title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=478 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Optimal tillage depths for enhancing rice yield, quality and lodging resistance in the rice production systems of northeast China link: https://peerj.com/articles/15739 last-modified: 2023-07-19 description: Long-term shallow tillage leads to poor development of root system and deterioration of soil quality. Field experiments were conducted during 2019–2021 to explore the effects of different tillage depths on rice root system, stem lodging resistance, rice yield and quality. The experimental treatments were comprised of four tillage depths i.e., 14 cm (TD 14) as the control, 17 cm (TD17), 20 cm (TD20), and 23 cm (TD23) by using a tractor- mounted hydraulic-adjustable. Results indicated that the TD17 treatment substantially improved the breaking resistance by 39.45–72.37% and decreased the lodging index by 11.73–29.94% of first to third node attribute, increased the stem diameter and unit length dry weight and decreased the internode length, compared with control. The TD17 treatment also reduced the chalkiness, chalkiness rate by 26.23% and 32.30%, respectively. Moreover, the viscosity value and cooking and eating quality of rice in TD17 treatment were improved 27.30% and 12.33%, respectively, compared to control. Moreover, the TD20 treatment enhanced the grain yield by 9.18% owing to the higher panicle number and grain number per panicle. The highest photosynthetic rate was also found in the TD20 treatment, which was significant higher 15.57% than TD14 treatment. Overall, the 17–20 cm was found the optimum tillage depth and therefore recommended to the farmers to get improved rice yield with minimum lodging in the rice production systems of the Northeast China. creator: Diankai Gong creator: Guijin Dai creator: Ying Chen creator: Guangxing Yu uri: https://doi.org/10.7717/peerj.15739 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gong et al. title: Prediction of sea ice area based on the CEEMDAN-SO-BiLSTM model link: https://peerj.com/articles/15748 last-modified: 2023-07-19 description: This article proposes a combined prediction model based on a bidirectional long short-term memory (BiLSTM) neural network optimized by the snake optimizer (SO) under complete ensemble empirical mode decomposition with adaptive noise. First, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) was used to decompose the sea ice area time series data into a series of eigenmodes and perform noise reduction to enhance the stationarity and smoothness of the time series. Second, this article used a bidirectional long short-term memory neural network optimized by the snake optimizer to fully exploit the characteristics of each eigenmode of the time series to achieve the prediction of each. Finally, the predicted values of each mode are superimposed and reconstructed as the final prediction values. Our model achieves a good score of RMSE: 1.047, MAE: 0.815, and SMAPE: 3.938 on the test set. creator: Qiao Guo creator: Haoyu Zhang creator: Yuhao Zhang creator: Xuchu Jiang uri: https://doi.org/10.7717/peerj.15748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: Recent research progress on the correlation between metabolic syndrome and Helicobacter pylori infection link: https://peerj.com/articles/15755 last-modified: 2023-07-19 description: BackgroundGlobally, metabolic syndrome (MS) and Helicobacter pylori (HP) infection, which have gained an epidemic status, are major challenges to human health, society, and medical professionals. Recent studies have demonstrated that MS is closely related to HP infection. Additionally, HP is an important risk factor for gastric cancer. However, systematic reviews on HP are lacking. This review aimed to summarize and analyze the potential correlation of HP infection with MS and its components, as well as the underlying mechanism, to provide reference and strategies for clinical prevention and treatment.MethodologyPrevious studies examining the correlation between HP and MS since 1990 were retrieved from the PubMed, Web of Science, and Embase databases. The potential correlation between HP infection and MS and its components was comprehensively analyzed. The keywords “Helicobacter pylori,” “HP,” “metabolic syndrome,” “hypertension,” “obesity,” “diabetes,” or “dyslipidemia” were used in all fields. No language restrictions were imposed.ResultsMS was strongly correlated to HP infection. The inflammatory response and inflammatory factors produced during HP infection are important etiological factors