title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1621 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Anther development in tribe Epidendreae: orchids with contrasting pollination syndromes link: https://peerj.com/articles/4383 last-modified: 2018-02-27 description: BackgroundEpidendreae is one of the most diverse tribes among the orchids with remarkable variation in life form, floral morphology and pollination syndromes. Its circumscription was recently revised and subtribes Agrostophyllinae and Calypsoinae were transferred into this tribe. One of the principal floral characters utilized in classification of orchids is the incumbency or bending of the column. This study records and compares late stages of anther, column and lip development, and discusses anther characters in fifteen representative taxa of five of the six subtribes in Epidendreae with respect to classification and pollination biology.MethodsA series of late floral stages were sampled and fixed for examination under scanning electron microscope.ResultsAnther incumbency or bending in this group varies from 90° to almost 180°. Incumbency in the late stages of development is reached in Bletiinae, Ponerinae, Pleurothallidinae and Laeliinae whereas incumbency is reached early in its development in Corallorhiza and Govenia of Calypsoinae.DiscussionOur observations indicate that the position of Chysis in subtribe Bletiinae needs revision based on differences in a number floral, and in particular of anther characters; and that Coelia only shares the early anther incumbency with Calypsoinae members, but not the rest of floral and anther characters. Anatomical characters such as crystals around the actinocytic stomata on the anther cap and sugar crystals in Laeliinae; lack of rostellum in Bletiinae; coalescent anther with the column, lack of trichomes and papillae on lip keels, and underdeveloped rostellum in Chysis; a mechanism by which the anther cap comes off (it is joined with the grooved lip by a claw) in Isochilus are all related to pollination syndromes and reproductive biology. creator: Benjamín Valencia-Nieto creator: Victoria Sosa creator: Judith Márquez-Guzmán uri: https://doi.org/10.7717/peerj.4383 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Valencia-Nieto et al. title: Seasonal variation in the abundance and distribution of Anomalocardia flexuosa (Mollusca, Bivalvia, Veneridae) in an estuarine intertidal plain link: https://peerj.com/articles/4332 last-modified: 2018-02-27 description: Spatial and temporal density and biomass of the infaunal mollusk Anomalocardia flexuosa (Linnaeus, 1767) evaluated a tidal plain at Goiana estuary (Northeast Brazil). Three hundred and sixty core samples were taken during an annual cycle from three intertidal habitats (A, B and C). Shell ranged from 2.20 to 28.48 mm (15.08 ± 4.08 mm). Recruitment occurred more intensely from January to March. Total (0–1,129 g m−2) differed seasons (rainy and dry), with highest values in the early rainy season (221.0 ± 231.44 g m−2); and lowest values in the late dry season (57.34 ± 97 g m−2). The lowest occurred during the late rainy (319 ± 259 ind m−2) and early dry (496 ± 607 ind m−2) seasons. Extreme environmental situations (e.g., river flow, salinity and water temperature) at the end of each season also affected density ranges (late dry: 0–5,798 ind m−2; late rainy: 0–1,170 ind m−2). A. flexuosa in the Goiana estuary presented a dominance of juvenile individuals (shell length < 20 mm), with high biomass main the recruitment period. Average shell length, density and biomass values suggest overfishing of the stock unit. A. flexuosa is an important food and income resource along its whole distribution range. The species was previously also known as Anomalocardia brasiliana (Gmelin, 1791). creator: Jacqueline S. Silva-Cavalcanti creator: Monica F. Costa creator: Luis H.B. Alves uri: https://doi.org/10.7717/peerj.4332 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Silva-Cavalcanti et al. title: Feature-by-feature comparison and holistic processing in unfamiliar face matching link: https://peerj.com/articles/4437 last-modified: 2018-02-26 description: Identity comparisons of photographs of unfamiliar faces are prone to error but imperative for security settings, such as the verification of face identities at passport control. Therefore, finding techniques to improve face-matching accuracy is an important contemporary research topic. This study investigates whether matching accuracy can be enhanced by verbal instructions that address feature comparisons or holistic processing. Findings demonstrate that feature-by-feature comparison strategy had no effect on face matching. In contrast, verbal instructions focused on holistic processing made face matching faster, but they impaired accuracy. Given the recent evidence for the heredity of face perception and the previously reported small or no improvements of face-matching ability, it seems reasonable to suggest that improving unfamiliar face matching is not an easy task, but it is presumably worthwhile to explore new methods for improvement