J. Andrew Aquilina
creator: Ren Zhang
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.1230
publisher: PeerJ Inc.
rights: © 2015 Yu et al.
abstract: Bacillus sp. CDB3 possesses a novel eight-gene ars cluster (ars1, arsRYCDATorf7orf8) with some unusual features in regard to expression regulation. This study demonstrated that the cluster is a single operon but can also produce a short three-gene arsRYC transcript. A hairpin structure formed by internal inverted repeats between arsC and arsD was shown to diminish the expression of the full operon, thereby probably acting as a transcription attenuator. A degradation product of the arsRYC transcript was also identified. Electrophoretic mobility shift analysis demonstrated that ArsR interacts with the ars1 promoter forming a protein-DNA complex that could be impaired by arsenite. However, no interaction was detected between ArsD and the ars1 promoter, suggesting that the CDB3 ArsD protein may not play a regulatory role. Compared to other ars gene clusters, regulation of the Bacillus sp. CDB3 ars1 operon is more complex. It represents another example of specific mRNA degradation in the transporter gene region and possibly the first case of attenuator-mediated regulation of ars operons.
bibliographic citation: Yu et al. (2015) Transcriptional and posttranscriptional regulation of Bacillus sp. CDB3 arsenic-resistance operon ars1. PeerJ 3:e1230 https://doi.org/10.7717/peerj.1230
date submitted: 2015-02-24
date accepted: 2015-08-16
issued: 2015-09-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Xuefei
author list: Agent
  family name: Zheng
  given name: Wei
author list: Agent
  family name: Bhat
  given name: Somanath
author list: Agent
  family name: Aquilina
  given name: J. Andrew
author list: Agent
  family name: Zhang
  given name: Ren
doi: 10.7717/peerj.1230
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-03
copyright: © 2015 Yu et al.
attribution name: Yu et al.

An explanation of the relationship between mass, metabolic rate and characteristic length for placental mammals
type: item
type: AcademicArticle
description: The Mass, Metabolism and Length Explanation (MMLE) was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. This paper reports on a modernized version of MMLE. MMLE deterministically computes the absolute value of Basal Metabolic Rate (BMR) and body mass for individual animals. MMLE is thus distinct from other examinations of these topics that use species-averaged data to estimate the parameters in a statistically best fit power law relationship such as BMR = a(bodymass)b. Beginning with the proposition that BMR is proportional to the number of mitochondria in an animal, two primary equations are derived that compute BMR and body mass as functions of an individual animal’s characteristic length and sturdiness factor. The characteristic length is a measureable skeletal length associated with an animal’s means of propulsion. The sturdiness factor expresses how sturdy or gracile an animal is. Eight other parameters occur in the equations that vary little among animals in the same phylogenetic group. The present paper modernizes MMLE by explicitly treating Froude and Strouhal dynamic similarity of mammals’ skeletal musculature, revising the treatment of BMR and using new data to estimate numerical values for the parameters that occur in the equations. A mass and length data set with 575 entries from the orders Rodentia, Chiroptera, Artiodactyla, Carnivora, Perissodactyla and Proboscidea is used. A BMR and mass data set with 436 entries from the orders Rodentia, Chiroptera, Artiodactyla and Carnivora is also used. With the estimated parameter values MMLE can calculate characteristic length and sturdiness factor values so that every BMR and mass datum from the BMR and mass data set can be computed exactly. Furthermore MMLE can calculate characteristic length and sturdiness factor values so that every body mass and length datum from the mass and length data set can be computed exactly. Whether or not MMLE can calculate a …
format: application/pdf
format: text/html
creator: Charles C. Frasier
subject: Biophysics
subject: Mathematical Biology
subject: Zoology
description: doi:10.7717/peerj.1228
publisher: PeerJ Inc.