for insulin resistance and MS. The co-occurrence of long-term chronic inflammation and immune dysfunction with MS may be the predisposing factor for HP infection. MS components, such as diabetes, hypertension, dyslipidemia, and obesity were also correlated with HP infection in one or both directions.ConclusionsHP infection and MS may promote the pathogenesis of each other. The contribution of HP infection and MS to gastric cancer cannot be ruled out based on co-occurrence. The MS components diabetes and obesity may be bidirectionally correlated with HP infection. creator: Qinli Xie creator: Yangjun He creator: Danni Zhou creator: Yi Jiang creator: Ying Deng creator: Ruoqing Li uri: https://doi.org/10.7717/peerj.15755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xie et al. title: Putative causal inference for the relationship between obesity and sex hormones in males: a bidirectional Mendelian randomization study link: https://peerj.com/articles/15760 last-modified: 2023-07-19 description: BackgroundObesity is a chronic disease with a high prevalence rate and is an established risk factor for human health. Body mass index (BMI) is a common and primary indicator used in assessing obesity. This work aims to investigate the putative causal relationship among BMI, sex hormone-binding globulin (SHBG), bioavailable testosterone (BioT), and estradiol levels.Materials and MethodsWe conducted a bidirectional Mendelian randomization study, using single-nucleotide polymorphisms (SNPs) strongly associated with BMI, SHBG, BioT, and estradiol as instrumental variables. All SNPs were identified from the genome-wide association study (GWAS) summary data of large sample studies recruiting more than 150,000 European adult male individuals. The inverse-variance-weighted (IVW) approach was used as a primary algorithm for putative causal estimation.ResultsGenetically predicted elevated BMI was associated with decreased SHBG (IVW, β = −0.103, 95% confidence interval [CI] [−0.113 to −0.092], P = 1.50 × 10−77) and BioT levels (IVW, β = −0.139, 95% CI [−0.165 to −0.113], P = 9.54 × 10−26) and high estradiol levels (IVW, β = 0.014, 95% CI [0.009–0.019], P = 2.19 × 10−7). Increased SHBG levels were causally associated with low BMI (IVW, β = −0.051, 95% CI [−0.098 to −0.005], P = 0.030) and BioT (IVW, β = −0.126, 95% CI [−0.175 to −0.077], P = 5.97 × 10−7) and high estradiol levels (IVW, β = 0.046, 95% CI [0.035–0.056], P = 6.51 × 10−17). Conversely, no evidence of an effect of estradiol imbalance on SHBG levels (IVW, β = 1.035, 95% CI [−0.854 to 2.926], P = 0.283) and BMI (IVW, β = 0.091, 95% CI [−0.094 to 0.276], P = 0.336) was obtained. However, increased BioT levels were causally associated with lower SHBG levels (IVW, β = −0.044, 95% CI [−0.061 to −0.026], P = 8.76 × 10−7), not BMI (IVW, β = −0.006, 95% CI [−0.035 to 0.023], P = 0.679).ConclusionsThe findings support a network putative causal relationship among BMI, SHBG, BioT, and estradiol. SHBG, BioT, and estradiol may partly mediate the effect of obesity on male health. Reasonably modulating BioT and estradiol, especially SHBG, facilitated the attenuation of the harmful effects of obesity on male health. creator: Bangbei Wan creator: Ning Ma creator: Zhi Zhou creator: Cai Lv uri: https://doi.org/10.7717/peerj.15760 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wan et al. title: Why can people with developmental prosopagnosia recognise some familiar faces? Insights from subjective experience link: https://peerj.com/articles/15497 last-modified: 2023-07-18 description: Developmental prosopagnosia is a relatively common visuo-cognitive condition, characterised by impaired facial identity recognition. Impairment severity appears to reside on a continuum, however, it is unknown whether instances of milder deficits reflect the successful use of spontaneous (typical) face recognition strategies, or the application of extraneous compensatory cues to recognition. Here, we explore this issue in two studies. First, 23 adults with developmental prosopagnosia were asked about their use of spontaneous versus compensatory face recognition techniques in everyday life, using a series of closed- and open-ended questions. Second, the same participants performed a computerised famous face recognition task where they were asked to provide reasons why they could make any successful identifications. Findings from both studies suggest that people with developmental prosopagnosia can successfully, and quite frequently, use compensatory strategies to recognition, and that these cues support the majority of