title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=991 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A nature-based health intervention at a military healthcare center: a randomized, controlled, cross-over study link: https://peerj.com/articles/10519 last-modified: 2021-01-04 description: We describe a mixed qualitative and quantitative research study in a military facility regarding the role of nature in well-being. Study intervention included two 20-minute walks. One walk was in an intentionally designed woodland environment (Green Road) and the other was on a busy campus road in a medical treatment facility (Urban Road). Twelve volunteers from a military facility participated in both walks in a cross-over experimental design. The two walking sessions were randomly ordered and preceded by pre-walk instructions appropriate to each road’s characteristics and incorporated focused attention and present moment orientation. A semi-structured post-walk interview, the primary outcome, was conducted after the conclusion of each walk. Qualitative data analyses consisted of sentiments and themes by using NVivo 12 software. The Green Road was unanimously rated as positive (100%). Responses to Urban Road were evenly distributed among positive (33.3%), negative (33.3%), and neutral/mixed (33.3%) sentiments. The Green Road yielded predominantly positive themes such as enjoyment of nature, relaxation, and feelings of privacy and safety. Urban Road produced significantly more negative themes such as concerns for safety, dislike of noise and other noxious experiences. Quantitative assessment of distress and mindfulness with Distress Thermometer (DT) and Mindful Attention Awareness Scale-state version (MAAS) demonstrated that a walk on the Green Road significantly decreased distress and increased mindfulness compared to a walk on the Urban Road. We also observed that pre-walk instructions could direct attention to both obvious and subtle elements of experience and enhance awareness. Results support the notion that an intentional nature-based environment may produce significantly more positive experiences and result in health-promoting benefits in a military health-care setting compared to an urban environment. Future studies with clinical populations could advance our understanding of the healing value of nature-based interventions. The impact of intentional green environments may be enhanced by well-designed instructions for both recreational and therapeutic use. creator: Rezvan Ameli creator: Perry Skeath creator: Preetha A. Abraham creator: Samin Panahi creator: Josh B. Kazman creator: Frederick Foote creator: Patricia A. Deuster creator: Niha Ahmad creator: Ann Berger uri: https://doi.org/10.7717/peerj.10519 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2021 Ameli et al. title: Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist link: https://peerj.com/articles/10533 last-modified: 2021-01-04 description: BackgroundGypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the species Lepidium subulatum, a dominant Iberian shrubby gypsophyte.MethodsWe tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier.ResultsResults showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, like FST and FIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants.DiscussionNatural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions. creator: Irene Martín-Rodríguez creator: Adrián Escudero creator: Alfredo García-Fernández uri: https://doi.org/10.7717/peerj.10533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Martín-Rodríguez et al. title: A feasibility study to determine the use of baited pots in Greenland halibut (Reinhardtius hippoglossoides) fisheries, supported by the use of underwater video observations link: https://peerj.com/articles/10536 last-modified: 2021-01-04 description: High incidental catches of Greenland shark (Somniosus microcephalus) in Nunavut’s Greenland halibut (Reinhardtius hippoglossoides) fishery has led to studies on the feasibility of capturing Greenland halibut with baited pots. In this study, catch rates among six experimental pots are compared. In addition to this, underwater video observations of Greenland halibut interacting with two of these experimental pot types are quantified in order to help provide recommendations on future pot designs. Catch rates of Greenland halibut differed among pots with different entrance mesh types, and none of the pots produced substantial amounts of bycatch. Strings of pots were deployed within a narrow corridor between baited gillnets targeting Greenland halibut, which may have affected catch results. Video observations revealed Greenland halibut entangled by their teeth significantly more often in entrance funnels constructed with 50 mm than with 19 mm clear monofilament netting and the entrance rate was 45% higher with the 19 mm netting. Greenland halibut that successfully entered a pot repeatedly became entangled by their teeth in 58 mm netting used in the side and end panels and in a horizontal panel used to separate the pot into a lower and upper chamber. The majority (80%) of Greenland halibut were observed to approach a pot