nonetheless. creator: Ahmed M. Megreya uri: https://doi.org/10.7717/peerj.4437 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Megreya title: Regenerative agriculture: merging farming and natural resource conservation profitably link: https://peerj.com/articles/4428 last-modified: 2018-02-26 description: Most cropland in the United States is characterized by large monocultures, whose productivity is maintained through a strong reliance on costly tillage, external fertilizers, and pesticides (Schipanski et al., 2016). Despite this, farmers have developed a regenerative model of farm production that promotes soil health and biodiversity, while producing nutrient-dense farm products profitably. Little work has focused on the relative costs and benefits of novel regenerative farming operations, which necessitates studying in situ, farmer-defined best management practices. Here, we evaluate the relative effects of regenerative and conventional corn production systems on pest management services, soil conservation, and farmer profitability and productivity throughout the Northern Plains of the United States. Regenerative farming systems provided greater ecosystem services and profitability for farmers than an input-intensive model of corn production. Pests were 10-fold more abundant in insecticide-treated corn fields than on insecticide-free regenerative farms, indicating that farmers who proactively design pest-resilient food systems outperform farmers that react to pests chemically. Regenerative fields had 29% lower grain production but 78% higher profits over traditional corn production systems. Profit was positively correlated with the particulate organic matter of the soil, not yield. These results provide the basis for dialogue on ecologically based farming systems that could be used to simultaneously produce food while conserving our natural resource base: two factors that are pitted against one another in simplified food production systems. To attain this requires a systems-level shift on the farm; simply applying individual regenerative practices within the current production model will not likely produce the documented results. creator: Claire E. LaCanne creator: Jonathan G. Lundgren uri: https://doi.org/10.7717/peerj.4428 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 LaCanne and Lundgren title: Merging cranial histology and 3D-computational biomechanics: a review of the feeding ecology of a Late Triassic temnospondyl amphibian link: https://peerj.com/articles/4426 last-modified: 2018-02-26 description: Finite Element Analysis (FEA) is a useful method for understanding form and function. However, modelling of fossil taxa invariably involves assumptions as a result of preservation-induced loss of information in the fossil record. To test the validity of predictions from FEA, given such assumptions, these results could be compared to independent lines of evidence for cranial mechanics. In the present study a new concept of using bone microstructure to predict stress distribution in the skull during feeding is put forward and a correlation between bone microstructure and results of computational biomechanics (FEA) is carried out. The bony framework is a product of biological optimisation; bone structure is created to meet local mechanical conditions. To test how well results from FEA correlate to cranial mechanics predicted from bone structure, the well-known temnospondyl Metoposaurus krasiejowensis was used as a model. A crucial issue to Temnospondyli is their feeding mode: did they suction feed or employ direct biting, or both? Metoposaurids have previously been characterised either as active hunters or passive bottom dwellers. In order to test the correlation between results from FEA and bone microstructure, two skulls of Metoposaurus were used, one modelled under FE analyses, while for the second one 17 dermal bone microstructure were analysed. Thus, for the first time, results predicting cranial mechanical behaviour using both methods are merged to understand the feeding strategy of Metoposaurus. Metoposaurus appears to have been an aquatic animal that exhibited a generalist feeding behaviour. This taxon may have used two foraging techniques in hunting; mainly bilateral biting and, to a lesser extent, lateral strikes. However, bone microstructure suggests that lateral biting was more frequent than suggested by Finite Element Analysis (FEA). One of the potential factors that determined its mode of life may have been water levels. During optimum water conditions, metoposaurids may have been more active ambush predators that were capable of lateral strikes of the head. The dry season required a less active mode of life when bilateral biting is particularly efficient. This, combined with their characteristically anteriorly positioned orbits, was optimal for ambush strategy. This ability to use alternative modes of food acquisition, independent of environmental conditions, might hold the key in explaining the very common occurrence of metoposaurids during the Late Triassic. creator: Dorota Konietzko-Meier creator: Kamil Gruntmejer creator: Jordi