Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model.

The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PLpro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PLpro with the inhibitory constant Ki values from 13.2 to 88.2 nanomolar. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.

Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model.

The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PLpro inhibitors that bind to the newly discovered Val70Ub site and the known BL2 groove pocket. Potent compounds inhibited PLpro with inhibitory constant Ki values from 13.2 to 88.2 nM. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 µM. Oral treatment with Jun12682 significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.

Pathology in Practice.

In collaboration with the American College of Veterinary Pathologists.

Pax5 and CD3 immunophenotyping of lymphoma in 2 central bearded dragons.

Two central bearded dragons (Pogona vitticeps), a 3-y-old male and a 5-y-old female, were diagnosed with different manifestations of lymphoma at the Kansas State Veterinary Diagnostic Laboratory between 2019 and 2020. The 3-y-old male was presented for postmortem evaluation and was in poor body condition. Microscopically, nearly all examined organs contained variable numbers of neoplastic round cells. Neoplastic cells in the stomach and liver had moderate immunoreactivity to CD3 consistent with multicentric T-cell lymphoma, and non-neoplastic lymphocytes infiltrating the stomach mass had strong immunoreactivity to Pax5. The 5-y-old female had an ulcerated oral mass located in the right lingual gingiva submitted as an excisional biopsy. Microscopically, the mass was composed of large numbers of neoplastic round cells in the epithelium and connective tissue that were strongly and diffusely positive for CD3 and frequently positive for Pax5, consistent with a dual-positive, localized, epitheliotropic T-cell lymphoma. Neoplastic and non-neoplastic lymphocytes did not stain with CD20 or CD79a. Neoplasms are increasingly reported as a cause of morbidity and mortality in reptiles. Our 2 cases illustrate various presentations of T-cell lymphoma and the effectiveness of CD3 and Pax5 immunohistochemistry in bearded dragons.

Biomechanical modeling of radiation dose-induced volumetric changes of the parotid glands for deformable image registration.

PURPOSE: Early animal studies suggest that parotid gland (PG) toxicity prediction could be improved by an accurate estimation of the radiation dose to sub-regions of the PG. Translation to clinical investigation requires voxel-level dose accumulation in this organ that responds volumetrically throughout treatment. To date, deformable image registration (DIR) has been evaluated for the PG using only surface alignment. We sought to develop and evaluate an advanced DIR technique capable of modeling these complex PG volume changes over the course of radiation therapy. MATERIALS AND METHODS: Planning and mid-treatment magnetic resonance images from 19 patients and computed tomography images from nine patients who underwent radiation therapy for head and neck cancer were retrospectively evaluated. A finite element model (FEM)-based DIR algorithm was applied between the corresponding pairs of images, based on boundary conditions on the PG surfaces only (Morfeus-spatial). To investigate an anticipated improvement in accuracy, we added a population model-based thermal expansion coefficient to simulate the dose distribution effect on the volume change inside the glands (Morfeus-spatialDose). The model accuracy was quantified using target registration error for magnetic resonance images, where corresponding anatomical landmarks could be identified. The potential clinical impact was evaluated using differences in mean dose, median dose, D98, and D50 of the PGs. RESULTS: In the magnetic resonance images, the mean (±standard deviation) target registration error significantly reduced by 0.25 ± 0.38 mm (p = 0.01) when using Morfeus-spatialDose instead of Morfeus-spatial. In the computed tomography images, differences in the mean dose, median dose, D98, and D50 of the PGs reached 2.9 ± 0.8, 3.8, 4.1, and 3.8 Gy, respectively, between Morfeus-spatial and Morfeus-spatialDose. CONCLUSION: Differences between Morfeus-spatial and Morfeus-spatialDose may be impactful when considering high-dose gradients of radiation in the PGs. The proposed DIR model can allow more accurate PG alignment than the standard model and improve dose estimation and toxicity prediction modeling.

Effects of music on behavior and physiological stress response of domestic cats in a veterinary clinic.