against the current. The downstream entrance was aligned with the current in 52% of the observed Greenland halibut approaches. Seventy percent of entry attempts and 67% of successful entries occurred when fish approached against the current and when the entrance was aligned with the current. These observations lead to recommendations that future studies consider developing a four entrance pot to ensure an entrance is always aligned with bottom currents. Based on these observations of entanglements, it is recommended to use 19 mm clear monofilament netting in the entrance funnel, 100 mm polyethylene netting in the exterior panels, and 19 mm polypropylene netting in the horizontal panel when targeting Greenland halibut. Three Greenland sharks were observed interacting with the pots in the video sets, but none were captured or damaged the pots during the potting experiments, providing validity to the use of pots to mitigate the capture of Greenland shark in Nunavut territorial waters. creator: Margaret H. Folkins creator: Scott M. Grant creator: Philip Walsh uri: https://doi.org/10.7717/peerj.10536 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Folkins et al. title: Soluble expression and purification of Bluetongue Virus Type 1 (BTV1) structure protein VP2 in Escherichia coli and its immunogenicity in mice link: https://peerj.com/articles/10543 last-modified: 2021-01-04 description: BackgroundThe VP2 on the surface of the virus particle is the main structural protein of BTV, which can induce the host to produce neutralizing antibodies and play an important role in the antiviral immunity process. This study aimed to obtain the soluble VP2 and analyze its immunogenicity.MethodsThe gene encoding the full-length VP2 of BTV1 was amplified by PCR. The products from restriction enzyme digestion and ligase reaction between VP2 and vector pET-28a were transformed into E.coli DH5α. After PCR and sequencing detection, the positive plasmid PET28a-VP2 was transformed into E.coli BL21(DE3) and Rosetta(DE3) competent cells, expression induced by IPTG. The fusion protein was expressed in the optimized conditions with the induction of IPTG, purified by affinity chromatography and identified by SDS-PAGE and Western blotting. A total of 5 Balb/c mice aged 6–8 weeks were immunized with the fusion protein at a dose of 30 µg per mouse. Each mouse was immunized three times at an interval of 3 weeks.ResultsThe recombinant plasmid PET28a-VP2 was successfully constructed. The expression strains were induced by 0.4 mmol/L IPTG at 16 °C for 10 h, and BTV1 VP2 was expressed in a soluble form. The purity of the recombinant VP2 protein (∼109 kDa) was about 90% in the concentration at 0.2 mg/ml afterpurification. The purified VP2 had good immunoreactivity with BTV1 positive serum. Taken together, thisstudy offered a route for producing soluble BTV VP2, which retains activity and immunogenicity, to bebeneficial to the research on developing BTV vaccine, and lay the foundation for further research on BTV. creator: Aiping Wang creator: Jiajia Yin creator: Jingming Zhou creator: Hongfang Ma creator: Yumei Chen creator: Hongliang Liu creator: Yanhua Qi creator: Chao Liang creator: Yankai Liu creator: Jinge Li creator: Gaiping Zhang uri: https://doi.org/10.7717/peerj.10543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: In vitro anticandidal activity and gas chromatography-mass spectrometry (GC-MS) screening of Vitex agnus-castus leaf extracts link: https://peerj.com/articles/10561 last-modified: 2021-01-04 description: BackgroundCandida infections are becoming more drug resistant; it is necessary to search for alternative medications to treat them. Therefore, the present study estimates the anticandidal activity of Vitex agnus-castus (VA-C) leaf extracts.MethodsWe used the agar well diffusion method to assess the anticandidal activity of three different VA-C leaf extracts (ethanol, methanol, and water) against three Candida species (Candida tropicalis, Candida albicans, and Candida ciferrii). The minimum inhibitory concentration (MIC) was estimated using the two-fold dilution method and the minimum fungicidal concentration (MFC) was determined using the classic pour plate technique. The MFC/MIC ratio was calculated to estimate the microbicidal or microbiostatic activity. A gas chromatography mass spectrometer was used to screen the phytochemicals of the VA-C leaf extracts (ethanol, methanol, and water).ResultsAll VA-C extracts ethanol, methanol, and water were significantly inhibited the growth of the test Candida species and the inhibition activity depended on the solvent used and the Candida species. The results showed that C. tropicalis was the most highly inhibited by all extracts followed by C. albicans and C. ciferrii. The MIC values were 12.5–25 µg/ml, and MFC values were 25–100 µg/ml. The ratios of MFC/MIC were two-fold to four-fold which was considered candidacidal activity. Ninety-five phytochemical compounds were identified by the GC-MS assay for the VA-C leaf extracts. The total number of compounds per extract differed. Methanol had 43 compounds, ethanol had 47 compounds, and water had 52 compounds. The highest compound