rights: © 2015 Frasier
abstract: The Mass, Metabolism and Length Explanation (MMLE) was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. This paper reports on a modernized version of MMLE. MMLE deterministically computes the absolute value of Basal Metabolic Rate (BMR) and body mass for individual animals. MMLE is thus distinct from other examinations of these topics that use species-averaged data to estimate the parameters in a statistically best fit power law relationship such as BMR = a(bodymass)b. Beginning with the proposition that BMR is proportional to the number of mitochondria in an animal, two primary equations are derived that compute BMR and body mass as functions of an individual animal’s characteristic length and sturdiness factor. The characteristic length is a measureable skeletal length associated with an animal’s means of propulsion. The sturdiness factor expresses how sturdy or gracile an animal is. Eight other parameters occur in the equations that vary little among animals in the same phylogenetic group. The present paper modernizes MMLE by explicitly treating Froude and Strouhal dynamic similarity of mammals’ skeletal musculature, revising the treatment of BMR and using new data to estimate numerical values for the parameters that occur in the equations. A mass and length data set with 575 entries from the orders Rodentia, Chiroptera, Artiodactyla, Carnivora, Perissodactyla and Proboscidea is used. A BMR and mass data set with 436 entries from the orders Rodentia, Chiroptera, Artiodactyla and Carnivora is also used. With the estimated parameter values MMLE can calculate characteristic length and sturdiness factor values so that every BMR and mass datum from the BMR and mass data set can be computed exactly. Furthermore MMLE can calculate characteristic length and sturdiness factor values so that every body mass and length datum from the mass and length data set can be computed exactly. Whether or not MMLE can calculate a …
bibliographic citation: Frasier (2015) An explanation of the relationship between mass, metabolic rate and characteristic length for placental mammals. PeerJ 3:e1228 https://doi.org/10.7717/peerj.1228
date submitted: 2014-12-18
date accepted: 2015-08-13
issued: 2015-09-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frasier
  given name: Charles C.
doi: 10.7717/peerj.1228
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-03
copyright: © 2015 Frasier
attribution name: Frasier

Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of ‘river dolphins’ in the Americas
type: item
type: AcademicArticle
description: In contrast to dominant mode of ecological transition in the evolution of marine mammals, different lineages of toothed whales (Odontoceti) have repeatedly invaded freshwater ecosystems during the Cenozoic era. The so-called ‘river dolphins’ are now recognized as independent lineages that converged on similar morphological specializations (e.g., longirostry). In South America, the two endemic ‘river dolphin’ lineages form a clade (Inioidea), with closely related fossil inioids from marine rock units in the South Pacific and North Atlantic oceans. Here we describe a new genus and species of fossil inioid, Isthminia panamensis, gen. et sp. nov. from the late Miocene of Panama. The type and only known specimen consists of a partial skull, mandibles, isolated teeth, a right scapula, and carpal elements recovered from the Piña Facies of the Chagres Formation, along the Caribbean coast of Panama. Sedimentological and associated fauna from the Piña Facies point to fully marine conditions with high planktonic productivity about 6.1–5.8 million years ago (Messinian), pre-dating the final closure of the Isthmus of Panama. Along with ecomorphological data, we propose that Isthminia was primarily a marine inhabitant, similar to modern oceanic delphinoids. Phylogenetic analysis of fossil and living inioids, including new codings for Ischyrorhynchus, an enigmatic taxon from the late Miocene of Argentina, places Isthminia as the sister taxon to Inia, in a broader clade that includes Ischyrorhynchus and Meherrinia, a North American fossil inioid. This phylogenetic hypothesis complicates the possible scenarios for the freshwater invasion of the Amazon River system by stem relatives of Inia, but it remains consistent with a broader marine ancestry for Inioidea. Based on the fossil record of this group, along with Isthminia, we propose that a marine ancestor of Inia invaded Amazonia during late Miocene eustatic sea-level highs.
format: application/pdf
format: text/html
creator: Nicholas D. Pyenson
creator: Jorge Vélez-Juarbe
creator: Carolina S. Gutstein
creator: Holly Little
creator: Dioselina Vigil
creator: Aaron O’Dea
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.1227
publisher: PeerJ Inc.
rights: © 2015 Pyenson et al.
abstract: In contrast to dominant mode of ecological transition in the evolution of marine mammals, different lineages of toothed whales (Odontoceti) have repeatedly invaded freshwater ecosystems during the Cenozoic era. The so-called ‘river dolphins’ are now recognized as independent lineages that converged on similar morphological specializations (e.g., longirostry). In South America, the two endemic ‘river dolphin’ lineages form a clade (Inioidea), with closely related fossil inioids from marine rock units in the South Pacific and North Atlantic oceans. Here we describe a new genus and species of fossil inioid, Isthminia panamensis, gen. et sp. nov. from the late Miocene of Panama. The type and only known specimen consists of a partial skull, mandibles, isolated teeth, a right scapula, and carpal elements recovered from the Piña Facies of the Chagres Formation, along the Caribbean coast of Panama. Sedimentological and associated fauna from the Piña Facies point to fully marine conditions with high planktonic productivity about 6.1–5.8 million years ago (Messinian), pre-dating the final closure of the Isthmus of Panama. Along with ecomorphological data, we propose that Isthminia was primarily a marine inhabitant, similar to modern oceanic delphinoids. Phylogenetic analysis of fossil and living inioids, including new codings for Ischyrorhynchus, an enigmatic taxon from the late Miocene of Argentina, places Isthminia as the sister taxon to Inia, in a broader clade that includes Ischyrorhynchus and Meherrinia, a North American fossil inioid. This phylogenetic hypothesis complicates the possible scenarios for the freshwater invasion of the Amazon River system by stem relatives of Inia, but it remains consistent with a broader marine ancestry for Inioidea. Based on the fossil record of this group, along with Isthminia, we propose that a marine ancestor of Inia invaded Amazonia during late Miocene eustatic sea-level highs.