OBJECTIVES: Our objective was to determine if feline-specific music played in a veterinary clinical setting would promote lower cat stress scores (CSSs), lower mean handling scale scores (HSs) and reduced neutrophil:lymphocyte ratios (NLRs) in cats during physical examinations. METHODS: Cats were exposed to one of three auditory stimuli tests - silence, classical music and cat-specific music - during three physical examinations 2 weeks apart. CSSs were recorded at pre- and post-auditory tests and during the examination period. The HSs were recorded at the physical examination period. The physiological stress was assessed via NLRs. RESULTS: The pre-auditory test showed no difference in CSS between cats listening to silence, classical music and cat music. CSSs for post-auditory tests and examination periods were not significantly different between silence and classical music; however, CSSs were significantly decreased in cats listening to cat music vs silence and in cats listening to cat music vs classical music. HSs were not different in cats listening to silence vs classical music, but were significantly lower in cats listening to cat music vs silence and classical music. No difference was found in NLRs among all three auditory stimuli tests. CONCLUSIONS AND RELEVANCE: Listening to cat-specific music prior to, and during, physical examination was associated with lower CSSs and lower HSs in cats, but had no effect on the physiological stress responses measured by NLRs. We conclude that cat-specific music may benefit cats by decreasing the stress levels and increasing the quality of care in veterinary clinical settings.

Disseminated Mycobacterium kansasii infection in a white-tailed deer and implications for public and livestock health.

We document a case of Mycobacterium kansasii, a rare, zoonotic bacterium, in a white-tailed deer (WTD; Odocoileus virginianus) in East Baton Rouge Parish, Louisiana. Grossly, the deer had fibrinous pleuropneumonia with yellow, mineralized nodules scattered throughout the lungs and extending to the pleura. The kidneys were enlarged and had numerous pale foci in the cortex. Microscopically, the pulmonary architecture was replaced by variably sized, multifocal-to-coalescing granulomas with peripheral histiocytes and fewer multinucleate giant cells, and necrotic centers with mineralization and hemorrhage. The latter rarely contained one to a few acid-fast, slender, 7-µm long bacteria, for which beaded morphology was sometimes evident. Similar acid-fast bacteria were also within histiocytes in the kidney. PCR assay of fresh lung sample and subsequent sequencing revealed a non-tuberculosis mycobacterium, M. kansasii. These lesions were similar to those that result from infection with M. bovis in WTD. Both M. bovis and M. kansasii are zoonotic. WTD are a reservoir of M. bovis, which is a major concern in regions in which WTD and cattle can come into close contact.

Biomechanical modeling of neck flexion for deformable alignment of the salivary glands in head and neck cancer images.

During head and neck (HN) cancer radiation therapy, analysis of the dose-response relationship for the parotid glands (PG) relies on the ability to accurately align soft tissue organs between longitudinal images. In order to isolate the response of the salivary glands to delivered dose, from deformation due to patient position, it is important to resolve the patient postural changes, mainly due to neck flexion. In this study we evaluate the use of a biomechanical model-based deformable image registration (DIR) algorithm to estimate the displacements and deformations of the salivary glands due to postural changes. A total of 82 pairs of CT images of HN cancer patients with varying angles of neck flexion were retrospectively obtained. The pairs of CTs of each patient were aligned using bone-based rigid registration. The images were then deformed using biomechanical model-based DIR method that focused on the mandible, C1 vertebrae, C3 vertebrae, and external contour. For comparison, an intensity-based DIR was also performed. The accuracy of the biomechanical model-based DIR was assessed using Dice similarity coefficient (DSC) for all images and for the subset of images where the PGs had a volume change within 20%. The accuracy was compared to the intensity-based DIR. The PG mean ± STD DSC were 0.63 ± 0.18, 0.80 ± 0.08, and 0.82 ± 0.15 for the rigid registration, biomechanical model-based DIR, and intensity based DIR, respectively, for patients with a PG volume change up to 20%. For the entire cohort of patients, where the PG volume change was up to 57%, the PG mean ± STD DSC were 0.60 ± 0.18, 0.78 ± 0.09, and 0.81 ± 0.14 for the rigid registration, biomechanical model-based DIR, and intensity based DIR, respectively. The difference in DSC of the intensity and biomechanical model-based DIR methods was not statistically significant when the volume change was less than 20% (two-sided paired t-test, p  = 0.12). When all volume changes were considered, there was a significant difference between the two registration approaches, although the magnitude was small. These results demonstrate that the proposed biomechanical model with boundary conditions on the bony anatomy can serve to describe the varying angles of neck flexion appearing in images during radiation treatment and to align the salivary glands for proper analysis of dose-response relationships. It also motivates the need for dose response modeling following neck flexion for cases where parotid gland response is noted.

Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes.

Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as "domestication syndrome." These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness ("tame foxes") and six foxes selectively bred for aggression ("aggressive foxes"). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication.

Ischaemic stroke in a 21-year-old with hereditary haemorrhagic telangiectasia.

A 21-year-old man presented with an acute ischaemic stroke. He had a history of epistaxis and a family history of hereditary haemorrhagic telangiectasia. We gave thrombolysis after some deliberation, and he made a good neurological recovery. This case highlights the link between hereditary haemorrhagic telangiectasia and ischaemic stroke, the potential risks of thrombolysis in such patients and the need to consider pulmonary arteriovenous malformations in patients with stroke.

Etching of surfactant from solution-processed, type-separated carbon nanotubes and impact on device behavior.

Semiconducting single-walled carbon nanotubes (SWCNTs) have great potential for use in electronic and optoelectronic devices. However, methods for synthesizing SWCNTs produce a mixture of metallic and semiconducting materials, which require additional processing to separate by electronic type. Purification and enrichment of the semiconducting fraction is readily achieved by using the centrifugation of aqueous suspensions of SWCNTs with the help of surfactants, but this leaves residual surfactant on the SWCNT surface that can impact their electronic and optical properties. Here, we present a detailed study of the sodium taurodeoxycholate (STDC) surfactant removal process during vacuum annealing, showing that it occurs through fragmentation of the surfactant, and that complete removal requires exceedingly high temperatures, which indicates strong binding to the SWCNTs. We then present an approach based on air oxidation and mild annealing to completely remove the surfactant while maintaining the SWCNT properties. Using this approach, we compare single SWCNT electronic devices with and without STDC and show that, despite the very strong surfactant binding, it does not affect device performance substantially.

Tunable electrical conductivity in metal-organic framework thin-film devices.

We report a strategy for realizing tunable electrical conductivity in metal-organic frameworks (MOFs) in which the nanopores are infiltrated with redox-active, conjugated guest molecules. This approach is demonstrated using thin-film devices of the MOF Cu3(BTC)2 (also known as HKUST-1; BTC, benzene-1,3,5-tricarboxylic acid) infiltrated with the molecule 7,7,8,8-tetracyanoquinododimethane (TCNQ). Tunable, air-stable electrical conductivity over six orders of magnitude is achieved, with values as high as 7 siemens per meter. Spectroscopic data and first-principles modeling suggest that the conductivity arises from TCNQ guest molecules bridging the binuclear copper paddlewheels in the framework, leading to strong electronic coupling between the dimeric Cu subunits. These ohmically conducting porous MOFs could have applications in conformal electronic devices, reconfigurable electronics, and sensors.

Physical removal of metallic carbon nanotubes from nanotube network devices using a thermal and fluidic process.

Electronic and optoelectronic devices based on thin films of carbon nanotubes are currently limited by the presence of metallic nanotubes. Here we present a novel approach based on nanotube alkyl functionalization to physically remove the metallic nanotubes from such network devices. The process relies on preferential thermal desorption of the alkyls from the semiconducting nanotubes and the subsequent dissolution and selective removal of the metallic nanotubes in chloroform. The approach is versatile and is applied to devices post-fabrication.

Influence of catalyst choices on transport behaviors of InAs NWs for high-performance nanoscale transistors.

