Predicting chronic wasting disease in white-tailed deer at the county scale using machine learning.

Continued spread of chronic wasting disease (CWD) through wild cervid herds negatively impacts populations, erodes wildlife conservation, drains resource dollars, and challenges wildlife management agencies. Risk factors for CWD have been investigated at state scales, but a regional model to predict locations of new infections can guide increasingly efficient surveillance efforts. We predicted CWD incidence by county using CWD surveillance data depicting white-tailed deer (Odocoileus virginianus) in 16 eastern and midwestern US states. We predicted the binary outcome of CWD-status using four machine learning models, utilized five-fold cross-validation and grid search to pinpoint the best model, then compared model predictions against the subsequent year of surveillance data. Cross validation revealed that the Light Boosting Gradient model was the most reliable predictor given the regional data. The predictive model could be helpful for surveillance planning. Predictions of false positives emphasize areas that warrant targeted CWD surveillance because of similar conditions with counties known to harbor CWD. However, disagreements in positives and negatives between the CWD Prediction Web App predictions and the on-the-ground surveillance data one year later underscore the need for state wildlife agency professionals to use a layered modeling approach to ensure robust surveillance planning. The CWD Prediction Web App is at https://cwd-predict.streamlit.app/ .

Role of global public sector research in discovering new drugs and vaccines.

Analysis of international public-sector contributions to Food and Drug Administration (FDA)-approved drugs and vaccines allows for a more thorough examination of the global biomedical innovation ecosystem by institution of origin. Using new and existing methods, we have identified 364 FDA-approved drugs and vaccines approved from 1973 to 2016 discovered in whole or in part by Public Sector Research Institutions (PSRIs) worldwide. We identified product-specific intellectual property contributions to FDA-approved small molecule and biologic drugs and vaccines from the FDA Orange Book, our peer network, published studies, and three new sources: reports of medical product manufacturers' payments to physicians and teaching hospitals under The Sunshine Act of 2010, a paper by Kneller and 64 royalty monetization transactions by academic institutions and/or their faculty that one of us (AS) maintains. We include a total of 293 drugs discovered either wholly by a US PSRI or jointly by a U.S. and a non-U.S. PSRI. 119 FDA-approved drugs and vaccines were discovered by PSRIs outside the U.S. Of these, 71 were solely discovered outside the US, while 48 also involved intellectual property contributions by US PSRIs. In the context of the global public sector landscape, the US dominates drug discovery, accounting for two-thirds of these drugs and many of the important, innovative vaccines introduced over the past 30 years. Contributions by Canada, UK, Germany, Belgium, Japan, and others each amount to 5.4% or less of the total. Supplementary Information: The online version contains supplementary material available at 10.1007/s10961-023-10007-z.

Commentary: University Technology Transfer Has Made a Significant Contribution to Fighting COVID-19 while Ensuring Global Access.

This paper reviews the response by public sector research organizations and their technology transfer offices to the COVID-19 pandemic. It shows that leading universities and technology transfer associations quickly enacted licensing principles for the duration of the pandemic to maximize availability and minimize delays in translating public sector research institutes' (PSRIs') COVID-19 inventions to the public - in both the developed and the developing world - while waiving payment of royalties. It discusses examples of vaccines, drugs, diagnostics and personal protective equipment that were developed in PSRIs and swiftly deployed throughout the world on socially responsible terms. It reviews the case cited by Herder et al. (2022) and concludes that their proposed mandates are unnecessary and may inhibit the free flow of healthcare innovation from bench to bedside.

Use of portable air cleaners to reduce aerosol transmission on a hospital coronavirus disease 2019 (COVID-19) ward.

