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Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

Demineralized root dentin and cementum are mostly collagen that shrinks significantly upon dehydration. Active root caries lesions manifest shrinkage upon dehydration, however during the remineralization of root caries lesions mineral is deposited on the outside of the lesion arresting the lesion and arrested lesions no longer manifest shrinkage upon dehydration. Optical coherence tomography is ideally suited for the measurement of that shrinkage for the assessment of lesion activity. In this study the shrinkage of natural root caries lesions on extracted teeth were measured using a CP-OCT system with a 3D printed appliance with an integrated air nozzle suitable for clinical use.

It is challenging to identify demineralized areas of root lesions due to cervical erosion, calculus formation, and heavy staining of dentin. We have found that root caries can be imaged with extremely high contrast at short wavelength IR (SWIR) wavelengths beyond 1500-nm. Lasers are well suited for the selective removal of caries lesions from tooth surfaces. A CO2 laser operating at a wavelength of 9.3-μm was combined with a thulium-doped fiber laser operating at 1880-nm for the selective removal of root caries lesions from extracted teeth. Serial SWIR reflectance images at 1880-nm were used to guide the CO2 laser for image-guided laser ablation. Cross polarization optical coherence tomography (CP-OCT) was used to assess the initial depth of the lesions before removal and assess the volume of sound and demineralized tissue removed by the CO2 laser. With this image-guided approach, we believe we can achieve highly selective lesion removal and minimal damage to surrounding sound tissues.

Near Infrared Reflectance (NIR) is a new imaging technology that detects dental caries (decay) on tooth occlusal surfaces and in the interproximal contact sites between teeth. Conventional techniques, mostly dental x-rays, do not provide the high sensitivity and specificity at the vulnerable pits and fissure regions. The contrast of demineralization on tooth surfaces changes with increasing severity and the magnitude of that change with depth depends on the wavelength. The purpose of this study is to determine how the contrast changes with depth as a function of wavelength. Demineralization of varying depth was produced in 1.5 × 1.5 mm exposed windows after 1, 2, 3, 4, and 5 days of exposure to a demineralizing solution at pH 4.5. Lesions were imaged at 405, 630, 850, 1300, 1460, 1535, 1675, and 1950-nm with multiple imaging systems. The highest lesion contrast was measured at 1950-nm.

The diagnosis of root caries and root fractures is of increasing importance due to our aging population. The objective of this study is to show that optical clearing agents can be used to increase the visibility of subsurface structures in tooth roots to aid in the diagnosis of root caries depth and extension and to differentiate from subsurface defects. Previous studies have shown that high refractive index fluids can increase the depth penetration of optical coherence tomography (OCT) for imaging caries lesions on tooth enamel. Extracted teeth with suspected root caries were imaged with (OCT) with and without the addition of water (W), glycerol (G), and propylene glycol (PG). The reflectance was monitored in sound and demineralized areas before and after application of W, G, and PG. The visibility of subsurface root canals was also measured before and after application of the respective fluids. In addition, shrinkage in lesion areas was measured after lesion dehydration to aid in the assessment of lesion activity. This study shows that optical clearing agents can be used to increase the performance of OCT for the diagnosis of root caries and other defects on root surfaces.

Through the provision of different types of social support, significant nonparental youth--adult relationships can facilitate youth's positive development across adolescence. However, despite the potential benefits of these relationships, there has been little consideration of how the relational process may vary across different adolescent stages. Utilizing qualitative methods, this study compared five types of social support processes (emotional, instrumental, companionship, validation, and informational) as reported by youth during early (n = 23) and late adolescence (n = 14). Differences emerged with regard to the general characteristics and nature of relationships between the early and late adolescent groups and additional differences emerged across the five types of social support. This study demonstrates how a developmental perspective may elucidate the processes that characterize and underlie youth's relationships with supportive nonparental adults. Findings provide implications to understand, promote and sustain these important relationships in the lives of youth.

Mental health is crucial throughout life and significantly influences overall well-being, yet it is often overlooked and stigmatized. Mental health issues among men are a significant public health concern due to societal norms that discourage emotional vulnerability and seeking help, leading to underreporting and inadequate access to necessary services. While research has explored these connections, a gap exists in understanding how these factors influence the mental health of young men specifically. The study was conducted in the college department of an institution in Malaybalay City, Bukidnon. It utilized an explanatory sequential research design, beginning with quantitative data collection to measure 106 male students' experiences with mental health expression and stigma, followed by qualitative methods to explore the experiences of 5 male students in-depth regarding their mental health expression. This study examines the factors influencing male students' willingness to communicate mental health expression. The study shows a strong positive correlation between adverse experiences and higher-level stigma, underscoring how societal attitudes discourage open communication. Moreover, the qualitative findings reveal that societal norms, personal experiences, and coping mechanisms play a role. Themes like stereotyping, social anxieties, and feelings of isolation emerged, highlighting students' challenges in seeking support. These qualitative insights support the quantitative data, which shows a high prevalence of stigma surrounding mental health. The study emphasizes the need to address these cultural and structural barriers to create a more supportive environment that reduces stigma and encourages help-seeking behavior among male students. [ABSTRACT FROM AUTHOR]