The influence of the catalyst materials on the electron transport behaviors of InAs nanowires (NWs) grown by a conventional vapor transport technique is investigated. Utilizing the NW field-effect transistor (FET) device structure, ~20% and ~80% of Au-catalyzed InAs NWs exhibit strong and weak gate dependence characteristics, respectively. In contrast, ~98% of Ni-catalyzed InAs NWs demonstrate a uniform n-type behavior with strong gate dependence, resulting in an average OFF current of ~10(-10) A and a high I(ON)/I(OFF) ratio of >10(4). The non-uniform device performance of Au-catalyzed NWs is mainly attributed to the non-stoichiometric composition of the NWs grown from a different segregation behavior as compared to the Ni case, which is further supported by the in situ TEM studies. These distinct electrical characteristics associated with different catalysts were further investigated by the first principles calculation. Moreover, top-gated and large-scale parallel-array FETs were fabricated with Ni-catalyzed NWs by contact printing and channel metallization techniques, which yield excellent electrical performance. The results shed light on the direct correlation of the device performance with the catalyst choice.

Ballistic InAs nanowire transistors.

Ballistic transport of electrons at room temperature in top-gated InAs nanowire (NW) transistors is experimentally observed and theoretically examined. From length dependent studies, the low-field mean free path is directly extracted as ~150 nm. The mean free path is found to be independent of temperature due to the dominant role of surface roughness scattering. The mean free path was also theoretically assessed by a method that combines Fermi's golden rule and a numerical Schrödinger-Poisson simulation to determine the surface scattering potential with the theoretical calculations being consistent with experiments. Near ballistic transport (~80% of the ballistic limit) is demonstrated experimentally for transistors with a channel length of ~60 nm, owing to the long mean free path of electrons in InAs NWs.

Contact printing of compositionally graded CdS(x)Se(1-x) nanowire parallel arrays for tunable photodetectors.

Spatially composition-graded CdS(x)Se(1-x) (x = 0-1) nanowires are grown and transferred as parallel arrays onto Si/SiO(2) substrates by a one-step, directional contact printing process. Upon subsequent device fabrication, an array of tunable-wavelength photodetectors is demonstrated. From the spectral photoconductivity measurements, the cutoff wavelength for the device array, as determined by the bandgap, is shown to cover a significant portion of the visible spectrum. The ability to transfer a collection of crystalline semiconductor nanowires while preserving the spatially graded composition may enable a wide range of applications, such as tunable lasers and photodetectors, efficient photovoltaics, and multiplexed chemical sensors.

Observation of degenerate one-dimensional sub-bands in cylindrical InAs nanowires.

One-dimensional (1D) sub-bands in cylindrical InAs nanowires (NWs) are electrically mapped as a function of NW diameter in the range of 15-35 nm. At low temperatures, stepwise current increases with the gate voltage are clearly observed and attributed to the electron transport through individual 1D sub-bands. The 2-fold degeneracy in certain sub-band energies predicted by simulation due to structural symmetry is experimentally observed for the first time. The experimentally obtained sub-band energies match the simulated results, shedding light on both the energies of the sub-bands as well as the number of sub-bands populated per given gate voltage and diameter. This work serves to provide better insight into the electrical transport behavior of 1D semiconductors.

Nanoscale semiconductor "X" on substrate "Y"--processes, devices, and applications.

Recent advancements in the integration of nanoscale, single-crystalline semiconductor 'X' on substrate 'Y' (XoY) for use in transistor and sensor applications are presented. XoY is a generic materials framework for enabling the fabrication of various novel devices, without the constraints of the original growth substrates. Two specific XoY process schemes, along with their associated materials, device and applications are presented. In one example, the layer transfer of ultrathin III-V semiconductors with thicknesses of just a few nanometers on Si substrates is explored for use as energy-efficient electronics, with the fabricated devices exhibiting excellent electrical properties. In the second example, contact printing of nanowire-arrays on thin, bendable substrates for use as artificial electronic-skin is presented. Here, the devices are capable of conformably covering any surface, and providing a real-time, two-dimensional mapping of external stimuli for the realization of smart functional surfaces. This work is an example of the emerging field of "translational nanotechnology" as it bridges basic science of nanomaterials with practical applications.