OBJECTIVE: To study the airflow, transmission, and clearance of aerosols in the clinical spaces of a hospital ward that had been used to care for patients with coronavirus disease 2019 (COVID-19) and to examine the impact of portable air cleaners on aerosol clearance. DESIGN: Observational study. SETTING: A single ward of a tertiary-care public hospital in Melbourne, Australia. INTERVENTION: Glycerin-based aerosol was used as a surrogate for respiratory aerosols. The transmission of aerosols from a single patient room into corridors and a nurses' station in the ward was measured. The rate of clearance of aerosols was measured over time from the patient room, nurses' station and ward corridors with and without air cleaners [ie, portable high-efficiency particulate air (HEPA) filters]. RESULTS: Aerosols rapidly travelled from the patient room into other parts of the ward. Air cleaners were effective in increasing the clearance of aerosols from the air in clinical spaces and reducing their spread to other areas. With 2 small domestic air cleaners in a single patient room of a hospital ward, 99% of aerosols could be cleared within 5.5 minutes. CONCLUSIONS: Air cleaners may be useful in clinical spaces to help reduce the risk of acquisition of respiratory viruses that are transmitted via aerosols. They are easy to deploy and are likely to be cost-effective in a variety of healthcare settings.

Evaluation of BD Barricor™ and PST™ blood collection tubes compared to serum for testing 11 therapeutic drugs on a Roche Cobas® 8000 platform.

INTRODUCTION: The type of blood collection tube used when obtaining samples for therapeutic drug monitoring (TDM) has important implications on the accuracy of results. Serum tubes without a gel separator are currently considered best practice. We sought to evaluate the performance of Barricor™, a novel plasma tube that utilizes an inert mechanical separator, as well as a gel-based tube (PST™) for testing acetaminophen, digoxin, gentamicin, methotrexate, phenobarbital, phenytoin, salicylate, vancomycin, valproic acid, carbamazepine, and theophylline on a Roche Cobas® 8000 platform. METHODS: Paired patient samples were collected from individuals taking at least one of the medications evaluated. These were supplemented with spiked specimens to ensure a minimum of 40 paired samples per drug. All drugs were measured within two hours of collection on Roche e602 or c502 instruments. Deming regression was used to assess bias between Barricor™ vs serum and PST™ vs serum. Seven-day refrigerated stability was also assessed in Barricor™, PST™, and serum tubes in a subset of samples (n = 10) for each drug. RESULTS: Drug concentrations in Barricor™ were similar to serum for each drug assessed. In contrast, a negative bias was observed in PST™ compared to serum tubes for carbamazepine (-7.6%) and phenytoin (-6.8%) although this did not surpass our total allowable error goal of 10%. All drugs recovered within ±10% of baseline value when samples were stored refrigerated for 7 days except for carbamazepine, phenytoin, and phenobarbital where significant analyte loss was observed within the first day in PST™ tubes. CONCLUSION: Barricor™ tubes are a suitable alternative to serum for TDM on the Roche Cobas® 8000 platform.

Preserving and enhancing social health in neurocognitive disorders.

PURPOSE OF REVIEW: The WHO updated concept of health includes social health alongside physical and mental health. No existing reviews have examined the evidence for preserving or enhancing social health in people living with neurocognitive disorders, such as mild cognitive impairment and dementia. The present review examines recent epidemiological studies and interventions with social health outcome measures, including interventions across multiple modalities and settings, from communities to assisted living facilities. RECENT FINDINGS: Epidemiological evidence shows that neurocognitive disorders are associated with poorer social support, and greater social isolation and loneliness. This highlights the importance of maintaining and enhancing social health in people living with neurocognitive disorders. Group activities involving dance or music have emerging evidence indicating improvements in social health in communities and assisted living facilities. More quantitative research is required on the social health benefits of cognitive/multicomponent interventions, community social groups, exercise groups and other interventions. Several socially assistive robots are being developed to help foster social participation and require further research. SUMMARY: There is evidence that group music or dance interventions can improve social health for people living with neurocognitive disorders. Larger trials with multiple social health outcome measures are required to investigate the social health benefits of exercise, cognitive/multicomponent and community social group interventions.

Inhibition of protein tyrosine phosphatase receptor type F suppresses Wnt signaling in colorectal cancer.

