Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of a Lytic Vibriophage OY1 and Its Biocontrol Effects Against Vibrio spp.

Vibrio species are important pathogens of marine animals and aquaculture populations and some of them can cause serious infections in humans through consumption of contaminated seafood and aquaculture products. Lytic bacteriophages can potentially alleviate Vibrio contamination in the aquaculture organisms and in the processing of aquatic products and have gained significant scientific attention in recent years. In the present study, bacteriophages were isolated from sewage of local aquatic products markets and grown using Vibrio mimicus CICC 21613 as host cells. The lytic vibriophage OY1 belonging to the newly proposed family Autographiviridae and the genus Maculvirus was identified by observation under electron microscope and comparative genomic analysis. The phage OY1 showed lytic activity against 24 among 32 tested strains belonging to eight Vibrio species. The complete phage OY1 genome consists of a single circular double-stranded DNA of 43,479 bp with a total GC content of 49.27% and was predicted to encode 40 open reading frames (ORFs). To evaluate its potential against vibrios, the one-step growth curve, thermal and pH stability, host range, and lytic activity of the OY1 phage against Vibrio species were evaluated. The results showed that phage OY1 had a range of thermal and pH tolerance, and exhibited a significant inhibitory effect on the growth of tested Vibrio species. Bacterial growth in the fish muscle extract juice (FMEJ) inoculated with Vibrio mimicus CICC 21613, Vibrio parahaemolyticus CICC 21617, Vibrio alginolyticus VJ14, and the mixed bacterial culture was reduced by 2.65 log CFU/ml, 2.42 log CFU/ml, 1.93 log CFU/ml, and 2.01 log CFU/ml, respectively, by incubation with phage OY1 at 25°C for 36 h. Phage OY1 also showed a strong ability to prevent biofilm formation and destroy formed Vibrio species biofilms. These results indicate that phage OY1 is a potential biocontrol agent against Vibrio species in the aquaculture industry and in food safety control.
CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement

The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
Strategies for the Prevention of Violence in Institutional Care: A Qualitative Interview Study With Ward Managers

Background The presence of violence within psychiatric and residential settings remains a challenge. Research on this problem has often focused on describing violence prevention strategies from either staffs' or service users' perspectives, and the views of ward managers has been largely overlooked. The aim of the present study was therefore to identify ward managers' strategies to prevent violence in institutional care, focusing on safety and values. Methods Data were collected using semi-structured interviews with 12 ward managers who headed four different types of psychiatric wards and two special residential homes for adolescents. Qualitative content analysis was applied, first using a deductive approach, in which quotes were selected within a frame of primary, secondary, and tertiary prevention, then by coding using an inductive approach to create themes and subthemes. Results Ward managers' strategies were divided into the four following themes: (1) Balancing being an active manager with relying on staff's abilities to carry out their work properly while staying mostly in the background; (2) Promoting value awareness and non-coercive practices in encounters with service users by promoting key values and adopting de-escalation techniques, as well as focusing on staff-service user relationships; (3) Acknowledging and strengthening staff's abilities and competence by viewing and treating staff as a critical resource for good care; and (4) Providing information and support to staff by exchanging information and debriefing them after violent incidents. Conclusions Ward managers described ethical challenges surrounding violence and coercive measures. These were often described as practical problems, so there seems to be a need for a development of higher ethical awareness based on a common understanding regarding central ethical values to be respected in coercive care. The ward managers seem to have a high awareness of de-escalation and the work with secondary prevention, however, there is a need to develop the work with primary and tertiary prevention. The service user group or user organizations were not considered as resources in violence prevention, so there is a need to ensure that all stakeholders are active in the process of creating violence prevention strategies.
Impact of Spatial Orientation Ability on Air Traffic Conflict Detection in a Simulated Free Route Airspace Environment