Marcé-Nogué creator: Adam Bodzioch creator: Josep Fortuny uri: https://doi.org/10.7717/peerj.4426 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Konietzko-Meier et al. title: Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding link: https://peerj.com/articles/4412 last-modified: 2018-02-26 description: The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. creator: Alexey Smirnov creator: Asta Zubrienė creator: Elena Manakova creator: Saulius Gražulis creator: Daumantas Matulis uri: https://doi.org/10.7717/peerj.4412 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Smirnov et al. title: Pharmacokinetics and safety of oral glyburide in dogs with acute spinal cord injury link: https://peerj.com/articles/4387 last-modified: 2018-02-26 description: BackgroundGlyburide (also known as glibenclamide) is effective in reducing the severity of tissue destruction and improving functional outcome after experimental spinal cord injury in rodents and so has promise as a therapy in humans. There are many important differences between spinal cord injury in experimental animals and in human clinical cases, making it difficult to introduce new therapies into clinical practice. Spinal cord injury is also common in pet dogs and requires new effective therapies, meaning that they can act as a translational model for the human condition while also deriving direct benefits from such research. In this study we investigated the pharmacokinetics and safety of glyburide in dogs with clinical spinal cord injury.MethodsWe recruited dogs that had incurred an acute thoracolumbar spinal cord injury within the previous 72 h. These had become acutely non-ambulatory on the pelvic limbs and were admitted to our veterinary hospitals to undergo anesthesia, cross sectional diagnostic imaging, and surgical decompression. Oral glyburide was given to each dog at a dose of 75 mcg/kg. In five dogs, we measured blood glucose concentrations for 10 h after a single oral dose. In six dogs, we measured serum glyburide and glucose concentrations for 24 h and estimated pharmacokinetic parameters to estimate a suitable dose for use in a subsequent clinical trial in similarly affected dogs.ResultsNo detrimental effects of glyburide administration were detected in any participating dog. Peak serum concentrations of glyburide were attained at a mean of 13 h after dosing, and mean apparent elimination half-life was approximately 7 h. Observed mean maximum plasma concentration was 31 ng/mL. At the glyburide dose administered there was no observable association between glyburide and glucose concentrations in blood.DiscussionOur data suggest that glyburide can be safely administered to dogs that are undergoing anesthesia, imaging and surgery for treatment of their acute spinal cord injury and can attain clinically-relevant serum concentrations without developing hazardous hypoglycemia. Serum glyburide concentrations achieved in this study suggest that a loading dose of 150 mcg/kg followed by repeat doses of 75 mcg/kg at 8-hourly intervals would lead to serum glyburide concentrations of 25–50 ng/mL within an acceptably short enough period after oral administration to be appropriate for a clinical trial in canine spinal cord injury. creator: Nick Jeffery creator: C. Elizabeth Boudreau creator: Megan Konarik creator: Travis Mays creator: Virginia Fajt uri: https://doi.org/10.7717/peerj.4387 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jeffery et al. title: A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand link: https://peerj.com/articles/4422 last-modified: 2018-02-23 description: We report on a discovery of Siamophryne troglodytesGen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA–16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytesGen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the “out of Indo-Eurasia” biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytesGen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it. creator: Chatmongkon Suwannapoom creator: Montri Sumontha creator: Jitthep Tunprasert creator: Thiti Ruangsuwan creator: Parinya Pawangkhanant creator: Dmitriy V. Korost creator: Nikolay A. Poyarkov uri: https://doi.org/10.7717/peerj.4422 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Suwannapoom et al. title: Assessment of three risk evaluation systems for patients aged ≥70 in East China: performance of SinoSCORE, EuroSCORE II and the STS risk evaluation system link: https://peerj.com/articles/4413 last-modified: 2018-02-23 description: ObjectivesTo assess and compare the predictive ability of three risk evaluation systems (SinoSCORE, EuroSCORE II and the STS risk evaluation system) in patients aged ≥70, and who underwent coronary artery bypass grafting (CABG) in East China.MethodsThree risk evaluation systems were applied to 1,946 consecutive patients who underwent isolated CABG from January 2004 to September 2016 in two hospitals. Patients were divided into two subsets according to their age: elderly group (age ≥70) with a younger group (age <70) used for comparison. The outcome of interest in this study was in-hospital mortality. The entire