title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=477 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Submarine groundwater discharge interacts with creek geomorphology to affect eastern oyster Crassostrea virginica growth rates in a coastal Georgia creek link: https://peerj.com/articles/15837 last-modified: 2023-08-04 description: Eastern oysters, Crassostrea virginica, are commercially important coastal species that provide many ecosystem services for coastal communities. Unfortunately, 85% of oyster reefs have been lost globally, prompting investments in restoration efforts to rebuild populations. Managers often consider several well-studied environmental and water quality parameters when making restoration site decisions. However, recent research suggests that submarine groundwater discharge (SGD) may play a role in driving the distribution of oysters in some estuaries. Specifically, SGD may result in localized areas of low dissolved oxygen and low pH that could inhibit oyster recruitment and survival. However, SGD may interact with other potential oyster stressors, including creek geomorphology. On point bars, sediment accumulation could alter growth rates of oysters and physiology, and it is possible that the two factors, SGD and creek geomorphology, could interact to impact oyster growth. We conducted a field experiment to examine the effects of SGD and creek geomorphology on oyster growth rates in a marsh-lined tidal creek in Georgia, USA. High and low SGD sites were paired within point bars and cut banks. Oysters were deployed in cages for 72 days and growth rates were determined. We found a significant interaction between SGD and creek geomorphology on oyster growth rates. Oysters grew at significantly faster rates at locations on accretionary point bars regardless of SGD flux, whereas, on erosional cut banks, high SGD flux significantly reduced oyster growth rate relative to low SGD flux. It appears that SGD may negatively influence oyster growth at specific creek locations, likely due to the presence of other stressors. Therefore, it is important to consider potential interacting and confounding stressors when managing oyster populations. As SGD is still a relatively understudied potential stressor for oysters, it is critical to continue to examine how groundwater might influence oysters in other locations and in combination with other stressors. Regardless, this study provides further evidence that SGD should be considered in future management efforts. creator: John M. Carroll creator: Walker de la Torre creator: Jacque L. Kelly uri: https://doi.org/10.7717/peerj.15837 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Carroll et al. title: Microvertebrate faunal assemblages of the Favel Formation (late Cenomanian-middle Turonian) of Manitoba, Canada link: https://peerj.com/articles/15493 last-modified: 2023-08-03 description: Microvertebrate assemblages of the Upper Cretaceous (late Cenomanian to mid-Turonian) Favel Formation of Manitoba are formally described for the first time. New vertebrate occurrences from the Favel Formation include the actinopterygians Caturidae indet., cf. Albulidae incertae sedis, Micropycnodon kansasensis, Pachyrhizodus minimus, Protosphyraena sp., Thryptodus loomisi, chondrichthyans Ischyrhiza cf. mira, I. texana, Ptychodus marginalis, P. occidentalis, and P. rhombodus, the avian cf. Ichthyornis sp., the reptile Testudines indet., and an unknown taxon referred to as Vertebrate A. Changes in faunal occurrences throughout the formation suggest an offshore open marine environment for the lower and middle horizons and nearshore marine for the upper horizon, represent ing mid- and late stages of the Greenhorn third-order marine cycle. This newly described diversity increases biogeographic affinities of the late Cenomanian to mid-Turonian vertebrate assemblages of Manitoba with central WIS localities in South Dakota and Kansas, providing additional support for a central vertebrate biogeographic subprovince during late Cenomanian to early Turonian times, as well as WIS localities further south in Texas decreasing the gradient of the north-south or central-south community boundary during early and mid-Turonian times. creator: Aaron A. Kilmury creator: Aaron Anderson creator: Dhuranka S. Wijesinghe creator: Ashley F. Verstraete creator: William Ezeana creator: Ashley E. Anderson creator: Kirstin S. Brink uri: https://doi.org/10.7717/peerj.15493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kilmury et al. title: GGA1 participates in spermatogenesis in mice under stress link: https://peerj.com/articles/15673 last-modified: 2023-08-03 description: BackgroundInfertility is recognized as a common and worrisome problem of human reproduction worldwide. Based on previous studies, male factors account for about half of all infertility cases. Exposure to environmental toxicants is an important contributor to male infertility. Bisphenol A (BPA) is the most prominent toxic environmental contaminant worldwide affecting the male reproductive system. BPA can impair the function of the Golgi apparatus which is important in spermatogenesis. GGA1 is known as Golgi-localized, gamma adaptin ear-containing, ARF-binding protein 1. Previously, it has been shown that GGA1 is associated with spermatogenesis in Drosophila, however, its function in mammalian spermatogenesis remains unclear.MethodsGga1 knockout mice were generated using