In the selection of job candidates who have the mental ability to become professional ATCOs, psychometric testing has been a ubiquitous activity in the ATM domain. To contribute to psychometric research in the ATM domain, we investigated the extent to which spatial orientation ability (SOA), as conceptualized in the spatial cognition and navigation literature, predicted air traffic conflict detection performance in a simulated free route airspace (FRA) environment. The implementation of free route airspace (FRA) over the past few years, notably in Europe, have facilitated air traffic services by giving greater flexibility to aviation operators in planning and choosing preferred air routes that can lead to quicker arrivals. FRA offers enhanced system safety and efficiency, but these benefits can be outweighed by the introduction of air traffic conflicts that are geometrically more complex. Such conflicts can arise from increased number and distribution of conflict points, as well as from elevated uncertainty in aircraft maneuvering (for instance, during heading changes). Overall, these issues will make conflict detection more challenging for air traffic controllers (ATCOs). Consequently, there is a need to select ATCOs with suitably high levels of spatial orientation ability (SOA) to ensure flight safety under FRA implementation. In this study, we tested 20 participants who are eligible for ATCO job application, and found that response time-based performance on a newly developed, open access, computerized spatial orientation test (SOT) predicted time to loss of minimum separation (tLMS) performance on an air traffic conflict detection task (AT-CDT) we designed. We found this predictive relationship to be significant to a moderately large extent under scenarios with high air traffic density (raw regression coefficient = 0.58). Moreover, we demonstrated our AT-CDT as a valid test in terms of eliciting well-known mental workload and spatial learning effects. We explained these findings in light of similar or overlapping mental processes that were most likely activated optimally under task conditions featuring approximately equal numbers of outcome-relevant stimuli. We conclude by discussing the further application of the SOT to the selection of prospective ATCOs who can demonstrate high levels of conflict detection performance in FRA during training simulations.
Health Disparities in Pharmacy Practice Within the Community: Let's Brainstorm for Solutions

Health disparity is defined as a type of health difference that is closely linked with social, economic and/or environmental disadvantage. Over the past two decades, major efforts have been undertaken to mitigate health disparities and promote health equity in the United States. Within pharmacy practice, health disparities have also been identified to play a role in influencing pharmacists' practice across various clinical settings. However, well-characterized solutions to address such disparities, particularly within pharmacy practice, are lacking in the literature. Recognizing that a significant amount of work will be necessary to reduce or eliminate health disparities, the University of California, Irvine (UCI) School of Pharmacy and Pharmaceutical Sciences held a webinar in June 2021 to explore pertinent issues related to this topic. During the session, participants were given the opportunity to propose and discuss innovative solutions to overcome health disparities in pharmacy practice. The goal of this perspective article is to distill the essence of the presentations and discussions from this interactive session, and to synthesize ideas for practical solutions that can be translated to practice to address this public health problem.
Blue Light Inhibits E. coli, but Decisive Parameters Remain Hidden in the Dark: Systematic Review and Meta-Analysis

Blue light (400–500 nm) alleviates overexposure risks associated to UV light and has therefore gained increased interest in multiple applications. This meta-analysis deals with decontamination of E. coli through the use of blue light based from nine recent publications identified via a systematic literature search. In these studies, various pathogenic and non-pathogenic E. coli strains grown in nutritional broths were exposed to wavelengths ranging from 395 to 460 nm. Five meta-analyses were performed using Cochrane’s software for meta-analyses (Review Manager): one including all studies to estimate the effect of E. coli reduction and four subgroup-analyses considering reported intensities, wavelengths, exposure dose as well as serovars/pathovars. Random effects models were used. All included studies used colony-forming units to estimate the impact of E. coli reduction. None of the included studies involved an organic matrix (e.g., skin, food related surface). Exposure to blue light had a significant and large reducing effect on viable counts of E. coli. However, substantial heterogeneity across studies was observed. Among subgroups, reported intensity and wavelength showed the clearest impact on E. coli reduction. With respect to the reported exposure dose, the picture across the spectrum was scattered, but effect sizes tend to increase with increasing exposure dose. Substantial heterogeneity was also present with respect to all serovar/pathovar subgroups among the included studies. The present body of reports does not display a strong basis for recommendation of relevant intensities, wavelengths and exposure doses for superficial blue light decontamination in medical or food safety contexts. A serious shortcoming in most studies is the absence of a clear documentation of inoculum preparation and of study parameters. We suggest improvement for study protocols for future investigations.
Handball Training and Competition With Facemasks in Galicia: The FISICOVID-DXTGALEGO Protocols Experience

