Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers.

Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.

Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections.

Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.

Thermal Conductivity Enhancement in Ion-Irradiated Hydrogenated Amorphous Carbon Films.

Amorphous solids are traditionally assumed to set the lower bound to the vibrational thermal conductivity of a material due to the high degree of structural disorder. Here, were demonstrate the ability to increase the thermal conductivity of amorphous solids through ion irradiation, in turn, altering the bonding network configuration. We report on the thermal conductivity of hydrogenated amorphous carbon implanted with C+ ions spanning fluences of 3 × 1014-8.6 × 1014 cm-2 and energies of 10-20 keV. Time-domain thermoreflectance measurements of the films' thermal conductivities reveal significant enhancement, up to a factor of 3, depending upon the preirradiation composition. Films with higher initial hydrogen content provide the greatest increase, which is complemented by an increased stiffening and densification from the irradiation process. This enhancement in vibrational transport is unique when contrasted to crystalline materials, for which ion implantation is known to produce structural degradation and significantly reduced thermal conductivities.

Impact of delayed prescription fill on readmission rates for chronic obstructive pulmonary disease and heart failure.

OBJECTIVES: In an effort to reduce reimbursement penalty from the Centers for Medicare & Medicaid Services, hospitals have looked to evaluate the effectiveness of existing programs as well as adopt innovative practices to reduce 30-day readmission rates. The objective of this study was to evaluate the impact of delaying prescription fill on 30-day readmission rates for patients with heart failure (HF) and chronic obstructive pulmonary disease (COPD). Identifying an association between delaying prescription fill and readmission rate would validate programs that provide patients with their medications before discharge. METHODS: A retrospective chart review was performed for all patients admitted to Henry County Medical Center with an HF or COPD exacerbation from January to October 2016. Outpatient pharmacies were contacted for each patient to determine time of prescription fill. Time of fill was compared with time of discharge, and patients were separated into 2 subgroups: those who filled within 48 hours of discharge and those who filled after 48 hours. The primary outcome was 30-day readmission rate, and a secondary end point was to identify patient characteristics associated with delayed prescription fills. RESULTS: A total of 104 patients were included in the study. COPD patients experienced a lower readmission rate when delaying prescription fill at least 48 hours (P = 0.23). HF patients experienced a higher readmission rate when delaying prescription fill at least 48 hours (P = 0.48). No baseline characteristics were associated with a significantly higher rate of delaying prescription fill. CONCLUSION: Delaying discharge prescription fills resulted in a nonsignificant increase in the rate of HF readmission but did not increase the rate of readmission for COPD. Rate of delaying prescription fill was not statistically greater for any of the baseline characteristics.

Full Characterization of the Mechanical Properties of 11-50 nm Ultrathin Films: Influence of Network Connectivity on the Poisson's Ratio.

Precise characterization of the mechanical properties of ultrathin films is of paramount importance for both a fundamental understanding of nanoscale materials and for continued scaling and improvement of nanotechnology. In this work, we use coherent extreme ultraviolet beams to characterize the full elastic tensor of isotropic ultrathin films down to 11 nm in thickness. We simultaneously extract the Young's modulus and Poisson's ratio of low-k a-SiC:H films with varying degrees of hardness and average network connectivity in a single measurement. Contrary to past assumptions, we find that the Poisson's ratio of such films is not constant but rather can significantly increase from 0.25 to >0.4 for a network connectivity below a critical value of ∼2.5. Physically, the strong hydrogenation required to decrease the dielectric constant k results in bond breaking, lowering the network connectivity, and Young's modulus of the material but also decreases the compressibility of the film. This new understanding of ultrathin films demonstrates that coherent EUV beams present a new nanometrology capability that can probe a wide range of novel complex materials not accessible using traditional approaches.

The effect of edge compliance on the contact between a spherical indenter and a high-aspect-ratio rectangular fin.

In the last two decades, significant progress has been made on developing new nanoscale mechanical property measurement techniques including instrumented indentation and atomic force microscopy based techniques. The changes in the tip-sample contact mechanics during measurements uniquely modify the displacement and force sensed by a measurement sensor and much effort is dedicated to correctly retrieve the sample mechanical properties from the measured signal. It turns out that in many cases, for the sake of simplicity, a simple contact mechanics model is adopted by overlooking the complexity of the actual contact geometry. In this work, a newly developed matrix formulation is used to solve the stress and strain equations for samples with edge geometries. Such sample geometries are often encountered in today's nanoscale integrated electronics in the form of high-aspect-ratio fins with widths in the range of tens of nanometers. In the matrix formulation, the fin geometries can be easily modeled as adjacent overlapped half-spaces and the contact problem can be solved by a numerical implementation of the conjugate gradient method. This method is very versatile in terms of contact geometry and contact interaction, either non-adhesive or adhesive. The discussion will incorporate a few model examples that are relevant for the nanoscale mechanics investigated by intermittent contact resonance AFM (ICR-AFM) on low-k dielectric fins of high-aspect-ratio. In such ICR-AFM measurements, distinct dependence of the contact stiffness was observed as a function of the applied force and distance from the edges of the fins. These dependences were correctly predicted by the model and used to retrieve the mechanical changes undergone by fins during fabrication and processing.

Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.

Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family's known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intrabacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show is capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi possess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Because single-protein metabolic modules such as flavoHb function independently, readily undergo GD and HGT, and are frequently involved in organismal defense and competition, we suggest that they represent "plug-and-play" proteins for ecological arms races.

Nanoscale tomographic reconstruction of the subsurface mechanical properties of low-k high-aspect ratio patterns.

In this work, intermittent contact resonance atomic force microscopy (ICR-AFM) was performed on high-aspect ratio a-SiOC:H patterned fins (100 nm in height and width from 20 to 90 nm) to map the depth and width dependencies of the material stiffness. The spatial resolution and depth sensitivity of the measurements were assessed from tomographic cross-sections over various regions of interest within the 3D space of the measurements. Furthermore, the depth-dependence of the measured contact stiffness over the scanned area was used to determine the sub-surface variation of the elastic modulus at each point in the scan. This was achieved by iteratively adjusting the local elastic profile until the depth dependence of the resulted contact stiffness matched the depth dependence of the contact stiffness measured by ICR-AFM at that location. The results of this analysis were assembled into nanoscale sub-surface tomographic images of the elastic modulus of the investigated SiOC:H patterns. A new 3D structure-property representation emerged from these tomographic images with direct evidence for the alterations sustained by the structures during processing.

Nanoscale Buckling of Ultrathin Low-k Dielectric Lines during Hard-Mask Patterning.

Commonly known in macroscale mechanics, buckling phenomena are now also encountered in the nanoscale world as revealed in today's cutting-edge fabrication of microelectronics. The description of nanoscale buckling requires precise dimensional and elastic moduli measurements, as well as a thorough understanding of the relationships between stresses in the system and the ensuing morphologies. Here, we analyze quantitatively the buckling mechanics of organosilicate fins that are capped with hard masks in the process of lithographic formation of deep interconnects. We propose an analytical model that quantitatively describes the morphologies of the buckled fins generated by residual stresses in the hard mask. Using measurements of mechanical properties and geometric characteristics, we have verified the predictions of the analytical model for structures with various degrees of buckling, thus putting forth a framework for guiding the design of future nanoscale interconnect architectures.

Toughening thin-film structures with ceramic-like amorphous silicon carbide films.

A significant improvement of adhesion in thin-film structures is demonstrated using embedded ceramic-like amorphous silicon carbide films (a-SiC:H films). a-SiC:H films exhibit plasticity at the nanoscale and outstanding chemical and thermal stability unlike most materials. The multi-functionality and the ease of processing of the films have potential to offer a new toughening strategy for reliability of nanoscale device structures.

Analysis of a taurine-dependent promoter in Sinorhizobium meliloti that offers tight modulation of gene expression.

BACKGROUND: Genetic models have been developed in divergent branches of the class Alphaproteobacteria to help answer a wide spectrum of questions regarding bacterial physiology. For example, Sinorhizobium meliloti serves as a useful representative for investigating rhizobia-plant symbiosis and nitrogen fixation, Caulobacter crescentus for studying cell cycle regulation and organelle biogenesis, and Zymomonas mobilis for assessing the potentials of metabolic engineering and biofuel production. A tightly regulated promoter that enables titratable expression of a cloned gene in these different models is highly desirable, as it can facilitate observation of phenotypes that would otherwise be obfuscated by leaky expression. RESULTS: We compared the functionality of four promoter regions in S. meliloti (P(araA), P(tauA), P(rhaR), and P(melA)) by constructing strains carrying fusions to the uidA reporter in their genomes and measuring beta-glucuronidase activities when they were induced by arabinose, taurine, rhamnose, or melibiose. P(tauA) was chosen for further study because it, and, to a lesser extent, P(melA), exhibited characteristics suitable for efficient modulation of gene expression. The levels of expression from P(tauA) depended on the concentrations of taurine, in both complex and defined media, in S. meliloti as well as C. crescentus and Z. mobilis. Moreover, our analysis indicated that TauR, TauC, and TauY are each necessary for taurine catabolism and substantiated their designated roles as a transcriptional activator, the permease component of an ABC transporter, and a major subunit of the taurine dehydrogenase, respectively. Finally, we demonstrated that P(tauA) can be used to deplete essential cellular factors in S. meliloti, such as the PleC histidine kinase and TatB, a component of the twin-arginine transport machinery. CONCLUSIONS: The P(tauA) promoter of S. meliloti can control gene expression with a relatively inexpensive and permeable inducer, taurine, in diverse alpha-proteobacteria. Regulated expression of the same gene in different hosts can be achieved by placing both tauR and P(tauA) on appropriate vectors, thus facilitating inspection of conservation of gene function across species.