cohort and subsets of patients were analyzed. The calibration and discrimination in total and in subsets were assessed by the Hosmer–Lemeshow and the C statistics respectively.ResultsInstitutional overall mortality was 2.52%. The expected mortality rates of SinoSCORE, EuroSCORE II and the STS risk evaluation system were 0.78(0.64)%, 1.43(1.14)% and 0.78(0.77)%, respectively. SinoSCORE achieved the best discrimination (the area under the receiver operating characteristic curve (AUC) = 0.829), followed by the STS risk evaluation system (AUC = 0.790) and EuroSCORE II (AUC = 0.769) in the entire cohort. In the elderly group, the observed mortality rate was 4.82% while it was 1.38% in the younger group. SinoSCORE (AUC = .829) also achieved the best discrimination in the elderly group, followed by the STS risk evaluation system (AUC = .730) and EuroSCORE II (AUC = 0.640) while all three risk evaluation systems all had good performances in the younger group. SinoSCORE, EuroSCORE II and the STS risk evaluation system all achieved positive calibrations in the entire cohort and subsets.ConclusionThe performance of the three risk evaluation systems was not ideal in the entire cohort. In the elderly group, SinoSCORE appeared to achieve better predictive efficiency than EuroSCORE II and the STS risk evaluation system. creator: Lingtong Shan creator: Wen Ge creator: Yiwei Pu creator: Hong Cheng creator: Zhengqiang Cang creator: Xing Zhang creator: Qifan Li creator: Anyang Xu creator: Qi Wang creator: Chang Gu creator: Yangyang Zhang uri: https://doi.org/10.7717/peerj.4413 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shan et al. title: Conservative treatment for patients with subacromial impingement: Changes in clinical core outcomes and their relation to specific rehabilitation parameters link: https://peerj.com/articles/4400 last-modified: 2018-02-23 description: BackgroundImpaired patient-reported shoulder function and pain, external-rotation strength, abduction strength, and abduction range-of-motion (ROM) is reported in patients with subacromial impingement (SIS). However, it is unknown how much strength and ROM improves in real-life practice settings with current care. Furthermore, outcomes of treatment might depend on specific rehabilitation parameters, such as the time spent on exercises (exercise-time), number of physiotherapy sessions (physio-sessions) and number of corticosteroid injections, respectively. However, this has not previously been investigated. The purpose of this study was to describe changes in shoulder strength, ROM, patient-reported function and pain, in real-life practice settings, and explore the association between changes in clinical core outcomes and specific rehabilitation parameters.MethodsPatients diagnosed with SIS at initial assessment at an outpatient hospital clinic using predefined criteria’s, who had not undergone surgery after 6 months, were included in this prospective cohort study. After initial assessment (baseline), all patients underwent treatment as usual, with no interference from the investigators. The outcomes Shoulder Pain and Disability Index (SPADI:0–100), average pain (NRS:0–10), external rotation strength, abduction strength and abduction ROM, pain during each test (NRS:0–10), were collected at baseline and at six month follow-up. Amount of exercise-time, physio-sessions and steroid-injections was recorded at follow-up. Changes in outcomes were analyzed using Wilcoxon Signed-Rank test, and the corresponding effect sizes (ES) were estimated. The associations between changes in outcomes and rehabilitation parameters were explored using multiple regression analyses.ResultsSixty-three patients completed both baseline and follow-up testing. Significant improvements were seen in SPADI (19 points, ES:0.53, p < 0.001) and all pain variables (median 1–1.5 points, ES:0.26–0.39, p < 0.01), but not in strength and ROM (ES:0.9–0.12, p > 0.2). A higher number of physio-sessions was significantly associated with larger improvements in external rotation strength (0.7 Newton/session, p = 0.046), and higher exercise-time was significantly associated with decrease in average pain (−0.2 points/1,000 min, p = 0.048).DiscussionPatient-reported function and pain improved after six months of current care, but strength and ROM did not improve. This is interesting, as strengthening exercises is part of most current interventions. While two significant associations were identified between self-reported rehabilitation parameters and outcomes, the small gains per physio-session or 1,000 min of exercise-time reduces the clinical relevance of these relationships. Collectively, the findings from this study indicate room for improvement of the current rehabilitation of SIS, especially with regard to core clinical outcomes, such as strength and range of motion. creator: Mikkel B. Clausen creator: Mikas B. Merrild creator: Adam Witten creator: Karl B. Christensen creator: Mette K. Zebis creator: Per Hölmich creator: Kristian Thorborg uri: https://doi.org/10.7717/peerj.4400 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Clausen et al.