instances of preserved familiar face recognition. In contrast, 16 of the 23 participants were able to spontaneously recognise familiar faces on at least some occasions, but there were vast individual differences in frequencies of success. These findings have important implications for our conceptualisation of the condition, as well as for diagnostic practice. creator: Emma Portch creator: Liam Wignall creator: Sarah Bate uri: https://doi.org/10.7717/peerj.15497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Portch et al. title: Functional trait diversity of Cyclanthaceae and its convergent evolution with Araceae in Neotropical forests link: https://peerj.com/articles/15557 last-modified: 2023-07-18 description: The Cyclanthaceae comprise a relatively small family of about 230 species and 12 genera in the Pandanales that is widespread in wet Neotropical forests. The great majority of species can be divided into three growth forms (understory herbs, epiphytes, and root-climbing hemiepiphytes) that share functional traits with similar growth forms present in the Araceae, a member of the Alismatales and not closely related. Our objectives were first to characterize the diversity, functional growth forms, and ecological traits of Cyclanthaceae at the La Selva Biological Station. Specific functional leaf and canopy traits of terrestrial herbs and epiphytes are very similar and associated with ecological success in both families. We further examined the functional traits of root-climbing hemiepiphytes, a specialized growth form that links the two families but rare in other families and argue that their specialized functional traits allow them to be considered as a distinct functional growth form. A key trait in distinguishing hemiepiphytes which are rare outside of the Cyclanthaceae and Araceae is the severance of the main stem hydraulic connection to the soil early in plant development. We used field data to examine the possible evolutionary pathways of developmental and ecological transition from terrestrial to hemiepiphyte growth forms. The broader ecological success of hemiepiphytic Araceae compared to Cyclanthaceae is hypothesized to result from the presence of heteroblasty in developing stems and leaves which allows more efficient utilization of complex canopy light environments of wet tropical forests. creator: Erin C. Riordan creator: Orlando Vargas Ramirez creator: Philip W. Rundel uri: https://doi.org/10.7717/peerj.15557 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Riordan et al. title: Pogonias courbina sperm characteristcs in its first reproductive season link: https://peerj.com/articles/15600 last-modified: 2023-07-18 description: Southern black drum (Pogonias courbina) is a species distributed along the western Atlantic Ocean, and it is the largest Sciaenidae observed in the coast of Rio Grande do Sul state, Brazil. However, it is listed as a vulnerable species at The IUCN Red List of Threatened Species™, and their fishing is prohibited. The objective of this study was to determine the sperm characteristics of P. courbina. Sperm samples of five young males (two-year-old fish) were collected through abdominal pressure. The sperm kinetics parameters were sperm motility (MOT) 10.7 ± 5.6%, curvilinear velocity (VCL) 120.07 ± 16.16 mm s ± 1, average path velocity (VAP) 75.64 ± 23.78 mm s ± 1, straight-line velocity (VSL) 62.49 ± 15.83 mm s ± 1, straightness (STR) 83.9 ± 5.3%, wobble (WOB) 61.9 ± 12.7%, beat cross frequency (BCF) 42.981 ± 4.627 Hz and progression (PRG) 1,805.4 ± 564.5 µm. The proportion of normal spermatozoa was 35.6 ± 6.1%. About the abnormalities observed, 22.7% occurred in the tail (short tail = 0.6 ± 0.5%, distally curled tail = 2.4 ± 1.6%, strongly curled tail = 1.9 ± 1.3%, broken tail = 7.9 ± 5.1%, folded tail = 5.5 ± 0.8%, loose tail = 4.4 ± 1.9%); 14.2% occurred in the head (degenerate head = 4.2 ± 1.6%, microcephaly = 1.8 ± 2.5%, loose head = 8.2 ± 2.1%) and 27.5% of the spermatozoa showed cytoplasmatic gouts (proximal gout = 20.0 ± 8.4%, distal gout = 7.5 ± 2.8%). Besides that, a correlation analysis was performed between sperm morphology and kinetics parameters, and the spermatozoa were measured for the morphometric parameters. There was a positive correlation between BCF and normal spermatozoa (r =  0.9269). A negative correlation occurred between BCF and loose head (r =  −0.9047); WOB and strongly curled tail (r =  −0.8911); and PROG and strongly curled tail (r =  −0.9191). The morphometric measures found for the head were length of 2.50 ± 0.21 µm and width of 2.12 ± 0.22 µm, and for the