bibliographic citation: Pyenson et al. (2015) Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of ‘river dolphins’ in the Americas. PeerJ 3:e1227 https://doi.org/10.7717/peerj.1227
date submitted: 2015-04-27
date accepted: 2015-08-13
issued: 2015-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pyenson
  given name: Nicholas D.
author list: Agent
  family name: Vélez-Juarbe
  given name: Jorge
author list: Agent
  family name: Gutstein
  given name: Carolina S.
author list: Agent
  family name: Little
  given name: Holly
author list: Agent
  family name: Vigil
  given name: Dioselina
author list: Agent
  family name: O’Dea
  given name: Aaron
doi: 10.7717/peerj.1227
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-01
copyright: © 2015 Pyenson et al.
attribution name: Pyenson et al.

Assessing uncertainty in sighting records: an example of the Barbary lion
type: item
type: AcademicArticle
description: As species become rare and approach extinction, purported sightings can be controversial, especially when scarce management resources are at stake. We consider the probability that each individual sighting of a series is valid. Obtaining these probabilities requires a strict framework to ensure that they are as accurately representative as possible. We used a process, which has proven to provide accurate estimates from a group of experts, to obtain probabilities for the validation of 32 sightings of the Barbary lion. We consider the scenario where experts are simply asked whether a sighting was valid, as well as asking them to score the sighting based on distinguishablity, observer competence, and verifiability. We find that asking experts to provide scores for these three aspects resulted in each sighting being considered more individually, meaning that this new questioning method provides very different estimated probabilities that a sighting is valid, which greatly affects the outcome from an extinction model. We consider linear opinion pooling and logarithm opinion pooling to combine the three scores, and also to combine opinions on each sighting. We find the two methods produce similar outcomes, allowing the user to focus on chosen features of each method, such as satisfying the marginalisation property or being externally Bayesian.
format: application/pdf
format: text/html
creator: Tamsin E. Lee
creator: Simon A. Black
creator: Amina Fellous
creator: Nobuyuki Yamaguchi
creator: Francesco M. Angelici
creator: Hadi Al Hikmani
creator: J. Michael Reed
creator: Chris S. Elphick
creator: David L. Roberts
subject: Ecology
subject: Mathematical Biology
description: doi:10.7717/peerj.1224
publisher: PeerJ Inc.
rights: © 2015 Lee et al.
abstract: As species become rare and approach extinction, purported sightings can be controversial, especially when scarce management resources are at stake. We consider the probability that each individual sighting of a series is valid. Obtaining these probabilities requires a strict framework to ensure that they are as accurately representative as possible. We used a process, which has proven to provide accurate estimates from a group of experts, to obtain probabilities for the validation of 32 sightings of the Barbary lion. We consider the scenario where experts are simply asked whether a sighting was valid, as well as asking them to score the sighting based on distinguishablity, observer competence, and verifiability. We find that asking experts to provide scores for these three aspects resulted in each sighting being considered more individually, meaning that this new questioning method provides very different estimated probabilities that a sighting is valid, which greatly affects the outcome from an extinction model. We consider linear opinion pooling and logarithm opinion pooling to combine the three scores, and also to combine opinions on each sighting. We find the two methods produce similar outcomes, allowing the user to focus on chosen features of each method, such as satisfying the marginalisation property or being externally Bayesian.
bibliographic citation: Lee et al. (2015) Assessing uncertainty in sighting records: an example of the Barbary lion. PeerJ 3:e1224 https://doi.org/10.7717/peerj.1224
date submitted: 2015-05-06
date accepted: 2015-08-11
issued: 2015-09-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Tamsin E.
author list: Agent
  family name: Black
  given name: Simon A.
author list: Agent
  family name: Fellous
  given name: Amina
author list: Agent
  family name: Yamaguchi
  given name: Nobuyuki
author list: Agent
  family name: Angelici
  given name: Francesco M.
author list: Agent
  family name: Al Hikmani
  given name: Hadi
author list: Agent
  family name: Reed
  given name: J. Michael
author list: Agent
  family name: Elphick
  given name: Chris S.
author list: Agent
  family name: Roberts
  given name: David L.
doi: 10.7717/peerj.1224
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-01
copyright: © 2015 Lee et al.
attribution name: Lee et al.

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