Pennsylvania State University
  • University Park, PA, United States
Recent publications
This study examined daily occurrences of behavioral and psychological symptoms of dementia (BPSD) and whether caregivers’ perceived distress towards BPSD varies throughout four phases of the day (i.e., morning, daytime, evening, and night). Family caregivers residing with relatives who were using adult day services (ADS) participated in an 8-day daily diary study (caregiver N = 173; caregiver-day N = 1,359). BPSD occurred most frequently in the evenings. ADS use, sleep disturbances, and dementia severity were significantly associated with BPSD occurrence for some phases of the day. Caregivers’ distress towards BPSD occurrences increased throughout the day (i.e., most stressful at night). However, caregivers showed lower reactivity to BPSD at night on days when their relatives used ADS. Evidence of temporal patterns of BPSD in community-dwelling older adults and caregiver distress demonstrated the importance of ADS use for BPSD reactivity and identified potential target windows and associated contextual factors for individualized interventions.
Wild lupine (Lupinus perennis) is a perennial plant originally found primarily throughout the United States and Canada in oak savannas, which are considered an ecotone between prairie and forest. Because of primary habitat loss, this early successional plant is declining and now persists in managed edge habitats such as power line rights-of-way and roadsides across much of its range. Many edge populations of wild lupine are small and isolated, which can hinder the reproduction of this pollinator-dependent plant. Here, we synthesize current literature about the biology and management of wild lupine and associated plants and insects. We also highlight current gaps of knowledge to guide future research on wild lupine and, more generally, on savanna-like habitats. The information provided here on lupine serves as a case study for how edge habitat conserves rare plant species reliant on disturbance. Overall, habitat characteristics that seem best for wild lupine include a gradient of canopy cover from moderate to open, well-drained soils, and a low abundance of understory woody plants. Land management, including prescribed burning, mowing, and mechanical thinning, can promote the conservation of wild lupine and other forest edge plants. However, additional research in regards to ideal management regimes and intensity is needed to further plant conservation in forest edge habitat.
Coral reefs are beginning to experience conditions unlike any in recent history. Understanding ecosystem function on future reefs will require reassessing ecological processes under novel environmental regimes. For many coastal reefs, severely degraded water quality will be a hallmark of these novel regimes. While herbivory has traditionally been considered essential for maintaining coral dominance, recent evidence from urban reefs suggests this pattern may be changing. Here, we reexamined the impacts of herbivores on a shallow, turbid reef exposed to extensive coastal development. We found that although herbivore biomass, size-structure, and grazing rates were significantly reduced relative to a nearby protected reef, coral cover on this shallow urban reef remained > 45%. In contrast, coral cover at the nearby protected site was roughly 50% lower. Differences in coral cover between the sites were due to greater cover of two groups of corals at the urban site: depth-generalist Orbicella spp., particularly O. faveolata, and Agaricia spp. with weedy life-history characteristics. Both groups are tolerant of low light but susceptible to coral bleaching. Our results suggest that diminished top-down pressure did not promote algal dominance. Instead, turbidity-induced reductions in available light drove community structure, leading to dominance of coral and algae species able to acclimate to low-light. Our study demonstrates how environmental context can alter the importance of critical processes on coral reefs and highlights the need to reexamine traditional paradigms in reef ecology to understand ecosystem function on future reefs.
Background Xanthomonas translucens pv. graminis (Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity. Results In this study, we produced high-quality, complete genome sequences of four strains of Xtg, complementing the recently obtained complete genome sequence of the Xtg pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related. A high number of transposases were exclusively found in Xtg and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of Xtg. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 plant cell wall degradative enzymes. Conclusion These results suggest a high adaptability of Xtg, conferred by the abundance of mobile genetic elements, which could play a crucial role in pathogen adaptation. The large amount of such elements in Xtg compared to other pathovars of the species could, at least partially, explain its high virulence and broad host range. Conserved features that were specific to Xtg were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of Xtg.
Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of 'internally-labeled' (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.
Relative humidity (RH) is an environmental variable that affects mosquito physiology and can impact pathogen transmission. Low RH can induce dehydration in mosquitoes, leading to alterations in physiological and behavioral responses such as blood-feeding and host-seeking behavior. We evaluated the effects of a temporal drop in RH (RH shock) on mortality and Mayaro virus vector competence in Ae. aegypti. While dehydration induced by humidity shock did not impact virus infection, we detected a significant effect of dehydration on mosquito mortality and blood-feeding frequency, which could significantly impact transmission dynamics.