Spectroscopic method for measuring refractive index.

A method for routine, but precise measurements of refractive index is described. The method is fast and accurate. It is based on the analysis of interference fringes, and uses positions of the fringe maxima and/or minima and a precise measurement of sample thickness to extract refractive index. An extremely dense dataset of refractive index values over the entire spectral range of interest can be routinely obtained.

Intervention based on social cognitive theory: evaluating adolescents' knowledge of OTC pain medications.

OBJECTIVE: To evaluate the effect of a social cognitive theory (SCT)-based intervention on the constructs of situational perception, behavioral capabilities, outcome expectations, outcome expectancies, and self-efficacy concerning over-the-counter (OTC) pain medications among an adolescent population. DESIGN: Pre-posttest control group design. SETTING: Rural high school in the southeastern United States, between February and March 2011. PARTICIPANTS: 203 high school students recruited from 10 classrooms. INTERVENTION: Classrooms were randomly assigned to an SCT-based education intervention group or the control group. Pre- and posttest data were collected from each group 2 weeks before and 2 weeks after the intervention was delivered. MAIN OUTCOME MEASURES: Change in the five selected constructs of SCT. RESULTS: Compared with the control group, significant improvements at posttest were observed in the intervention group for outcome expectations of OTC pain medications ( P ≤ 0.05) and behavioral capabilities ( P ≤ 0.05). CONCLUSION: The results suggest that lessons based on SCT to improve the outcome expectations that an adolescent population places on the consumption of OTC pain medications may assist in developing the knowledge and skills needed to consume these products properly.

Nanoscale mapping of contact stiffness and damping by contact resonance atomic force microscopy.

In this work, a new procedure is demonstrated to retrieve the conservative and dissipative contributions to contact resonance atomic force microscopy (CR-AFM) measurements from the contact resonance frequency and resonance amplitude. By simultaneously tracking the CR-AFM frequency and amplitude during contact AFM scanning, the contact stiffness and damping were mapped with nanoscale resolution on copper (Cu) interconnects and low-k dielectric materials. A detailed surface mechanical characterization of the two materials and their interfaces was performed in terms of elastic moduli and contact damping coefficients by considering the system dynamics and included contact mechanics. Using Cu as a reference material, the CR-AFM measurements on the patterned structures showed a significant increase in the elastic modulus of the low-k dielectric material compared with that of a blanket pristine film. Such an increase in the elastic modulus suggests an enhancement in the densification of low-k dielectric films during patterning. In addition, the subsurface response of the materials was investigated in load-dependent CR-AFM point measurements and in this way a depth dimension was added to the common CR-AFM surface characterization. With the new proposed measurement procedure and analysis, the present investigation provides new insights into characterization of surface and subsurface mechanical responses of nanoscale structures and the integrity of their interfaces.

The influence of symbols on the short-term recall of pharmacy-generated prescription medication information in a low health literate sample.

The effect of symbols on conveying health information has been studied in a variety of contexts and populations. This investigation assessed whether short-term recall of prescription medication information could be enhanced in a low health literate population through the use of symbols. Participants recruited from various nonpharmacy educational service locations were randomly assigned to receive a prescription medication information leaflet in either a text-only, text with symbols, or symbols-only format and then administered the Rapid Estimate of Adult Literacy in Medicine (REALM). Only those with REALM scores indicative of a sixth grade or lower reading level were included in data analysis. An 8-item, interviewer-administered questionnaire was used to assess participants' recall of information contained in the leaflet. A fictitious medication was used to control for participants' past experiences with medications. Results of statistical testing revealed that the three groups did not differ with respect to their ability to recall the medication information, F(2, 157) = 0.943, p = .392. The symbols used in this investigation were not found to enhance the short-term recall of the medication information presented. These findings should not be considered a wholesale indictment of the use of symbols within health care and in pharmacies. Rather, they should serve as a caution to their widespread use without careful consideration.

Resolving the Subsurface Structure and Elastic Modulus of Layered Films via Contact Resonance Atomic Force Microscopy.

