PeerJ最新文献

In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived long non-coding RNA (TElncRNA) in response to cold stress remains unclear. In this study, several Pe-TElncRNAs were identified from Moso bamboo transcriptome data. qRT-PCR analysis showed that the expression of a novel Pe-TElncRNA2 in Moso bamboo seedlings reached its highest level at 8 hours of cold treatment at 4 °C and was significantly higher in the stems compared to the leaves, roots, and buds. Furthermore, cellular localization analysis revealed that Pe-TElncRNA2 expression was significantly higher in the cytoplasm than in the nucleus. Pe-TElncRNA2 overexpression in Moso bamboo protoplasts showed that Pe-TElncRNA2 positively regulated the expression of FZR2, NOT3, ABCG44 and AGD6 genes. Further validation of this lncRNA in Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity and proline content, as well as maximum photochemical efficiency PS II in dark-adapted leaves (F _v/F _m), in the transgenic plants compared to the wild-type controls. Conversely, malondialdehyde (MDA) content, a lipid peroxidation marker (a marker of oxidative stress), was significantly reduced in the transgenic plants. Notably, the expression levels of both Pe-TElncRNA2 and the genes that were regulated by this lncRNA were upregulated in the transgenic plants after two days of cold stress treatment. These findings elucidate the critical role of LTR retrotransposon-derived lncRNAs in mediating cold stress responses in Moso bamboo.

Crustacean zooplanktons are key secondary and tertiary producers in marine ecosystems, yet their genomic resources remain poorly understood. To advance biodiversity research on crustacean zooplankton, this study evaluated the effectiveness of genome skimming, a method that assembles genetic regions, including mitogenome, from shotgun genome sequencing data. Because the small amount of DNA available is a limitation in zooplankton genetics, different input DNA amounts (1 pg-10 ng) were prepared for library construction for genome skimming using two large species: Euphausia pacifica (Euphausiacea) and Calanus glacialis (Copepoda). Additionally, de novo assembly was used to obtain long contigs from short reads because reference-guided assembly can not be applied to all crustacean zooplankton. Evaluation of the raw sequence reads showed increased proportions of high-quality and distinct reads (low duplication levels) for large DNA inputs. By contrast, low sequence quality and high sequence duplication were observed for ≤ 10 pg DNA samples, owing to increased DNA amplification cycles. Complete mitogenomes, including all 37 genes, were successfully retrieved for ≥ 10 pg (E. pacifica) and ≥ 100 pg (C. glacialis) of DNA. Despite the large estimated genome sizes of these zooplankton species, only ≥ 1 and ≥ 3 M reads were sufficient for mitogenome assembly for E. pacifica and C. glacialis, respectively. Nuclear ribosomal repeats and histone 3 were identified in the assembled contigs. As obtaining sufficient DNA amounts (≥ 100 pg) is feasible even from small crustacean zooplankton, genome skimming is a powerful approach for robust phylogenetics and population genetics in marine zooplankton.

Background: Defensive nursing practices, which prioritize legal protection over patient care, are becoming increasingly common. This study aims to explore the prevalence and factors associated with defensive nursing practices among nurses in Egypt, considering the impact of workplace violence and legal threats.

Methods: A descriptive cross-sectional study was conducted from February to April 2024 using a self-report online questionnaire. The target population included clinical nurses working in various hospitals in Egypt. A sample size of 1,267 nurses was achieved through convenience sampling. The questionnaire assessed demographic data, experiences of workplace violence, legal consequences, and defensive nursing practices, categorized into positive and negative behaviors.

Results: The sample consisted of 1,267 nurses, predominantly female (75.9%), with a mean age of 28.57 years. Positive defensive practices, such as detailed documentation (79%) and thorough explanation of procedures (58.5%), were highly prevalent. Negative practices included avoiding high-risk procedures (15.9%) and patients more likely to file lawsuits (13.6%). Older nurses and those with higher educational qualifications were more likely to engage in positive defensive practices. Nurses who experienced workplace violence or legal threats were significantly more likely to avoid high-complication procedures.