concentrations were: 4,5-Dichloro-1,3-dioxolan-2-one in ethanol and methanol, 1H-Indene, 2,3-dihydro-1,1,2,3,3-pentamethyl in ethanol, Isobutyl 4-hydroxybenzoate in methanol, and Benzoic acid and 4-hydroxy- in water. These phytochemical compounds belong to different bioactive chemical group such as polyphenols, fatty acids, terpenes, terpenoids, steroids, aldehydes, alcohols, and esters, and most of which have anticandidal activity.ConclusionsVA-C leaf extracts may be useful alternatives to anticandidal drugs, based on their effectiveness against all test Candida species at low concentrations. However, appropriate toxicology screening should be conducted before use. creator: Ibtisam Mohammed Ababutain creator: Azzah Ibrahim Alghamdi uri: https://doi.org/10.7717/peerj.10561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ababutain and Alghamdi title: Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry link: https://peerj.com/articles/10619 last-modified: 2021-01-04 description: BackgroundOral cancer progresses from hyperplastic epithelial lesions through dysplasia to invasive carcinoma. The critical needs in oral cancer treatment are expanding our knowledge of malignant tumour progression and the development of useful approaches to prevent dysplastic lesions. This study was designed to gain insights into the underlying metabolic transformations that occur during the process of oral carcinogenesis.MethodsWe used gas chromatography-mass spectrometry (GC-MS) in conjunction with multivariate statistical techniques to observe alterations in serum metabolites in a 4-Nitroquinoline 1-oxide (4NQO)-induced rat tongue carcinogenesis model. Thirty-eight male rats were randomly divided into two groups, including the 4NQO-induced model group of 30 rats and the healthy control group of five rats. Animals were sacrificed at weeks 9, 13, 20, 24, and 32, post-4NQO treatment. Tissue samples were collected for histopathological examinations and blood samples were collected for metabolomic analysis. Partial least squares discriminate analysis (PLS-DA) models generated from GC-MS metabolic profile data showed robust discrimination from rats with oral premalignant and malignant lesions induced by 4NQO, and normal controls.ResultsThe results found 16 metabolites associated with 4NQO-induced rat tongue carcinogenesis. Dysregulated arachidonic acid, fatty acid, and glycine metabolism, as well as disturbed tricarboxylic acid (TCA) cycle and mitochondrial respiratory chains were observed in the animal model. The PLS-DA models of metabolomic results demonstrated good separations between the 4NQO-induced model group and the normal control group.ConclusionWe found several metabolites modulated by 4NQO and provide a good reference for further study of early diagnosis in oral cancer. creator: Shuyun Ge creator: Haiwen Zhou creator: Zengtong Zhou creator: Lin Liu creator: Jianing Lou uri: https://doi.org/10.7717/peerj.10619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ge et al. title: Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2 link: https://peerj.com/articles/10666 last-modified: 2021-01-04 description: SARS-CoV-2 genome encodes four structural proteins that include the spike glycoprotein, membrane protein, envelope protein and nucleocapsid phosphoprotein (N-protein). The N-protein interacts with viral genomic RNA and helps in packaging. As SARS-CoV-2 spread to almost all countries worldwide within 2–3 months, it also acquired mutations in its RNA genome. Therefore, this study was conducted with an aim to identify the variations present in N-protein of SARS-CoV-2. Here, we analysed 4,163 reported sequence of N-protein from United States of America (USA) and compared them with the first reported sequence from Wuhan, China. Our study identified 107 mutations that reside all over the N-protein. Further, we show the high rate of mutations in intrinsically disordered regions (IDRs) of N-protein. Our study show 45% residues of IDR2 harbour mutations. The RNA-binding domain (RBD) and dimerization domain of N-protein also have mutations at key residues. We further measured the effect of these mutations on N-protein stability and dynamicity and our data reveals that multiple mutations can cause considerable alterations. Altogether, our data strongly suggests that N-protein is one of the mutational hotspot proteins of SARS-CoV-2 that is changing rapidly and these mutations can potentially interferes with various aspects of N-protein functions including its interaction with RNA, oligomerization and signalling events. creator: Gajendra Kumar Azad uri: https://doi.org/10.7717/peerj.10666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Azad title: DHA content in milk and biohydrogenation pathway in rumen: a review link: https://peerj.com/articles/10230 last-modified: 2020-12-22 description: Docosahexaenoic acid (DHA) is an essential human nutrient that may promote neural health and development. DHA occurs naturally in milk in concentrations that are influenced by many factors, including the dietary intake of the cow and the rumen microbiome. We reviewed the literature of milk DHA content and the biohydrogenation pathway in rumen of