Cheatgrass ( Bromus tectorum ) is one of the most problematic invasive plants in the western United States. Invasion by annual grasses disrupts nutrient cycling and negatively affects above- and below-ground biodiversity. Land managers use chemical herbicides, mechanical controls, cultural practices, and bioherbicides to combat this invasive plant. Recently, the biocontrol agent Pseudomonas fluorescens D7 has been touted as a non-chemical herbicide that offers lasting control of cheatgrass. However, experimental results report limited effectiveness under field conditions. To understand the underlying cause of the variable efficacy of this commercially available bioherbicide, soil samples from an active cheatgrass invasion treated with P. fluorescens D7 were collected and screened using high-throughput sequencing. At 18 months post-application, the bioherbicide had limited lasting effects on bacterial community composition, and no reads assigned to P. fluorescens D7 were found in our sequence data. We suggest that the failure to establish may partially explain the inability of this biocontrol agent to suppress B. tectorum under field conditions. IMPORTANCE Cheatgrass is one of North America’s most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P . fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens D7 at 18 months post-application.
Severity of neurobehavioral deficits in children born from adverse pregnancies, such as maternal alcohol consumption and diabetes, does not always correlate with the adversity’s duration and intensity. Therefore, biological signatures for accurate prediction of the severity of neurobehavioral deficits, and robust tools for reliable identification of such biomarkers, have an urgent clinical need. Here, we demonstrate that significant changes in the alternative splicing (AS) pattern of offspring lymphocyte RNA can function as accurate peripheral biomarkers for motor learning deficits in mouse models of prenatal alcohol exposure (PAE) and offspring of mother with diabetes (OMD). An aptly trained deep-learning model identified 29 AS events common to PAE and OMD as superior predictors of motor learning deficits than AS events specific to PAE or OMD. Shapley-value analysis, a game-theory algorithm, deciphered the trained deep-learning model’s learnt associations between its input, AS events, and output, motor learning performance. Shapley values of the deep-learning model’s input identified the relative contribution of the 29 common AS events to the motor learning deficit. Gene ontology and predictive structure–function analyses, using Alphafold2 algorithm, supported existing evidence on the critical roles of these molecules in early brain development and function. The direction of most AS events was opposite in PAE and OMD, potentially from differential expression of RNA binding proteins in PAE and OMD. Altogether, this study posits that AS of lymphocyte RNA is a rich resource, and deep-learning is an effective tool, for discovery of peripheral biomarkers of neurobehavioral deficits in children of diverse adverse pregnancies.
Purpose Generalization has been defined and instantiated in a variety of ways over the last half-century, and this lack of consistency has created challenges for speech-language pathologists to plan for, implement, and measure generalization in aphasia treatment protocols. This tutorial provides an overview of generalization with a focus on how it relates to aphasia intervention, including a synthesis of existing principles of generalization and examples of how these can be embedded in approaches to aphasia treatment in clinical and research settings. Method Three articles collectively listing 20 principles of generalization formed the foundation for this tutorial. The seminal work of Stokes and Baer (1977) focused attention on generalization in behavioral change following treatment. Two aphasia-specific resources identified principles of generalization in relation to aphasia treatment (Coppens & Patterson, 2018; Thompson, 1989). A selective literature review was conducted to identify evidence-based examples of each of these 20 principles from the extant literature. Results Five principles of generalization were synthesized from the original list of 20. Each principle was supported by studies drawn from the aphasia treatment literature to exemplify its application. Conclusions Generalization is an essential aspect of meaningful aphasia intervention. Successful generalization requires the same dedication to strategic planning and outcome measurement as the direct training aspect of intervention. Although not all people with aphasia are likely to benefit equally from each of the principles reviewed herein, our synthesis provides information to consider for maximizing generalization of aphasia treatment outcomes. Supplemental Material
The 6th International Consensus Conference on Concussion in Sport, Amsterdam 2022, addressed sport-related concussion (SRC) in adults, adolescents, and children. We highlight the updated evidence-base and recommendations regarding SRC in children (5–12 years) and adolescents (13–18 years). Prevention strategies demonstrate lower SRC rates with mouthguard use, policy disallowing bodychecking in ice hockey, and neuromuscular training in adolescent rugby. The Sport Concussion Assessment Tools (SCAT) demonstrate robustness with the parent and child symptom scales, with the best diagnostic discrimination within the first 72 hours postinjury. Subacute evaluation (>72 hours) requires a multimodal tool incorporating symptom scales, balance measures, cognitive, oculomotor and vestibular, mental health, and sleep assessment, to which end the Sport Concussion Office Assessment Tools (SCOAT6 [13+] and Child SCOAT6 [8–12]) were developed. Rather than strict rest, early return to light physical activity and reduced screen time facilitate recovery. Cervicovestibular rehabilitation is recommended for adolescents with dizziness, neck pain, and/or headaches for greater than 10 days. Active rehabilitation and collaborative care for adolescents with persisting symptoms for more than 30 days may decrease symptoms. No tests and measures other than standardized and validated symptom rating scales are valid for diagnosing persisting symptoms after concussion. Fluid and imaging biomarkers currently have limited clinical utility in diagnosing or assessing recovery from SRC. Improved paradigms for return to school were developed. The variable nature of disability and differences in evaluating para athletes and those of diverse ethnicity, sex, and gender are discussed, as are ethical considerations and future directions in pediatric SRC research.