tail it was length of 37.97 ± 2.01 µm. It was possible to verify that the animals have sperm characteristics that indicate reproductive aptitude, but an abnormal behavior on sperm activation and high presence of the cytoplasmic gout abnormality indicates that the animals are not fully mature in their first reproductive season. This work contributes to a better understanding of the P. courbina spermatic parameters, what can be allies to recovery this species population in nature and promote its production in fish farms. creator: Jhony Lisboa Benato creator: Danilo Streit Jr creator: Nathalia Dos Santos Teixeira creator: Rômulo Batista Rodrigues creator: Thaiza Rodrigues de Freitas creator: Marcelo Okamoto creator: Ricardo Rodrigues creator: Raquel Santos dos Santos creator: Renata Villar Dantas creator: Ana Paula de Abreu Balbinot creator: Rodrigo Ribeiro Bezerra de Oliveira creator: Lucas Campos Maltez creator: Olivia Menossi creator: Luis Andre Sampaio uri: https://doi.org/10.7717/peerj.15600 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Benato et al. title: Pesticide dynamics in three small agricultural creeks in Hesse, Germany link: https://peerj.com/articles/15650 last-modified: 2023-07-18 description: BackgroundDue to their high biodiversity, small water bodies play an important role for freshwater ecosystems. Nonetheless, systematic pesticide monitoring in small creeks with a catchment <30 km2 is rarely conducted.MethodsIn this study, event-driven water samples were taken from May until November 2017 and March until July 2018 after 20 rain events at three sampling sites with catchment areas of <27 km2 in the Wetterau, a region with intensive agriculture in Southern Hesse, Germany. Additionally, enriched extracts of the native water samples from the campaign in 2018 were used for the Microtox assay to determine baseline toxicity to invertebrates over time and sum of toxic units (STU) were calculated to compare the potential toxicity of the samples.ResultsOverall, 37 pesticides and 17 transformation products were found, whereby the herbicide metamitron (79 µg/L) showed the highest concentration. Regularly, pesticide concentrations peaked at the time of the highest water level within each sampling event. Within each sampling event maximum pesticide concentration was mostly reached in water samples taken during the first two hours. The sum of the time-weighted mean concentration values of all pesticides was between 2.0 µg/L and 7.2 µg/L, whereby the measured concentrations exceeded their regulatory acceptable concentration (RAC) at 55% of all sampling events for at least one pesticide. The mean EC50 values varied between 28.6 ± 13.1 to 41.3 ± 12.1 REF (relative enrichment factor). The results indicated that several samples caused baseline toxicity, whereby the highest activity was measured at the time of highest water levels and pesticides concentrations, and then steadily decreased in parallel with the water level. Median STUs of invertebrates ranged from −2.10 to −3.91, of algae/aquatic plants from −0.79 to −1.84 and of fish from −2.47 to −4.24. For one of the three sampling sites, a significant linear correlation between baseline toxicity and STUinvertebratewas found (r2 = 0.48).ConclusionThe results of the present study suggest that (1) current pesticide monitoring programs underestimate risks posed by the exposure to pesticides for aquatic organisms and (2) pre-authorization regulatory risk assessment schemes are insufficient to protect aquatic environments. creator: Sarah Betz-Koch creator: Björn Jacobs creator: Jörg Oehlmann creator: Dominik Ratz creator: Christian Reutter creator: Arne Wick creator: Matthias Oetken uri: https://doi.org/10.7717/peerj.15650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Betz-Koch et al. title: Basil functional and growth responses when cultivated via different aquaponic and hydroponics systems link: https://peerj.com/articles/15664 last-modified: 2023-07-18 description: BackgroundAquaponics is an innovative farming system that combines hydroponics and aquaculture, resulting in the production of both crops and fish. Decoupled aquaponics is a new approach introduced in aquaponics research for the elimination of certain system bottlenecks, specifically targeting the optimization of crops and fish production conditions. The aquaponics-related literature predominantly examines the system’s effects on crop productivity, largely overlooking the plant functional responses which underlie growth and yield performance. The aim of the study was the integrated evaluation of basil performance