dairy cows aim to enhance the DHA content. DHA in milk is mainly derived from two sources: α-linolenic acid (ALA) occurring in the liver and consumed as part of the diet, and overall dietary intake. Rumen biohydrogenation, the lymphatic system, and blood circulation influence the movement of dietary intake of DHA into the milk supply. Rumen biohydrogenation reduces DHA in ruminal environmental and limits DHA incorporation into milk. The fat-1 gene may increase DHA uptake into the body but this lacks experimental confirmation. Additional studies are needed to define the mechanisms by which different dietary sources of DHA are associated with variations of DHA in milk, the pathway of DHA biohydrogenation in the rumen, and the function of the fat-1 gene on DHA supply in dairy cows. creator: Guoxin Huang creator: Yangdong Zhang creator: Qingbiao Xu creator: Nan Zheng creator: Shengguo Zhao creator: Kaizhen Liu creator: Xueyin Qu creator: Jing Yu creator: Jiaqi Wang uri: https://doi.org/10.7717/peerj.10230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Lack of guilt, shame, and remorse following weight stigma expression: a real-time assessment pilot study link: https://peerj.com/articles/10294 last-modified: 2020-12-22 description: ObjectiveWeight stigma is pervasive and is associated with negative health and psychological outcomes. Few studies have examined weight stigma perpetration or the emotions individuals experience after perpetrating weight stigma. This study used experience sampling to explore the nature and frequency of weight stigma behaviors and cognitions and moral emotions (shame, guilt, remorse, pride) in the perpetrator following weight stigma perpetration.MethodsParticipants were college students (N = 31, 77.1% female). Participants completed baseline measures of anti-fat attitudes and one week of experience sampling phone prompts assessing: (1) weight stigma behaviors and cognitions and (2) moral emotions. Generalized estimating equation analyses were used to model trajectories of moral emotions after weight stigma events.ResultsThirty-one participants reported 1,008 weight stigma events over 7.5 days. Feelings of guilt, shame, and remorse decreased after weight stigma perpetration. Individuals also reported feeling less proud after engaging in weight stigma.ConclusionsWeight stigma occurs frequently as reported by perpetrators. A lack of remorse, guilt, and shame is evident in undergraduates after they express weight stigma; however, individuals in this study also reported feeling less pride after perpetration. This study highlights the need for future studies to explore the expression of weight stigma from the perspective of perpetrators instead of targets. Results highlight the pervasiveness and normative nature of weight stigma perpetration in everyday life and the need to better understand the emotional response following weight stigma perpetration as a potential mechanism of its perpetuation. creator: Paige J. Trojanowski creator: Lauren Breithaupt creator: Sonakshi Negi creator: Joseph Wonderlich creator: Sarah Fischer uri: https://doi.org/10.7717/peerj.10294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Trojanowski et al. title: The relationship between anti-Müllerian hormone (AMH) levels and pregnancy outcomes in patients undergoing assisted reproductive techniques (ART) link: https://peerj.com/articles/10390 last-modified: 2020-12-22 description: A variety of predictors are available for ovarian stimulation cycles in assisted reproductive technology (ART) forecasting ovarian response and reproductive outcome in women including biomarkers such as anti- Müllerian hormone (AMH). The aim of our present study was to compare the relationship between AMH levels and pregnancy outcomes in patients undergoing intra-cytoplasmic sperm injection (ICSI). Overall, fifty patients (n = 50), aged 20–45 years were recruited for the present prospective study. Three AMH levels were presented with high often poly cystic ovarian syndrome (PCOS) amongst 52.4% patients, 40.5% in normal and 7.1% in low to normal, correspondingly. There was statistically significant relationship between AMH and day of embryo transfer (p < 0.05). The Pearson analysis between AMH, age, E2 and FSH displayed no statistically significant relationship between E2 and AMH (p < 0.05) and negative correlation between FSH and age (p > 0.05). The area under the receiver operating characteristic curve for E2 was 0.725 and for AMH levels as predictors of CPR was 0.497 indicating E2 as better predictor than AMH. The number of oocytes, mature oocytes and fertilized oocytes all presented a weak positive relationship to AMH. Our results confirm the clinical significance of AMH to accurately predict ovarian reserve as a marker and its limitations to use as predictor for a positive pregnancy outcome. Additional prospective studies should be conducted to validate the predictive capability of AMH levels for the outcome of clinical pregnancy. creator: Shalini Umarsingh creator: Jamila Khatoon Adam creator: Suresh Babu Naidu Krishna uri: https://doi.org/10.7717/peerj.10390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Umarsingh et al.