Conclusion: The study identified a high engagement in both positive and negative defensive practices among nurses in Egypt. These practices are influenced by factors such as age, education level, and experiences of workplace violence and legal threats. The findings underscore the need for strategies to support nurses, reduce reliance on defensive practices, and ensure better patient outcomes.

Yersinia ruckeri is the causative agent of yersiniosis or enteric red mouth disease (ERM) that causes significant economic losses in the salmonid aquaculture industry. Due to an increasing number of outbreaks, lack of effective vaccines and the bacteria's ability to survive in the environment for long periods, there is a necessity for novel measures to control ERM. New techniques capable of rapidly detecting Y. ruckeri are critical to aid effective control programs. Molecular methods, like real-time polymerase chain reaction, can detect Y. ruckeri; however, that methodology is not field-deployable and cannot support local decision-making during an outbreak. We present a field-deployable molecular assay using loop mediated isothermal amplification (LAMP) and water filtering method for the detection of Y. ruckeri eDNA from water samples to improve current surveillance methods. The assay was optimised to amplify the glutamine synthetase gene (glnA) of Y. ruckeri in under 20 min. The assay demonstrated high specificity and sensitivity, as it did not amplify any non-target bacteria typically present in water sources. It achieved a limit of detection (LOD) of 0.5 × 10^-7 ng/µl, significantly surpassing the LOD of 0.5 × 10^-4 ng/µl obtained through conventional polymerase chain reaction (cPCR). When applied to environmental water samples spiked with transformed Escherichia coli containing the G-block of the Yersinia ruckeri (glnA) target gene, the Yr-LAMP method exhibited an analytical sensitivity of 0.08 cells/µl from the initial filtered water sample. Notably, the cumulative time for sample preparation and amplification was under 1 h. The simplicity of the developed field-deployable Yr-LAMP assay makes it suitable as a routine procedure to monitor fish for ERM infection. This will enable informed decision-making on mitigating pathogen prevalence in aquaculture farms.

Background: The risk of potential drug‒drug interactions is highest in oldest-old people. Thus, the aim of this study was to investigate the frequency and type of potential drug‒drug interactions in population-based oldest-old people.

Methods: The type of study was descriptive. Ethical permission was obtained (13.04.2022/153). All participants were informed, and their written consent was obtained. The "oldest-old" were defined as those who were ≥85 years of age during the study period and living in Turkiye. These people were reached from every region of Turkiye via the snowball method and were visited at their homes. Data were collected via face-to-face interviews. Age, sex, city of residence, and generic names of regularly used medications were recorded. The medications used were analyzed according to the Beers 2019® Criteria and UpToDate® Lexicomp® drug interaction guides. SPSS was used for statistical analysis, and p < 0.05 was considered statistically significant.

Results: Data were collected from the 549 oldest-old people throughout Turkiye. Among the participants, 61.2% (n = 336) were women. The median age of the women was 88.00 years (minimum = 85, maximum = 101), and the median age of the men was 88.00 years (minimum = 85, maximum = 102). The distributions of men and women in the different age groups were similar (p = 0.341). The distributions of men and women across regions were similar (p = 0.826), most of whom (n = 300, 54.6%) had ≥1 potential drug‒drug interaction, according to the UpToDate analysis. The median number of medications used continuously was 4.0 (minimum = 0, maximum = 19). The median number of potential drug‒drug interactions was 1.0 (minimum = 0, maximum = 21). As the number of medications used increased, the number of potential drug‒drug interactions also increased (r = 0.737; p = 0.001). The number of potential drug‒drug interactions decreased with increasing age (r = -0.104; p = 0.015). According to the Beers 2019® Criteria, potential drug‒drug interactions were detected in only eight patients. The concordance between the Beers 2019® Criteria and the UpToDate®Lexicomb® drug interaction data was poor compared with the number of potential drug‒drug interactions (kappa = 0.024, p < 0.001). Central nervous system medications are a common group that can cause potential drug‒drug interactions according to both guidelines. Moreover, potentially inappropriate medications defined by the Beers 2019® Criteria were the most common causes of potential drug‒drug interactions, according to UpToDate®Lexicomb® drug interactions. The frequency of potential drug‒drug interactions was found to be high in the population-based oldest-old people interviewed in Turkiye. It has been determined that the use of more than one guide in the evaluation of potential drug‒drug interactions is safer.