Baseline trachoma surveys in Côte d'Ivoire (2019) identified seven evaluation units (EUs) with a trachomatous inflammation–follicular (TF) prevalence ≥10%, but a trachomatous trichiasis (TT) prevalence in individuals ≥15 y of age below the elimination threshold (0.2%). Two of these EUs, Bondoukou 1 and Bangolo 2, were selected for a follow-up survey to understand the epidemiology of trachoma using additional indicators of Chlamydia trachomatis infection (DNA from conjunctival swabs) and exposure (anti-Pgp3 and Ct694 antibodies from dried blood spots [DBSs]). A two-stage cluster sampling methodology was used to select villages and households. All individuals 1–9 y of age from each selected household were recruited, graded for trachoma and had a conjunctival swab and DBS collected. Conjunctival swabs and DBSs were tested using Cepheid GeneXpert and a multiplex bead assay, respectively. The age-adjusted TF and infection prevalence in 1- to 9-year-olds was <1% and <0.3% in both EUs. Age-adjusted seroprevalence was 5.3% (95% confidence interval [CI] 1.5 to 15.6) in Bondoukou 1 and 8.2% (95% CI 4.3 to 13.7) in Bangolo 2. The seroconversion rate for Pgp3 was low, at 1.23 seroconversions/100 children/year (95% CI 0.78 to 1.75) in Bondoukou 1 and 1.91 (95% CI 1.58 to 2.24) in Bangolo 2. Similar results were seen for CT694. These infection, antibody and clinical data provide strong evidence that trachoma is not a public health problem in either EU.
Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a “paddle-shaped” PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
Despite a vaccine, hepatitis B virus (HBV) remains a world-wide source of infections and deaths. We develop a whole-cell computational platform combining spatial and kinetic models describing the infection cycle of HBV in a hepatocyte host. We simulate key parts of the infection cycle with this whole-cell platform for 10 min of biological time, to predict infection progression, map out virus-host and virus-drug interactions. We find that starting from an established infection, decreasing the copy number of the viral envelope proteins shifts the dominant infection pathway from capsid secretion to re-importing the capsids into the nucleus, resulting in more nuclear-localized viral covalently closed circular DNA (cccDNA) and boosting transcription. This scenario can mimic the consequence of drugs designed to manipulate viral gene expression. Mutating capsid proteins facilitates capsid destabilization and disassembly at nuclear pore complexes, resulting in an increase in cccDNA copy number. However, excessive destabilization leads to premature cytoplasmic disassembly and does not increase the cccDNA counts. Finally, our simulations can predict the best drug dosage and its administration timing to reduce the cccDNA counts. Our adaptable computational platform can be parameterized to study other viruses and identify the most central viral pathways that can be targeted by drugs.
Biomass gasification has significantly advanced in terms of performance and is increasingly used in rural off-grid electricity applications. The downdraft gasifier is primarily used in biomass gasification applications, in which it functions as a reactor into which biomass and gasifying air are introduced to generate producer gas that is then used in an engine generator to produce electricity. However, the safety and stability of biomass gasification remain challenging and depend on several factors, such as the startup heating process, which can affect risks of fire, explosion, and toxic gas emissions. As the biomass gasification is associated with high temperatures and demands safety measures, its startup process should follow a rigorous procedure that ensures reliable operation and minimizes the risk of hazard issues. This study presents a gasifier startup heating process based on a proposed safety protocols hazard analysis. The study indicates that the heating temperature in startup processes has been identified as a critical factor due to its role in impacting safety. The findings indicate that the biomass gasification process has significant risks, including the potential for fire, explosion, and release of environmental emissions via multiple pathways. The methods proposed here could lead to reduced risk from the abovementioned issues.
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22,299 members
Bing Pan
  • Department of Recreation, Park, and Tourism Management
Gordon N. Fleming
  • Department of Physics
Michelle Gayle Newman
  • Department of Psychology
Jordan Road, 16563, University Park, PA, United States
Head of institution
Dr. Eric Barron