Wnt signaling dysregulation promotes tumorigenesis in colorectal cancer (CRC). We investigated the role of PTPRF, a receptor-type tyrosine phosphatase, in regulating Wnt signaling in CRC. Knockdown of PTPRF decreased cell proliferation in patient-derived primary colon cancer cells and established CRC cell lines. In addition, the rate of proliferation as well as colony formation ability were significantly decreased in tumor organoids grown in 3D, whereas the number of differentiated tumor organoids were markedly increased. Consistently, knockdown of PTPRF resulted in a decrease in the expression of genes associated with cancer stem cells downstream of Wnt/ß-catenin signaling. Treating PTPRF knockdown cells with GSK3 inhibitor rescued the expression of Wnt target genes suggesting that PTPRF functions upstream of the ß-catenin destruction complex. PTPRF was found to interact with LRP6 and silencing PTPRF largely decreased the activation of LRP6. Interestingly, this PTPRF-mediated activation of Wnt signaling was blocked in cells treated with clathrin endocytosis inhibitor. Furthermore, knockdown of PTPRF inhibited xenograft tumor growth in vivo and decreased the expression of Wnt target genes. Taken together, our studies identify a novel role of PTPRF as an oncogenic protein phosphatase in supporting the activation of Wnt signaling in CRC.

Characterization of mRNA polyadenylation in the apicomplexa.

Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15-20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two-poly(A) polymerase and CPSF73-of the 19 proteins used as queries in this analysis. As the human subunits that recognize the AAUAAA polyadenylation signal (PAS) were not immediately obvious, a computational analysis of sequences adjacent to experimentally-determined apicomplexan poly(A) sites was conducted. The results of this study showed that there exists in apicomplexans an A-rich region that corresponds in position to the AAUAAA PAS. The set of experimentally-determined sites in one species, Sarcocystis neurona, was further analyzed to evaluate the extent and significance of alternative poly(A) site choice in this organism. The results showed that almost 80% of S. neurona genes possess more than one poly(A) site, and that more than 780 sites showed differential usage in the two developmental stages-extracellular merozoites and intracellular schizonts-studied. These sites affected more than 450 genes, and included a disproportionate number of genes that encode membrane transporters and ribosomal proteins. Taken together, these results reveal that apicomplexan species seem to possess a poly(A) signal analogous to AAUAAA even though genes that may encode obvious counterparts of the AAUAAA-recognizing proteins are absent in these organisms. They also indicate that, as is the case in other eukaryotes, alternative polyadenylation is a widespread phenomenon in S. neurona that has the potential to impact growth and development.

Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer.

Erbin belongs to the LAP (leucine-rich repeat and PDZ domain) family of scaffolding proteins that plays important roles in orchestrating cell signaling. Here, we show that Erbin functions as a tumor suppressor in colorectal cancer. Analysis of Erbin expression in colorectal cancer patient specimens revealed that Erbin was downregulated at both mRNA and protein levels in tumor tissues. Knockdown of Erbin disrupted epithelial cell polarity and increased cell proliferation in 3D culture. In addition, silencing Erbin resulted in increased amplitude and duration of signaling through Akt and RAS/RAF pathways. Erbin loss induced epithelial-mesenchymal transition, which coincided with a significant increase in cell migration and invasion. Erbin interacted with kinase suppressor of Ras 1 (KSR1) and displaced it from the RAF/MEK/ERK complex to prevent signal propagation. Furthermore, genetic deletion of Erbin in Apc knockout mice promoted tumorigenesis and significantly reduced survival. Tumor organoids derived from Erbin/Apc double knockout mice displayed increased tumor initiation potential and activation of Wnt signaling. Results from gene set enrichment analysis revealed that Erbin expression associated positively with the E-cadherin adherens junction pathway and negatively with Wnt signaling in human colorectal cancer. Taken together, our study identifies Erbin as a negative regulator of tumor initiation and progression by suppressing Akt and RAS/RAF signaling in vivoSignificance: These findings establish the scaffold protein Erbin as a negative regulator of EMT and tumorigenesis in colorectal cancer through direct suppression of Akt and RAS/RAF signaling. Cancer Res; 78(17); 4839-52. ©2018 AACR.

Respiratory and behavioral dysfunction following loss of the GABAA receptor α4 subunit.