cultivated under coupled and decoupled aquaponic systems compared with a hydroponic one, in terms of growth and functional parameters in a pilot-scale aquaponics greenhouse.MethodsWe focused on the efficiency of the photosynthetic process and the state of the photosynthetic machinery, assessed by instantaneous gas exchange measurements as well as photosynthetic light response curves, and in vivo chlorophyll a fluorescence. Light use efficiency was estimated through leaf reflectance determination. Photosynthetic pigments content and leaf nutritional state assessments completed the picture of basil functional responses to the three different treatments/systems. The plant’s functional parameters were assessed at 15-day intervals. The experiment lasted for two months and included an intermediate and a final harvest during which several basil growth parameters were determined.ResultsCoupled aquaponics resulted in reduced growth, which was mainly ascribed to sub-sufficient leaf nutrient levels, a fact that triggered a series of negative feedbacks on all aspects of their photosynthetic performance. These plants experienced a down-regulation of PSII activity as reflected in the significant decreases of quantum yield and efficiency of electron transport, along with decreased photosynthetic pigments content. On the contrary, decoupled aquaponics favored both growth and photochemistry leading to higher light use efficiency compared with coupled system and hydroponics, yet without significant differences from the latter. Photosynthetic light curves indicated constantly higher photosynthetic capacity of the decoupled aquaponics-treated basil, while also enhanced pigment concentrations were evident. Basil functional responses to the three tested production systems provided insights on the underlying mechanisms of plant performance highlighting key-points for systems optimization. We propose decoupled aquaponics as an effective system that may replace hydroponics supporting high crops productivity. We suggest that future works should focus on the mechanisms involved in crop and fish species function, the elucidation of which would greatly contribute to the optimization of the aquaponics productivity. creator: Anastasia Mourantian creator: Maria Aslanidou creator: Eleni Mente creator: Nikolaos Katsoulas creator: Efi Levizou uri: https://doi.org/10.7717/peerj.15664 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mourantian et al. title: Variation in Pheidole nodus (Hymenoptera: Formicidae) functional morphology across urban parks link: https://peerj.com/articles/15679 last-modified: 2023-07-18 description: BackgroundHabitat fragmentation and consequent population isolation in urban areas can impose significant selection pressures on individuals and species confined to urban islands, such as parks. Despite many comparative studies on the diversity and structure of ant community living in urban areas, studies on ants’ responses to these highly variable ecosystems are often based on assemblage composition and interspecific mean trait values, which ignore the potential for high intraspecific functional trait variation among individuals.MethodsHere, we examined differences in functional traits among populations of the generalist ant Pheidole nodus fragmented between urban parks. We used pitfall trapping, which is more random and objective than sampling colonies directly, despite a trade-off against sample size. We then tested whether trait-filtering could explain phenotypic differences among urban park ant populations, and whether ant populations in different parks exhibited different phenotypic optima, leading to positional shifts in anatomical morphospace through the regional ant meta-population.ResultsIntraspecific morphological differentiation was evident across this urban region. Populations had different convex hull volumes, positioned differently over the morphospace.ConclusionsFragmentation and habitat degradation reduced phenotypic diversity and, ultimately, changed the morphological optima of populations in this urban landscape. Considering ants’ broad taxonomic and functional diversity and their important role in ecosystems, further work over a variety of ant taxa is necessary to ascertain those varied morphological response pathways operating in response to population segregation in urban environments. creator: Yi Luo creator: Qing-Ming Wei creator: Chris Newman creator: Xiang-Qin Huang creator: Xin-Yu Luo creator: Zhao-Min Zhou uri: https://doi.org/10.7717/peerj.15679 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo et al.