Background: The BRAF V600E mutation was proven associated with papillary thyroid cancer (PTC) which has more aggressive behavior and could affect the outcome of PTC. The objective of this study was to observe more contrast-enhanced ultrasound (CEUS) time-intensity curve (TIC)-based quantitative parameters in nodules and surrounding parenchyma and analyze the association between the TIC-based quantitative parameters and BRAF V600E mutation status in patients with PTC.

Methods: A retrospective analysis of 447 PTC patients was conducted. Prior to thyroidectomy or fine needle aspiration (FNA), all patients had CEUS and had their BRAF V600E mutations examined. Based on their mutation status, the patients were split into two groups. The two groups were compared in terms of sex, age, quantitative CEUS characteristics, pathological findings, vascular invasion, capsular invasion, and cervical lymph node metastases.

Results: A total of 240 patients were in the mutation negative group and 207 patients were in the BRAF mutation positive group. The BRAF-positive group exhibited significantly higher arrival time (AT) and time to peak enhancement (TTP) of the nodules, among other direct quantitative characteristics. The BRAF-positive mutant nodules showed significantly higher arrival time change and time to peak change compared to the surrounding parenchyma for indirect quantitative metrics.

Conclusion: The time-dependent quantitative parameters of CEUS time intensity curve in nodules and surrounding parenchyma have clinical value in distinguishing BRAF V600E mutation positive nodules from gene mutation negative nodules. Quantitative CEUS characteristics may be beneficial in detecting the BRAF V600E mutation status and informing the subsequent clinical choice.

Background: Wetlands, globally, face significant threats from human activities, and waterbirds, as key indicators of wetland health, are essential to maintaining ecological balance. Any long-term conservation measures should prioritize coordinated habitat preservation, wetland restoration, and sustainable management practices involving local communities. Monitoring and analyzing waterbird population trends are critical for understanding restoration, conservation, and management practices.

Methods: The present study was carried out in five bird sanctuaries Chitrangudi, Kanjirankulam (Ramsar sites), Therthangal, Sakkarakottai, and Mel-Kel Selvanoor of Tamil Nadu, Southeast coast of India, over one year (April 2022 to March 2023). Monthly surveys using direct and block methods, with additional fortnightly visits during the breeding season, were conducted from vantage points to record species diversity, nesting activity, and conservation threats. Assessments of the residential status, national status (SOIB), and Convention for Migratory species (CMS) status were done along with the alpha and beta biodiversity profiles, principal component analysis, Pearson correlation and other statistical methods performed to assess breeding waterbirds community structure. Threats to the breeding waterbirds were categorised into high, medium, and low impacts based on degree of severity and irreversibility.

Results: The avifaunal checklist revealed a diversity of waterbird species utilizing the sanctuaries for breeding. Notable findings include two Near-Threatened species like, Asian Woolly-necked Stork Ciconia episcopus, and Spot-billed Pelican Pelecanus philippensis, where Asian Woolly-necked Stork recorded only in Therthangal Bird Sanctuary. Avifauna of each sanctuary with breeding waterbirds in parenthesis is as follows: Chitragundi 122 (13); Mel-Kel Selvanoor 117 (19); Therthangal 96 (23); Sakkarakottai 116 (17) and Kanjirankulam 123 (14). The breeding activity (incubation in nests) was from November to February except for Glossy Ibis and Oriental Darter whose breeding started in December; Spot-billed Duck and Knob-billed Duck breed only during January and February. Among the 131 species recorded from all the sanctuaries, 78% were resident birds; 27% were breeding waterbirds, and 21% were Winter visitors. The SOIB and CMS statuses underscore the necessity of implementing effective conservation measures to protect breeding habitats amid anthropogenic pressures. Water unavailability and nest tree unavailability in the sanctuaries are found to be the high degree threats to breeding waterbirds than others. This research provides critical baseline data for the forest department's future wetland management plans.