the CRISPR/Cas9 system. Gga1-/- male mice and wild-type littermates received intraperitoneal (i.p.) injections of BPA (40 µg/kg) once daily for 2 weeks. Histological and immunofluorescence staining were performed to analyze the phenotypes of these mice.ResultsMale mice lacking Gga1 had normal fertility without any obvious defects in spermatogenesis, sperm count and sperm morphology. Gga1 ablation led to infertility in male mice exposed to BPA, along with a significant reduction in sperm count, sperm motility and the percentage of normal sperm. Histological analysis of the seminiferous epithelium showed that spermatogenesis was severely disorganized, while apoptotic germ cells were significantly increased in the Gga1 null mice exposed to BPA. Our findings suggest that Gga1 protects spermatogenesis against damage induced by environmental pollutants. creator: Haoyun Jiao creator: Yinghong Chen creator: Tingting Han creator: Qiyu Pan creator: Fei Gao creator: Guoping Li uri: https://doi.org/10.7717/peerj.15673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jiao et al. title: Development, physicochemical characterization and in-vitro biocompatibility study of dromedary camel dentine derived hydroxyapatite for bone repair link: https://peerj.com/articles/15711 last-modified: 2023-08-03 description: This study aimed to produce hydroxyapatite from the dentine portion of camel teeth using a defatting and deproteinizing procedure and characterize its physicochemical and biocompatibility properties. Biowaste such as waste camel teeth is a valuable source of hydroxyapatite, the main inorganic constituent of human bone and teeth which is frequently used as bone grafts in the biomedical field. Fourier Transform infrared (FTIR), and micro-Raman spectroscopy confirmed the functional groups as-sociated with hydroxyapatite. X-ray diffraction (XRD) studies showed camel dentine-derived hydroxyapatite (CDHA) corresponded with hydroxyapatite spectra. Scanning electron micros-copy (SEM) demonstrated the presence of dentinal tubules measuring from 1.69–2.91 µm. The inorganic phases of CDHA were primarily constituted of calcium and phosphorus, with trace levels of sodium, magnesium, potassium, and strontium, according to energy dispersive X-ray analysis (EDX) and inductively coupled plasma mass spectrometry (ICP-MS). After 28 days of incubation in simulated body fluid (SBF), the pH of the CDHA scaffold elevated to 9.2. in-vitro biocompatibility studies showed that the CDHA enabled Saos-2 cells to proliferate and express the bone marker osteonectin after 14 days of culture. For applications such as bone augmentation and filling bone gaps, CDHA offers a promising material. However, to evaluate the clinical feasibility of the CDHA, further in-vivo studies are required. creator: Zohaib Khurshid creator: Mohammed Farhan A. Alfarhan creator: Yasmin Bayan creator: Javed Mazher creator: Necdet Adanir creator: George J. Dias creator: Paul R. Cooper creator: Jithendra Ratnayake uri: https://doi.org/10.7717/peerj.15711 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Khurshid et al. title: Earthworms neutralize the influence of components of particulate pollutants on soil extracellular enzymatic functions in subtropical forests link: https://peerj.com/articles/15720 last-modified: 2023-08-03 description: Human activities are increasing the input of atmospheric particulate pollutants to forests. The components of particulate pollutants include inorganic anions, base cations and hydrocarbons. Continuous input of particulate pollutants may affect soil functioning in forests, but their effects may be modified by soil fauna. However, studies investigating how soil fauna affects the effects of particulate pollutants on soil functioning are lacking. Here, we investigated how earthworms and the particulate components interact in affecting soil enzymatic functions in a deciduous (Quercus variabilis) and a coniferous (Pinus massoniana) forest in southeast China. We manipulated the addition of nitrogen (N, ammonium nitrate), sodium (Na, sodium chloride) and polycyclic aromatic hydrocarbons (PAHs, five mixed PAHs) in field mesocosms with and without Eisenia fetida, an earthworm species colonizing forests in eastern China. After one year, N and Na addition increased, whereas PAHs decreased soil enzymatic functions, based on average Z scores of extracellular enzyme activities. Earthworms generally stabilized soil enzymatic functions via neutralizing the effects of N, Na and PAHs addition in the deciduous but not in the coniferous forest. Specifically, earthworms neutralized the effects of N and Na addition on soil pH and the effects of the addition of PAHs on soil microbial biomass. Further, both particulate components and earthworms changed the correlations among soil enzymatic and other ecosystem functions in the deciduous forest, but the effects depended on the type of particulate components. Generally, the effects of particulate components and earthworms on soil enzymatic functions were weaker in the coniferous than the deciduous forest. Overall, the results indicate that earthworms stabilize soil enzymatic functions in the deciduous but not the coniferous forest irrespective of the type of particulate components. This suggests that earthworms may neutralize the influence of atmospheric particulate pollutants on ecosystem functions, but the neutralization may be restricted to deciduous forests. creator: Junbo Yang creator: Jingzhong Lu creator: Yinghui Yang creator: Kai Tian creator: Xiangshi Kong creator: Xingjun Tian creator: Stefan Scheu uri: https://doi.org/10.7717/peerj.15720 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Prevalence of bone loss surrounding dental implants as detected in cone beam computed tomography: a cross-sectional study link: https://peerj.com/articles/15770 last-modified: 2023-08-03 description: ObjectivesThe objective of this study was to assess the prevalence of crestal, and apical bone loss (CBL & ABL) associated with dental implants in CBCT scans. The second objective was to assess the radiographic stage of implant disease and the visible predisposing factors.Materials and MethodsThe CBCT scans that were taken from January 2015 to January 2022 in King Saud Medical City were screened to examine the marginal and periapical condition of dental implants. Information related to demographic variables, stage of bone loss, and radiographically evident predisposing factors were collected. The results were analyzed using descriptive statistics, chi-square test, and logistic regression analysis.ResultsIn total, 772 implant scans were analyzed. The prevalence of crestal bone loss and apical bone loss around the implants were 6.9% and 0.4% respectively. The amount of bone loss was moderate in 52.8% of cases of CBL and 100% mild in cases of ABL. The risk factors for CBL were patient age (p < 0.001), implant location (p < 0.001), bone loss in proximal teeth (p < 0.001), and adjacent edentulous sites (p < 0.001). The risk factors for ABL were adjacent periapical infection (p < 0.001) and endodontic therapy (p = 0.024).ConclusionThe prevalence of CBL and ABL was low. The CBCT can be used as a diagnostic tool for studying the prevalence of bone loss associated with peri-implant disease and relevant risk factors. The implantation of CBCT to evaluate the success and the prognosis of dental implants or the treatment of peri-implant diseases can be further considered in future research. creator: Fahda N. Algahtani creator: Mamata Hebbal creator: Moath M. Alqarni creator: Rahaf Alaamer creator: Anwar Alqahtani creator: Rahaf A. Almohareb creator: Reem Barakat creator: Manal M. Abdlhafeez uri: https://doi.org/10.7717/peerj.15770 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Algahtani et al. title: Effects of harvest stages and lactic acid bacteria additives on the nutritional quality of silage derived from triticale, rye, and oat on the Qinghai-Tibet Plateau link: https://peerj.com/articles/15772 last-modified: 2023-08-03 description: BackgroundTriticale (×Triticosecale Wittmack L.), rye (Secale cereale L.), and oat (Avena sativa L.) are the main forage crops on the Qinghai–Tibet Plateau, but there has been relatively little research on the silage produced from these three species.MethodsPlants were harvested at the heading, flowering, grouting, milky, and dough stages and then used to produce silage with and without additives (Sila-Max and Sila-Mix). The nutritional quality of the resulting silages was analyzed.ResultsTriticale was revealed to be more suitable than oat or rye for producing silage on the Qinghai–Tibet Plateau. On the basis of the dry matter yield (DMY), triticale and rye should be harvested at the milky stage to optimize silage quality, whereas oat should be harvested at the dough stage. The lactic acid bacteria additives Sila-Max and Sila-Mix had no significant effect on the nutritional quality of the three silages regardless of when the samples were harvested. Overall, triticale produced higher quality silage than oat or rye. More specifically, triticale variety ‘Gannong No.2’ harvested at the milky stage is ideal for silage production. creator: Jun Ma creator: Hanling Dai creator: Hancheng Liu creator: Wenhua Du uri: https://doi.org/10.7717/peerj.15772 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ma et al. title: Risk factors for high CAD-RADS scoring in CAD patients revealed by machine learning methods: a retrospective study link: https://peerj.com/articles/15797 last-modified: 2023-08-03 description: ObjectiveThis study aimed to investigate a variety of machine learning (ML) methods to predict the association between cardiovascular risk factors and coronary artery disease-reporting and data system (CAD-RADS) scores.MethodsThis is a retrospective cohort study. Demographical, cardiovascular risk factors and coronary CT angiography (CCTA) characteristics of the patients were obtained. Coronary artery disease (CAD) was evaluated using CAD-RADS score. The stenosis severity component of the CAD-RADS was stratified into two groups: CAD-RADS score 0-2 group and CAD-RADS score 3–5 group. CAD-RADS scores were predicted with random forest (RF), k-nearest neighbors (KNN), support vector machines (SVM), neural network (NN), decision tree classification (DTC) and linear discriminant analysis (LDA). Prediction sensitivity, specificity, accuracy and area under the curve (AUC) were calculated. Feature importance analysis was utilized to find the most important predictors.ResultsA total of 442 CAD patients with CCTA examinations were included in this study. 