Objective COVID-19 caused a complete stop in non-professional sports. The use of face masks for team sports is not a widely used measure in non-professional sports. The study aimed to evaluate the perception about using the mask and the adaptation difficulties related to training and competition in team sports following the FISICOVID-DXTGALEGO protocol. Methods Seven hundred eighty-seven handball players from the Galician Handball Federation were followed during their return to participation after months of confinement through an electronic questionnaire of perception and experience on the use of a mask. Results There is an excellent adaptation to the mask in training and competition with medium and high correlations. The 86,41% of players reported an adaptation to the mask in 3 weeks with a three times a week training frequency. The negative opinion on the mask was drastically reduced (-66.86%) after use. The 80,44% of players considered the use of a mask as an essential measure to resume competitions. Conclusions It is very feasible to adapt to training and compete with a mask (hygienic or surgical) in a short period. The use of a mask following these protocols changed previous opinions on the disadvantages of the mask during training and competition.
The Development of Education of Public Health Nurses for Applying Genomics in Preventive Health Care

Genetics and genomics have become one of the most important development areas in healthcare. For this reason, it is essential that nursing professionals take their role to offer their skills in implementing genomics in health promotion. The education of public health nurses is taking vital steps in training the health promoters who are able to take the genome-based knowledge into account in precision healthcare. Tampere University of Applied Sciences managed to integrate genomics into the studies of public health nursing. This article describes the process of development and lays emphasis on the importance of genomic education of public health nurses.
Environmental and Genetic Factors Involved in Plant Protection-Associated Secondary Metabolite Biosynthesis Pathways

Plant specialized metabolites (PSMs) play essential roles in the adaptation to harsh environments and function in plant defense responses. PSMs act as key components of defense-related signaling pathways and trigger the extensive expression of defense-related genes. In addition, PSMs serve as antioxidants, participating in the scavenging of rapidly rising reactive oxygen species, and as chelators, participating in the chelation of toxins under stress conditions. PSMs include nitrogen-containing chemical compounds, terpenoids/isoprenoids, and phenolics. Each category of secondary metabolites has a specific biosynthetic pathway, including precursors, intermediates, and end products. The basic biosynthetic pathways of representative PSMs are summarized, providing potential target enzymes of stress-mediated regulation and responses. Multiple metabolic pathways share the same origin, and the common enzymes are frequently to be the targets of metabolic regulation. Most biosynthetic pathways are controlled by different environmental and genetic factors. Here, we summarized the effects of environmental factors, including abiotic and biotic stresses, on PSM biosynthesis in various plants. We also discuss the positive and negative transcription factors involved in various PSM biosynthetic pathways. The potential target genes of the stress-related transcription factors were also summarized. We further found that the downstream targets of these Transcription factors (TFs) are frequently enriched in the synthesis pathway of precursors, suggesting an effective role of precursors in enhancing of terminal products. The present review provides valuable insights regarding screening targets and regulators involved in PSM-mediated plant protection in non-model plants.
Porous Media Microstructure Determines the Diffusion of Active Matter: Experiments and Simulations

Active swimmers are known to accumulate along external boundaries owing to their persistent self-motion, resulting in a significant reduction in their effective mobility through heterogeneous and tortuous materials. The dynamic interplay between the slowdown experienced by the active constituents near boundaries and their long-time diffusivity is critical for understanding and predicting active transport in porous media. In this work, we study the impact of boundary layer accumulation on the effective diffusivity of active matter by analyzing the motion of active Brownian particles in an array of fixed obstacles. We combine Janus particle experiments, Brownian dynamics simulations, and a theoretical analysis based on the Smoluchowski equation. We find that the shape, curvature, and microstructure of the obstacles play a critical role in governing the effective diffusivity of active particles. Indeed, even at dilute packing fractions of obstacles, ϕ = 12%, we observed a 25% reduction in the effective diffusivity of active particles, which is much larger than the hindrance experienced by passive Brownian particles. Our combined experimental and computational results demonstrate a strong coupling between the active force and the porous media microstructure. This work provides a framework to predict and control the transport of active matter in heterogeneous materials.
A Novel Missense Variant in Actin Binding Domain of MYH7 Is Associated With Left Ventricular Noncompaction