Habitat quality and availability are crucial for the survival and reproduction of animal species. Intraspecific and seasonal differences in habitat selection reflect adaptations to changing biological requirements and environmental factors. To investigate the effects of season (breeding and non-breeding) and sex on microhabitat selection in snakes, here we employed field surveys to analyze microhabitat selection data for Stejneger's bamboo pitviper (Viridovipera stejnegeri) across different sexes and seasons. Results indicated that although no significant difference was observed between groups, marked differences in certain microhabitat factors were noted. Specifically: (1) Non-breeding season females (NBF) displayed distinct differences in altitude, slope position, distance from roads compared to other groups. (2) Temperature exerted a lesser effect on non-breeding season individuals compared to breeding season individuals. Additionally, distance from roads only significantly impacted breeding season males, not females. (3) Regarding sexual differences, males and females differed in slope position and distance from residential sites, reflecting their distinct ecological requirements. Regarding seasons, differences in habitat selection between breeding and non-breeding seasons were primarily related to temperature, indicating behavioral changes linked to seasons. (4) Non-breeding season females exhibited the narrowest microhabitat niche width and the least microhabitat niche overlap with other groups, potentially due to their pronounced foraging requirements, which compel them to explore limited habitats with higher human disturbance but richer food sources. This study contributes novel insights into the habitat selection behaviors of snakes.

Background: This study aimed to evaluate the fracture resistance of immediate and delayed restorations after root canal treatment (RCT).

Methods: Sixty human intact premolar teeth were used. Teeth were prepared disto-occlusally. After RCT, teeth were randomly divided into two groups according to restoration times (immediate or 3 months delayed). The three month delay was imitated by thermomechanical aging. Then, samples were divided into six subgroups (n = 10). While I (Composite resin), II (Flowable bulk-fill) and III (Ribbond+Flowable bulk-fill) were restored immediately, Groups IV, V and VI were restored with temporary filling material and stored in distilled. After subjected to thermo-cycling (2,500 cycles, 5-55 °C) and exposed to 60,000 cycles in a chewing simulator, Group IV (Composite resin), V (Flowable bulk-fill) and VI (Ribbond+Flowable bulk-fill) were restored. All of the teeth were fractured on the universal testing machine. Failure modes were analyzed using scanning electron microscope. Data were analyzed using the Shapiro-Wilk and two-way ANOVA tests (p < 0.05).

Results: The highest fracture resistance was recorded in Group III while the lowest in Group VI. No statistically significant difference was observed among groups (p > 0.05). Most of the repairable fractures were seen in Groups I and II.

Conclusion: Delaying the permanent restorations of teeth for 3 months did not affect fracture resistance. However, it was suggested to avoid delaying restorations for obtaining repairable surfaces.

The paper aims to understand how humans reach for a single target object in multi-object scenes. In a previous empirical study, human subjects were asked to execute reaches to a single target among non-targets (choice reaching task). In the current work, we re-analysed the human data and implemented a neurobiologically-plausible cognitive robotics model (choice reaching with a LEGO arm robot, CoRLEGO) that mimics human reaches in the choice reaching task. The results from the experiment confirmed the commonly made assumption that proximity and similarity between objects (also termed perceptual grouping) affect the quality of the reaches. However, what was novel here was that modelling the reaches also allowed to temporally separate these factors, as the start of the movement was affected by both factors while the reach trajectory was affected only by proximity between target and distractor objects indicating that human information processing of visual stimuli applies these factors in a serial fashion. In particular, our model architecture and the optimised parameter settings suggest that object proximity directly influences the movement onset. In addition, our computational model confirmed this interpretation but also revealed that the relationship between the two factors may be affected by how the participants balanced speed (starting time of the movement) and accuracy of reaching (straightness of reaches). Future research will need to test whether this plausible prediction is correct.