Effects of plastic film mulching on the spatiotemporal distribution of soil water, temperature, and photosynthetic active radiation in a cotton field
Plastic film mulching (PFM) affects the spatiotemporal distribution of soil moisture and temperature, which in turn affects cotton growth and the spatiotemporal distribution of canopy photosynthetically active radiation (PAR). Due to the spatial heterogeneity of soil moisture, temperature and limited monitoring methods, the issues such as relatively few sampling points and long sampling intervals in most existing studies prevent the accurate quantification of spatiotemporal changes in moisture and temperature along soil profile. To investigate the effects of PFM on spatiotemporal changes in soil moisture, temperature, and canopy PAR in cotton fields, two field trials of plastic film-mulched (M) and nonmulched (NM) cultivations were performed in 2018 and 2019. The grid method was used for the soil information continuous monitoring and multiple-time fixed-site canopy PAR monitoring during the duration of cotton growth. Two-year field trial data showed that, M cultivation increased soil moisture by approximately 13.6%–25% and increased temperature by 2–4 °C in the 0–50 cm soil layer before the first irrigation (June 20) and by 1–2 °C in the 70–110 cm soil layer, compared with NM cultivation. In addition, the temperature difference between the two treatments gradually decreased with the increase in irrigation and air temperature. The M treatment reached the peak PAR interception rate 10 days earlier than the NM treatment. In 2018 and 2019, the PAR peak value under the M treatment was 4.62% and 1.8% higher than that under the NM treatment, respectively, but the PAR interception rate was decreased rapidly in the late growth stage. Overall, PFM had an effect on soil moisture retention during the whole growth period and greatly increased the soil temperature before budding stage, thus promoted the early growth of cotton. Considering this, we suggest that the irrigation quota and frequency could be appropriately decreased in the case of plastic film mulching cultivation. For nonmulching cultivation, the irrigation quota and frequency should be increased, and it is necessary to take measures to improve the soil temperature before middle July.
Yang et al. (2022) Effects of plastic film mulching on the spatiotemporal distribution of soil water, temperature, and photosynthetic active radiation in a cotton field. PeerJ 10:e13894 https://doi.org/10.7717/peerj.13894
CPUE standardization for southern bluefin tuna (Thunnus maccoyii) in the Korean tuna longline fishery, accounting for spatiotemporal variation in targeting through data exploration and clustering
Accounting for spatial and temporal variation in targeting is a concern in many catch per unit effort (CPUE) standardization exercises. In this study we standardized southern bluefin tuna (Thunnus maccoyii, SBT) CPUE from the Korean tuna longline fishery (1996–2018) using generalized linear models (GLMs) with operational set by set data. Data were first explored to investigate the operational characteristics of Korean tuna longline vessels fishing for SBT, such as the spatial and temporal distributions of effort, and changes in the nominal catch rates among major species and species composition. Then we estimated SBT CPUE by area used for the stock assessment in the CCSBT (Commission for the Conservation of Southern Bluefin Tuna) and identified two separate areas in which Korean tuna longline vessels have targeted SBT and albacore tuna (T. alalunga), with targeting patterns varying spatially, seasonally and longer term. We applied two approaches, data selection and cluster analysis of species composition, and compared their ability to address concerns about the changing patterns of targeting through time. Explanatory variables for the GLM analyses were year, month, vessel identifier, fishing location (5° cell), number of hooks, moon phase, and cluster. GLM results for each area suggested that location, year, targeting, and month effects were the principal factors affecting the nominal CPUE. The standardized CPUEs for both areas decreased until the mid-2000s and have shown an increasing trend since that time.