Since its discovery, atomic force microscopy (AFM) has become widely used for surface characterization, evolving from a tool for probing surface topography to a versatile method for characterizing mechanical, electrical, chemical, magnetic, and electro-optical properties of surfaces at the nanoscale. Developments of several AFM-based techniques have enabled even subsurface imaging, which is routinely being carried out at the qualitative level of feature detection for localized subsurface inhomogeneities. We surmise, however, that a quantitative three-dimensional (3D) subsurface characterization can emerge from the AFM mechanical response of flat buried interfaces, and present here a methodology for determining the depth of a film and its mechanical properties. Using load-dependent contact resonance atomic force microscopy (CR-AFM) and accurate modeling of the contact between the AFM tip and a layered sample, we determine the relationship between the measured resonance frequency of the AFM probe and the contact stiffness. Our subsequent statistical analysis reveals an intrinsic and sample-specific interdependence between the depth and modulus sensitivities of CR-AFM. This interdependence prevents the simultaneous accurate determination of both depth and modulus from measurements on a single-layered sample. If the elastic moduli of the sample components are predetermined from separate investigations of bulk samples (or otherwise known), then this methodology accurately yields the location of the interface between the layers of the sample; as such, it can serve as a nondestructive and robust technique for probing layer thickness, subsurface features, and elastic properties of materials used in semiconductor electronics, additive manufacturing, or biomaterials.

SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 pandemic.

Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals, but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here we present the data from Snapshot USA 2020, a second annual national mammal survey of the USA. This project involved 152 scientists setting camera traps in a standardized protocol at 1485 locations across 103 arrays in 43 states for a total of 52,710 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in 2 years that includes data from both during and before the COVID-19 pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total, we recorded 117,415 detections of 78 species of wild mammals, 9236 detections of at least 43 species of birds, 15,851 detections of six domestic animals and 23,825 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences among years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.

Health literacy and the quality of pharmacist-patient communication among those prescribed anticoagulation therapy.

BACKGROUND: Adequate counseling from a pharmacist concerning anticoagulation therapy is crucial to the wellbeing of patients. No studies have fully examined the relationship between health literacy, patient-pharmacist communication, and anticoagulation control. OBJECTIVE(S): To evaluate the relationship between health literacy and the perceived quality of patient-pharmacist communication among those receiving anticoagulation therapy. METHODS: This investigation utilized structured telephone interviews to evaluate the relationship between health literacy and perceived quality patient-pharmacist communication among patients receiving anticoagulation therapy. Two hundred-twenty participants prescribed anticoagulation therapy continuously for at least 6-months served as the sample for this study. A previously validated one-item screening tool was utilized to estimate health literacy. The primary outcome was patients' perceptions regarding the general communication process with pharmacists, according to the Interpersonal Process of Care questionnaire. RESULTS: Patients possessing inadequate health literacy reported significantly less favorable ratings for the perceived quality of pharmacist communication on the domains of general clarity (p = 0.02), responsiveness to patient concerns (p=<0.01), empowerment (p = 0.01), and consideration of patients' desire and ability to comply with recommendations (p = 0.01). Inadequate health literacy was found to be independently associated with poorer quality interpersonal processes of care across the domains of responsiveness to patient concerns and empowerment, (ß = -0.207, P = <0.01 and ß = -0.137, P = 0.04, respectively). Patients with inadequate health literacy did not differ significantly from those with adequate health literacy in terms of time within therapeutic INR range or percent of INRs in therapeutic range over the previous 12 months. CONCLUSIONS: Patients receiving anticoagulation therapy and possessing inadequate health literacy appear more likely to percieve poorer communication with pharmacists. This seems especially true as it relates to the percieved time and attention pharmacist devote to the communication encounter, as well as the sense pharmacists provide patients concerning their ability to influence health outcomes.

SNAPSHOT USA 2019: a coordinated national camera trap survey of the United States.

With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August-24 November of 2019). We sampled wildlife at 1,509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the United States. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as will future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.

Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria.

Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV via binding to, and stabilization of, DNA cleavage complexes. Optimization of this series led to the identification of compound 25, which has potent activity against Gram-positive bacteria, a favorable in vitro safety profile, and excellent in vivo pharmacokinetic properties. Compound 25 was found to be efficacious against fluoroquinolone-sensitive Staphylococcus aureus infection in a mouse thigh model at lower doses than moxifloxacin. An X-ray crystal structure of the ternary complex formed by topoisomerase IV from Klebsiella pneumoniae, compound 25, and cleaved DNA indicates that this compound does not engage in a water-metal ion bridge interaction and forms no direct contacts with residues in the quinolone resistance determining region (QRDR). This suggests a structural basis for the reduced impact of QRDR mutations on antibacterial activity of 25 compared to fluoroquinolones.