234 (52.9%) subjects were CAD-RADS score 0–2 group and 208 (47.1%) were CAD-RADS score 3–5 group. CAD-RADS score 3-5 group had a high prevalence of hypertension (66.8%), hyperlipidemia (50%) and diabetes mellitus (DM) (35.1%). Age, systolic blood pressure (SBP), mean arterial pressure, pulse pressure, pulse pressure index, plasma fibrinogen, uric acid and blood urea nitrogen were significantly higher (p < 0.001), and high-density lipoprotein (HDL-C) lower (p < 0.001) in CAD-RADS score 3–5 group compared to the CAD-RADS score 0–2 group. Nineteen features were chosen to train the models. RF (AUC = 0.832) and LDA (AUC = 0.81) outperformed SVM (AUC = 0.772), NN (AUC = 0.773), DTC (AUC = 0.682), KNN (AUC = 0.707). Feature importance analysis indicated that plasma fibrinogen, age and DM contributed most to CAD-RADS scores.ConclusionML algorithms are capable of predicting the correlation between cardiovascular risk factors and CAD-RADS scores with high accuracy. creator: Yueli Dai creator: Chenyu Ouyang creator: Guanghua Luo creator: Yi Cao creator: Jianchun Peng creator: Anbo Gao creator: Hong Zhou uri: https://doi.org/10.7717/peerj.15797 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dai et al. title: Uncovering the Grinnellian niche space of the cryptic species complex Gammarus roeselii link: https://peerj.com/articles/15800 last-modified: 2023-08-03 description: BackgroundThe discovery of cryptic species complexes within morphologically established species comes with challenges in the classification and handling of these species. We hardly know to what extent species within a species complex differ ecologically. Such knowledge is essential to assess the vulnerability of individual genetic lineages in the face of global change. The abiotic conditions, i.e., the Grinnellian niche that a genetic lineage colonizes, provides insights into how diverse the ecological requirements of each evolutionary lineage are within a species complex.Material and MethodsWe sampled the cryptic species complex of the amphipod Gammarus roeselii from Central Germany to Greece and identified genetic lineages based on cytochrome c oxidase subunit I (COI) barcoding. At the same time, we recorded various abiotic parameters and local pollution parameters using a series of in vitro assays to then characterize the Grinnellian niches of the morphospecies (i.e., Gammarus roeselii sensu lato) as well as each genetic lineage. Local pollution can be a significant factor explaining current and future distributions in times of increasing production and release of chemicals into surface waters.ResultsWe identified five spatially structured genetic lineages in our dataset that differed to varying degrees in their Grinnellian niche. In some cases, the niches were very similar despite the geographical separation of lineages, supporting the hypothesis of niche conservatism while being allopatrically separated. In other cases, we found a small niche that was clearly different from those of other genetic lineages.ConclusionThe variable niches and overlaps of different dimensions make the G. roeselii species complex a promising model system to further study ecological, phenotypic and functional differentiation within this species complex. In general, our results show that the Grinnellian niches of genetically distinct molecular operational taxonomic units (MOTUs) within a cryptic species complex can differ significantly between each other, calling for closer inspection of cryptic species in a conservational and biodiversity context. creator: Jana Kabus creator: Sarah Cunze creator: Andrea Dombrowski creator: Ioannis Karaouzas creator: Spase Shumka creator: Jonas Jourdan uri: https://doi.org/10.7717/peerj.15800 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kabus et al. title: The effect of three different pre-match warm-up structures on male professional soccer players’ physical fitness link: https://peerj.com/articles/15803 last-modified: 2023-08-03 description: BackgroundOptimizing the soccer players’ match preparation is one of the most relevant concerns of coaches for strength and conditioning training. Thus, the aim of this study was to analyze the effects of three pre-match warm-up structures on the physical condition of male professional soccer players.Materials & MethodsSeventeen male professional soccer players (age: 20.9 ± 2.4 years) of one Tunisian Professional Soccer League team participated in this study. Players performed three times a typical pre-match warm-up (WU) [aerobic phase (AE); neuromuscular phase (NM); velocity phase (VL); and ball-specific phase (BS) variating the order of the included phases/exercises: WU1 (AE + BS + NM + VL); WU2 (AE + NM + VL + BS); and WU3 (AE + VL + BS + NM). After each warm-up phase, players completed the following physical fitness tests: linear sprint test, countermovement jump test, 15-m ball dribbling agility test and ball shooting test. Additionally, the rate of perceived exertion (RPE) was registered after each warm-up.ResultsThe results indicated significant differences between WU1 and WU3, with better results in the ball shooting test and RPE in WU3. In addition, there were no significant differences in the other variables and between other warm-up structures. These findings could be of great interest for coaches to the strength and conditioning coaches for professional soccer teams in order to improve the players physical performance and perceived exertion. creator: Mehdi Ben Brahim creator: Alejandro Sal-de-Rellán creator: Adrián García-Valverde creator: Hussain Yasin creator: Javier Raya-González uri: https://doi.org/10.7717/peerj.15803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ben Brahim et al.