Hoyle et al. (2022) CPUE standardization for southern bluefin tuna (Thunnus maccoyii) in the Korean tuna longline fishery, accounting for spatiotemporal variation in targeting through data exploration and clustering. PeerJ 10:e13951 https://doi.org/10.7717/peerj.13951
Plant traits and environment: floating leaf blade production and turnover of Nymphoides peltata (S.G. Gmel.) O. Kuntze (Menyanthaceae)
Background Nymphaeid macrophytes, rooting in the sediment of water bodies and characterized by floating leaves, play an important role in wetland ecosystems. The present research deals with the effects of limited space, limited nutrient availability, water temperature and an unexpected inundation on the production, turnover and plasticity of floating leaves of the globally widespread species Nymphoides peltata (Fringed waterlily). Methods The effects of these environmental conditions were studied in two plots in outdoor concrete tanks (CT1, CT2, mesocosms simulating occurrence in small ponds) and in two plots in the floodplain oxbow lake Bemmelse Strang (BS1, BS2). Plot CT1 was situated in a stand coexisting with helophytes, plot CT2 in a monospecific stand, plot BS1 in the center and plot BS2 at the open water border of a monospecific stand. All floating leaf blades within the plots were marked at appearance at the water surface and subsequently length, width and damage of each leaf and maximum and minimum water temperatures were measured bi-weekly. Area and biomass of leaf blades were calculated based on leaf length and width and were used to calculate turnover rates and production. Results The growth period started in May and ended mid-October with continuous production of floating leaves during nearly the whole vegetation period. In the tanks the water level was very stable, but the lake underwent an inundation by river water, causing a sudden loss of existing leaves. Considering environmental conditions and based on the assumed ranking from low to high nutrient availability, the ranking of the plots was CT1, CT2, BS1, BS2. This order was found for maximum leaf life span and maximum leaf length, and the reverse order was found for number of leaves, new leaves per day and duration of the vegetation period. Turnover rates appeared to be relatively similar for plots CT1, CT2 and BS1, but for the deeper border plot BS2 lower ratios were found. These results indicate that increased enclosure with expected nutrient limitation causes (1) the production of high numbers of small leaves with larger totals for leaf area and biomass, (2) a shift towards increased sexual reproduction by the production of more flowering stem leaves.
Klok et al. (2022) Plant traits and environment: floating leaf blade production and turnover of Nymphoides peltata (S.G. Gmel.) O. Kuntze (Menyanthaceae). PeerJ 10:e13976 https://doi.org/10.7717/peerj.13976
Association of military-specific reaction time performance with physical fitness and visual skills
Background The aim of the present study was to explore whether military-specific reaction time (RT) test performance is affected by individuals’ physical and visual skills. Method In a single testing session, the military-specific Simple and Go, No-Go RT, aerobic power (20-m Multistage Shuttle Run test), maximal upper- and lower-body mechanical capacities (bench press and squat against different loads), and visual skills (multiple object tracking and dynamic visual acuity) of 30 young men (15 active-duty military personnel and 15 sport science students) were evaluated. Results The main findings revealed that the Simple RT and Go, No-Go RT presented (1) with aerobic power non-significant small correlations in military personnel (r = −0.39 and −0.35, respectively) and non-significant negligible correlations in sport science students (r = −0.10 and 0.06, respectively), (2) inconsistent and generally non-significant correlations with the maximal mechanical capacities of the upper- and lower-body muscles (r range = −0.10, 0.67 and −0.27, 0.48, respectively), (3) non-significant correlations with visual skills (r magnitude ≥ 0.58) with the only exception of the Go, No-Go RT that was significantly correlated to all visual variables in the group of students (i.e., students who achieved better results during visual tests had shorter RT; r magnitude ≥ 0.58), and (4) none of the physical and visual variables significantly predicted the Simple RT or Go, No-Go RT. Conclusion Altogether, these results indicate that military-specific RT performance is generally independent of physical and visual skills in both military personnel and active university students.