γ-Aminobutyric acid type A (GABAA) receptor plasticity participates in mediating adaptation to environmental change. Previous studies in rats demonstrated that extrasynaptic GABAA receptor subunits and receptors in the pons, a brainstem region involved in respiratory control, are upregulated by exposure to sustained hypobaric hypoxia. In these animals, expression of the mRNA encoding the extrasynaptic α4 subunit rose after 3 days in sustained hypoxia, while those encoding the α6 and δ subunits increased dramatically by 2 weeks. However, the participation of extrasynaptic subunits in maintaining respiration in normoxic conditions remains unknown. To examine the importance of α4 in a normal environment, respiratory function, motor and anxiety-like behaviors, and expression of other GABAA receptor subunit mRNAs were compared in wild-type (WT) and α4 subunit-deficient mice. Loss of the α4 subunit did not impact frequency, but did lead to reduced ventilatory pattern variability. In addition, mice lacking the subunit exhibited increased anxiety-like behavior. Finally, α4 subunit loss resulted in reduced expression of other extrasynaptic (α6 and δ) subunit mRNAs in the pons without altering those encoding the most prominent synaptic subunits. These findings on subunit-deficient mice maintained in normoxia, in conjunction with earlier findings on animals maintained in chronic hypoxia, suggest that the expression and regulation of extrasynaptic GABAA receptor subunits in the pons is interdependent and that their levels influence respiratory control as well as adaptation to stress.

Cytotoxicity and Selectivity in Skin Cancer by SapC-DOPS Nanovesicles.

Squamous cell carcinoma (SCC) and melanoma are malignant human cancers of the skin with an annual mortality that exceed 10,000 cases every year in the USA alone. In this study, the lysosomal protein saposin C (SapC) and the phospholipid dioloylphosphatidylserine (DOPS) were assembled into cancer-selective nanovesicles (SapC-DOPS) and successfully tested using several in vitro and in vivo skin cancer models. Using MTT assay that measures the percentage of cell death, SapC-DOPS cytotoxic effect on three skin tumor cell lines (squamous cell carcinoma, SK-MEL-28, and MeWo) was compared to two normal nontumorigenic skin cells lines, normal immortalized keratinocyte (NIK) and human fibroblast cell (HFC). We observed that the nanovesicles selectively killed the skin cancer cells by inducing apoptotic cell death whereas untransformed skin cancer cells remained unaffected. Using subcutaneous skin tumor xenografts, animals treated with SapC-DOPS by subcutaneous injection showed a 79.4 % tumor reduced compared to the control after 4 days of treatment. We observed that the nanovesicles killed skin cancer cells by inducing apoptotic cell death compared to the control as revealed by TUNEL staining of xenograft tumor sections.

The role of public-sector research in the discovery of drugs and vaccines.

BACKGROUND: Historically, public-sector researchers have performed the upstream, basic research that elucidated the underlying mechanisms of disease and identified promising points of intervention, whereas corporate researchers have performed the downstream, applied research resulting in the discovery of drugs for the treatment of diseases and have carried out development activities to bring them to market. However, the boundaries between the roles of the public and private sectors have shifted substantially since the dawn of the biotechnology era, and the public sector now has a much more direct role in the applied-research phase of drug discovery. METHODS: We identified new drugs and vaccines approved by the Food and Drug Administration (FDA) that were discovered by public-sector research institutions (PSRIs) and classified them according to their therapeutic category and potential therapeutic effect. RESULTS: We found that during the past 40 years, 153 new FDA-approved drugs, vaccines, or new indications for existing drugs were discovered through research carried out in PSRIs. These drugs included 93 small-molecule drugs, 36 biologic agents, 15 vaccines, 8 in vivo diagnostic materials, and 1 over-the-counter drug. More than half of these drugs have been used in the treatment or prevention of cancer or infectious diseases. PSRI-discovered drugs are expected to have a disproportionately large therapeutic effect. CONCLUSIONS: Public-sector research has had a more immediate effect on improving public health than was previously realized.

The Bayh-Dole Act turns 30.

On 12 December 1980, in the waning days of the lame duck session of the 96th Congress, the U.S. Senate passed the University and Small Business Patent Procedures Act, now known as the Bayh-Dole Act, a seemingly obscure act that allowed universities to claim title to inventions that had been made with federal funding. It is unlikely that many present that day realized what a dramatic impact that act would have. Data clearly show that it played a critical role in rejuvenating the entire U.S. economic system, transforming it from a manufacturing base to an innovation base. Yet ironically, the act has passionate critics.