The livelihoods of the majority of Uganda's population depend on declining environmental resources. The sustainability of the natural environment requires that the people who are interdependent with it, as well as the structures of governance and leadership around them, understand the implications of resource degradation and take deliberate steps towards restoration. The interdependency of human and environment conditions in Uganda requires multidisciplinary attention and this paper reflects a contribution to this end. Socio‐cultural perceptions and relations with a vulnerable environment are put into dialogue with the physical status of environmental resources in Alebtong District, Uganda. Southern epistemological perspectives are considered in relation to Western scientific paradigms. Culturally responsive socio‐cultural research data are related to MODIS NDVI data, using time series analyses and NDVI as a proxy for productivity. The research confirms the declining availability and condition of natural resources and the acknowledgement of local influence on this condition. Despite this, deliberate community and governance efforts towards conservation and restoration varied from non‐existent to insufficient. The causes for this inconsistency revolve around conflicting priorities. This paper demonstrates and discusses the difficult trade‐offs in decision‐making about natural resources that rural communities face, and supports new partnership models as a route to improvement. [ABSTRACT FROM AUTHOR]

Background Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a common approach to active surveillance, but its sensitivity for detecting colonization is uncertain. Methods Daily rectal or fecal swab samples and associated clinical data were collected over 12 months from patients in one 25-bed medical intensive care unit (ICU) in Chicago, IL and tested for the following MDROs: vancomycin-resistant enterococci; third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales; and carbapenem-resistant Enterobacterales. MDRO detection by (1) admission and discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. Results Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of MDRO acquisitions among medical ICU patients. Few (7%) MDRO carriers were identified by clinical cultures alone. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. Conclusions Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance. [ABSTRACT FROM AUTHOR]

Context: Understanding fire and inundation impacts on wetland vegetation communities is crucial for effective post-fire wetland management. Aims: We aimed to determine the impact of post-fire inundation on plant community structure and seedling germination and establishment after a large wildfire. We asked two questions, namely (1) did fire, drought or inundation affect plant communities the most; and (2) did fire or inundation affect seedling germination and establishment? Methods: Using a before–after–control–impact (BACI) design, we monitored vegetation changes in water-couch wetland communities before and after a wildfire. Also, soil samples were collected from burnt and unburnt sites and assessed for impacts of fire and post-fire inundation regimes on seed germination and seedling establishment. Key results: Inundation variables had more pronounced and more consistent impacts on vegetation measures than did fire or drought variables. Fire impacts were mainly short-term, with impact thresholds at 72 and 143 days after fire. Low germination levels and zero seedling survival were observed without inundation. Conclusions: Fire was a major but short-term contributor to wetland vegetation change, whereas drought had longer-term impacts, and inundation regimes had the greatest impacts. Implications: Providing a range of inundation conditions post-fire may enhance wetland vegetation recovery and have modifying effects on invasive species. Understanding fire and inundation impacts on wetland vegetation communities is crucial for effective post-fire wetland management. Here, we measured fire and inundation impacts on water-couch marshland in the Gwydir Wetlands and showed that fire was a major but short-term contributor to wetland vegetation change, whereas drought had longer-term impacts, and inundation regimes had the greatest impacts. This article belongs to the collection Environmental flows in northern Murray–Darling Basin: what we know about the science and management after a decade of practice. [ABSTRACT FROM AUTHOR]

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), is an invasive pest species that has incurred massive economic damages in areas cultivating economically important crops like corn, rice, cotton and many others. Known to be a native of the Western Hemisphere, FAW has since then established itself in many parts of Africa, Asia and Australia and Oceania. The Philippines had been among the Asian countries vulnerable to FAW invasion, which was validated in June 2019. This study aims to characterize the existing strains and haplotypes of FAW and describe the genetic structure and the signature of its recent demographic history nationwide. COI sequences reveal the predominance of rice‐strain over the corn‐strain FAW, while Tpi sequences are more accurate in defining the corn‐strain found in corn and sugarcane. Discordant COI‐Tpi configurations frequently occur the most in the entire FAW population at 65.29%. Nucleotide and haplotype diversity are low with an average of 0.005976 and 0.4019 respectively. In addition to non‐significant values in neutrality tests suggesting neutral evolution, the low nucleotide and haplotype diversity indicate population contraction from founder effect. Variations are mostly found within regions, and genetic structure is moderate among regions (FST = 0.14375). These results can be attributed to low selective pressures accompanying its establishment, or more likely due to recent migration and/or human‐assisted factors such as trade. Implications on pest management and prospective studies in the future are also discussed in this study. [ABSTRACT FROM AUTHOR]