Janicijevic et al. (2022) Association of military-specific reaction time performance with physical fitness and visual skills. PeerJ 10:e14007 https://doi.org/10.7717/peerj.14007
Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty
Orthologs separate after lineages split from each other and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS), as proxy for functional divergence. We used five working definitions of orthology, including reciprocal best hits (RBH), among other definitions based on network analyses and clustering. The results showed that orthologs, by all definitions tested, had values of dN/dS noticeably lower than those of paralogs, suggesting that orthologs generally tend to be more functionally stable than paralogs. The differences in dN/dS ratios remained suggesting the functional stability of orthologs after eliminating gene comparisons with potential problems, such as genes with high codon usage biases, low coverage of either of the aligned sequences, or sequences with very high similarities. Separation by percent identity of the encoded proteins showed that the differences between the dN/dS ratios of orthologs and paralogs were more evident at high sequence identity, less so as identity dropped. The last results suggest that the differences between dN/dS ratios were partially related to differences in protein identity. However, they also suggested that paralogs undergo functional divergence relatively early after duplication. Our analyses indicate that choosing orthologs as probably functionally coherent remains the right approach in comparative genomics.
Escorcia-Rodríguez et al. (2022) Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty. PeerJ 10:e13843 https://doi.org/10.7717/peerj.13843
An insight into the invasion of breast ductal carcinoma in situ based on clinical, pathological and hematological data
Background Ductal carcinoma in situ (DCIS) has become a non-negligible part of breast cancers owing to the greatly increased incidence. While its natural history was not fully elucidated, which is the reason for current controversies in clinical treatment. Exploration of this issue from a clinical perspective is meaningful. Methods Medical records of 389 patients diagnosed with DCIS or DCIS with invasive ductal carcinoma (IDC) were reviewed. All of them received appropriate medical care in our center. All 324 patients in training cohort were divided into invasion and non-invasion groups based on pathology. Differences in DCIS immunohistochemical markers and hematological indicators between them were analyzed. In the invasion group, differences between DCIS and matched IDC were compared to explore changes in the tumor heterogeneity during invasion. Conclusions are validated in the validation cohort of 65 patients. Results Patients in invasion and non-invasion groups were balanced in baseline characteristics and no statistically significant differences were noticed for DCIS immunohistochemical markers. For hematological indicators, high expression of platelet >291.50) (odds ratio, 2.46; CI [1.35–4.46]; p = 0.003) and SII (>347.20) (odds ratio, 2.54; CI [1.56–4.12]; p < 0.001) were established as independent predictors for invasion by logistic analysis and were validated in the validation cohort. Ki-67 of IDC was significantly higher than that of matched DCIS (p < 0.001). HER2 expression and histological grade of DCIS were separately linearly related to those of IDC. Conclusion The change in hematological indicators is an independent predictor for invasion and can be incorporated into the treatment decision-making process for DCIS. Invasion tumor cells exhibit a stronger proliferative capacity compared with the in-situ ones. There are linear relationships in HER2 expression and histological grades between DCIS and matched IDC. DCIS subclones with different histological grades will develop into invasive carcinomas separately.
Liu et al. (2022) An insight into the invasion of breast ductal carcinoma in situ based on clinical, pathological and hematological data. PeerJ 10:e13966 https://doi.org/10.7717/peerj.13966
Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean
Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise FST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species, where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts.
García-Urueña et al. (2022) Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean. PeerJ 10:e13854 https://doi.org/10.7717/peerj.13854
Be aware of the allele-specific bias and compositional effects in multi-template PCR
High-throughput sequencing of amplicon libraries is the most widespread and one of the most effective ways to study the taxonomic structure of microbial communities, even despite growing accessibility of whole metagenome sequencing. Due to the targeted amplification, the method provides unparalleled resolution of communities, but at the same time perturbs initial community structure thereby reducing data robustness and compromising downstream analyses. Experimental research of the perturbations is largely limited to comparative studies on different PCR protocols without considering other sources of experimental variation related to characteristics of the initial microbial composition itself. Here we analyse these sources and demonstrate how dramatically they effect the relative abundances of taxa during the PCR cycles. We developed the mathematical model of the PCR amplification assuming the heterogeneity of amplification efficiencies and considering the compositional nature of data. We designed the experiment—five consecutive amplicon cycles (22–26) with 12 replicates for one real human stool microbial sample—and estimated the dynamics of the microbial community in line with the model. We found the high heterogeneity in amplicon efficiencies of taxa that leads to the non-linear and substantial (up to fivefold) changes in relative abundances during PCR. The analysis of possible sources of heterogeneity revealed the significant association between amplicon efficiencies and the energy of secondary structures of the DNA templates. The result of our work highlights non-trivial changes in the dynamics of real-life microbial communities due to their compositional nature. Obtained effects are specific not only for amplicon libraries, but also for any studies of metagenome dynamics.