Cardiomyopathies are a group of common heart disorders that affect numerous people worldwide. Left ventricular non-compaction (LVNC) is a structural disorder of the ventricular wall, categorized as a type of cardiomyopathy that mostly caused by genetic disorders. Genetic variations are underlying causes of developmental deformation of the heart wall and the resultant contractile insufficiency. Here, we investigated a family with several affected members exhibiting LVNC phenotype. By whole-exome sequencing (WES) of three affected members, we identified a novel heterozygous missense variant (c.1963C>A:p.Leu655Met) in the gene encoding myosin heavy chain 7 (MYH7). This gene is evolutionary conserved among different organisms. We identified MYH7 as a highly enriched myosin, compared to other types of myosin heavy chains, in skeletal and cardiac muscles. Furthermore, MYH7 was among a few classes of MYH in mouse heart that highly expresses from early embryonic to adult stages. In silico predictions showed an altered actin-myosin binding, resulting in weaker binding energy that can cause LVNC. Moreover, CRISPR/Cas9 mediated MYH7 knockout in zebrafish caused impaired cardiovascular development. Altogether, these findings provide the first evidence for involvement of p.Leu655Met missense variant in the incidence of LVNC, most probably through actin-myosin binding defects during ventricular wall morphogenesis.
Exploring Variability of Trichodesmium Photophysiology Using Multi-Excitation Wavelength Fast Repetition Rate Fluorometry

Fast repetition rate fluorometry (FRRf) allows for rapid non-destructive assessment of phytoplankton photophysiology in situ yet has rarely been applied to Trichodesmium. This gap reflects long-standing concerns that Trichodesmium (and other cyanobacteria) contain pigments that are less effective at absorbing blue light which is often used as the sole excitation source in FRR fluorometers—potentially leading to underestimation of key fluorescence parameters. In this study, we use a multi-excitation FRR fluorometer (equipped with blue, green, and orange LEDs) to investigate photophysiological variability in Trichodesmium assemblages from two sites. Using a multi-LED measurement protocol (447+519+634 nm combined), we assessed maximum photochemical efficiency (Fv/Fm), functional absorption cross section of PSII (σPSII), and electron transport rates (ETRs) for Trichodesmium assemblages in both the Northwest Pacific (NWP) and North Indian Ocean in the vicinity of Sri Lanka (NIO-SL). Evaluating fluorometer performance, we showed that use of a multi-LED measuring protocol yields a significant increase of Fv/Fm for Trichodesmium compared to blue-only excitation. We found distinct photophysiological differences for Trichodesmium at both locations with higher average Fv/Fm as well as lower σPSII and non-photochemical quenching (NPQNSV) observed in the NWP compared to the NIO-SL (Kruskal–Wallis t-test df = 1, p < 0.05). Fluorescence light response curves (FLCs) further revealed differences in ETR response with a lower initial slope (αETR) and higher maximum electron turnover rate (ETRPSIImax) observed for Trichodesmium in the NWP compared to the NIO-SL, translating to a higher averaged light saturation EK (= ETRPSIImax/αETR) for cells at this location. Spatial variations in physiological parameters were both observed between and within regions, likely linked to nutrient supply and physiological stress. Finally, we applied an algorithm to estimate primary productivity of Trichodesmium using FRRf-derived fluorescence parameters, yielding an estimated carbon-fixation rate ranging from 7.8 to 21.1 mgC mg Chl-a–1 h–1 across this dataset. Overall, our findings demonstrate that capacity of multi-excitation FRRf to advance the application of Chl-a fluorescence techniques in phytoplankton assemblages dominated by cyanobacteria and reveals novel insight into environmental regulation of photoacclimation in natural Trichodesmium populations.
Association Study of TAF1 Variants in Parkinson’s Disease

Increasing evidence reveals sex as an important factor in the development of Parkinson’s disease (PD), but associations between genes on the sex chromosomes and PD remain unknown. TAF1 is a gene located on the X chromosome which is known to cause X-linked syndromic mental retardation-33 (MRXS33) and X-linked Dystonia-Parkinsonism (XDP). In this study, we conducted whole-exome sequencing (WES) among 1,917 patients with early-onset or familial PD and 1,652 controls in a Chinese population. We detected a hemizygous frameshift variant c. 29_53dupGGA(CAG)2CTACCATCA(CTG)2C (p.A19Dfs*50) in two unrelated male patients. Further segregation analysis showed an unaffected family member carried this variant, which suggested the penetrance of the variant may be age-related and incomplete. To verify the effects of TAF1 on PD, genetic analyses were carried separately by gender. Analysis of rare variants by optimal sequence kernel association (SKAT-O) test showed a nominally significant difference in variant burden between the male PD patients and controls (2.01 vs. 1.38%, p = 0.027). In the female group, none of the variant types showed significant association with PD in this study. In conclusion, we found rare variants in TAF1 may be implicated in PD, but further genetic and functional analyses were needed.