Korvigo et al. (2022) Be aware of the allele-specific bias and compositional effects in multi-template PCR. PeerJ 10:e13888 https://doi.org/10.7717/peerj.13888
Cardiorespiratory function, resting metabolic rate and heart rate variability in coal miners exposed to hypobaric hypoxia in highland workplace
Background Owing to intermittent/acute exposure to hypobaric hypoxia, highland miners may often suffer, the physiological characteristics between highland and lowland miners, however, are rarely reported. The objective of this study was to compare the physiological characteristics of coal miners working at disparate altitudes. Methods Twenty-three male coal mining workers acclimating to high altitude for 30 ± 6 days in Tibet (highland group; approx. 4500 m above sea level; 628.39 millibar), and 22 male coal mining workers in Hebei (lowland group; less than 100 m above sea level; 1021.82 millibar) were recruited. Tests were conducted to compare ventilatory parameters, circulation parameters, resting metabolic rate (RMR), and heart rate variability (HRV) indices between the two groups in resting state. Results Ventilation volume per minute (VE) of the highland group was markedly raised compared to that of the lowland group (11.70 ± 1.57 vs. 8.94 ± 1.97 L/min, p = 0.000). In the meanwhile, O2 intake per heart beat (VO2/HR) was strikingly decreased (3.54 ± 0.54 vs. 4.36 ± 0.69 ml/beat, p = 0.000). Resting metabolic rate relevant to body surface area (RMR/BSA) was found no significant difference between the two groups. Evident reduction in standard deviation of NN intervals (SDNN) and remarkable increase in ratio of low- and high- frequency bands (LF/HF) were manifest in highland miners compared to that of lowland ones (110.82 ± 33.34 vs. 141.44 ± 40.38, p = 0.008 and 858.86 ± 699.24 vs. 371.33 ± 171.46, p = 0.003; respectively). Conclusions These results implicate that long-term intermittent exposure to high altitude can lead miners to an intensified respiration, a compromised circulation and a profound sympathetic-parasympathetic imbalance, whereas the RMR in highland miners does not distinctly decline.
Yang et al. (2022) Cardiorespiratory function, resting metabolic rate and heart rate variability in coal miners exposed to hypobaric hypoxia in highland workplace. PeerJ 10:e13899 https://doi.org/10.7717/peerj.13899
Prior experience of captivity affects behavioural responses to ‘novel’ environments
Information ecology theory predicts that prior experience influences current behaviour, even if the information is acquired under a different context. However, when individuals are tested to quantify personality, cognition, or stress, we usually assume that the novelty of the test is consistent among individuals. Surprisingly, this ‘gambit of prior experience’ has rarely been explored. Therefore, here we make use of a wild population of great tits (Parus major) to test if prior experience of handling and captivity influences common measures of exploration (open field tests in two novel contexts: room and cage arenas), social response (simulated using a mirror), and behavioural stress (breathing rate). We found that birds with prior experience of captivity (caught previously for unrelated learning and foraging experiments) were more exploratory, but this depended on age: exploration and captivity experience (in terms of both absolute binary experience and the length of time spent in captivity) were associated more strongly in young (first-winter) birds than in adults. However, there was no association of prior experience of captivity with social response and breathing rate, and nor did the measures of exploration correlate. Together our results suggest that re-testing of individuals requires careful consideration, particularly for younger birds, and previous experiences can carry over and affect behaviours differently.
Kluen et al. (2022) Prior experience of captivity affects behavioural responses to ‘novel’ environments. PeerJ 10:e13905 https://doi.org/10.7717/peerj.13905