Identification of a Biomarker Panel for Early Detection of Lung Cancer Patients.

Lung cancer is the most common cause of cancer-related mortality worldwide, characterized by late clinical presentation (49-53% of patients are diagnosed at stage IV) and consequently poor outcomes. One challenge in identifying biomarkers of early disease is the collection of samples from patients prior to symptomatic presentation. We used blood collected during surgical resection of lung tumors in an iTRAQ isobaric tagging experiment to identify proteins effluxing from tumors into pulmonary veins. Forty proteins were identified as having an increased abundance in the vein draining from the tumor compared to "healthy" pulmonary veins. These protein markers were then assessed in a second cohort that utilized the mass spectrometry (MS) technique: Sequential window acquisition of all theoretical fragment ion spectra (SWATH) MS. SWATH-MS was used to measure proteins in serum samples taken from 25 patients <50 months prior to and at lung cancer diagnosis and 25 matched controls. The SWATH-MS analysis alone produced an 11 protein marker panel. A machine learning classification model was generated that could discriminate patient samples from patients within 12 months of lung cancer diagnosis and control samples. The model was evaluated as having a mean AUC of 0.89, with an accuracy of 0.89. This panel was combined with the SWATH-MS data from one of the markers from the first cohort to create a 12 protein panel. The proteome signature developed for lung cancer risk can now be developed on further cohorts.

Management of Five Hundred Patients With Gut Failure at a Single Center: Surgical Innovation Versus Transplantation With a Novel Predictive Model.

OBJECTIVE(S): To define the evolving role of integrative surgical management including transplantation for patients gut failure (GF). METHODS: A total of 500 patients with total parenteral nutrition-dependent catastrophic and chronic GF were referred for surgical intervention particularly transplantation and comprised the study population. With a mean age of 45 ±â€Š17 years, 477 (95%) were adults and 23 (5%) were children. Management strategy was guided by clinical status, splanchnic organ functions, anatomy of residual gut, and cause of GF. Surgery was performed in 462 (92%) patients and 38 (8%) continued medical treatment. Definitive autologous gut reconstruction (AGR) was achievable in 378 (82%), primary transplant in 42 (9%), and AGR followed by transplant in 42 (9%). The 84 transplant recipients received 94 allografts; 67 (71%) liver-free and 27 (29%) liver-contained. The 420 AGR patients received a total of 790 reconstructive and remodeling procedures including primary reconstruction, interposition alimentary-conduits, intestinal/colonic lengthening, and reductive/decompressive surgery. Glucagon-like peptide-2 was used in 17 patients. RESULTS: Overall patient survival was 86% at 1-year and 68% at 5-years with restored nutritional autonomy (RNA) in 63% and 78%, respectively. Surgery achieved a 5-year survival of 70% with 82% RNA. AGR achieved better long-term survival and transplantation better (P = 0.03) re-established nutritional autonomy. Both AGR and transplant were cost effective and quality of life better improved after AGR. A model to predict RNA after AGR was developed computing anatomy of reconstructed gut, total parenteral nutrition requirements, cause of GF, and serum bilirubin. CONCLUSIONS: Surgical integration is an effective management strategy for GF. Further progress is foreseen with the herein-described novel techniques and established RNA predictive model.

AMONDYS 45 (Casimersen), a Novel Antisense Phosphorodiamidate Morpholino Oligomer: Clinical Considerations for Treatment in Duchenne Muscular Dystrophy.

AMONDYS 45 (casimersen) is an antisense oligonucleotide therapy used to treat Duchenne muscular dystrophy (DMD), a rare genetic disorder characterized by a mutation in the DMD gene. Symptoms include progressive muscle weakness, respiratory and cardiac complications, and premature death. Casimersen targets a specific mutation in the DMD gene that results in the absence of dystrophin protein, a key structural component of muscle fibers. While there is currently no cure for DMD, exon-skipping therapy works by restoring the reading frame of the mutated gene, allowing the production of a partially functional dystrophin protein. Clinical trials of casimersen have shown promising results in increasing dystrophin production, as measured by polymerase chain reaction (PCR) droplets when compared to placebo. In a randomized double-blind trial, patients who received casimersen had significantly higher dystrophin levels when compared to those who received placebo. Casimersen therapy is administered through repeated intravenous infusions, although the optimal dosage and duration of treatment are still under investigation. Based on the completed and ongoing clinical trials, casimersen has been well tolerated, with most adverse events being mild and unrelated to casimersen. In 2021, AMONDYS 45 (casimersen) received approval from the US Food and Drug Administration (FDA) for the treatment of Duchene muscular dystrophy in patients with a mutation of the DMD gene that is amenable to exon 45 skipping. These collective findings indicate that casimersen has the potential to elicit functional changes in individuals with DMD, although further studies are necessary to comprehensively evaluate the specific functional improvements. Regardless, the FDA approval and ongoing clinic trials mark a significant milestone in the development of DMD treatments and offer hope for those affected by this debilitating disease.

Durable contraception in the female domestic cat using viral-vectored delivery of a feline anti-Müllerian hormone transgene.

Eighty percent of the estimated 600 million domestic cats in the world are free-roaming. These cats typically experience suboptimal welfare and inflict high levels of predation on wildlife. Additionally, euthanasia of healthy animals in overpopulated shelters raises ethical considerations. While surgical sterilization is the mainstay of pet population control, there is a need for efficient, safe, and cost-effective permanent contraception alternatives. Herein, we report evidence that a single intramuscular treatment with an adeno-associated viral vector delivering an anti-Müllerian hormone transgene produces long-term contraception in the domestic cat. Treated females are followed for over two years, during which transgene expression, anti-transgene antibodies, and reproductive hormones are monitored. Mating behavior and reproductive success are measured during two mating studies. Here we show that ectopic expression of anti-Müllerian hormone does not impair sex steroids nor estrous cycling, but prevents breeding-induced ovulation, resulting in safe and durable contraception in the female domestic cat.

Alzheimer's disease biomarker discovery using in silico literature mining and clinical validation.

BACKGROUND: Alzheimer's Disease (AD) is the most widespread form of dementia in the elderly but despite progress made in recent years towards a mechanistic understanding, there is still an urgent need for disease modification therapy and for early diagnostic tests. Substantial international efforts are being made to discover and validate biomarkers for AD using candidate analytes and various data-driven 'omics' approaches. Cerebrospinal fluid is in many ways the tissue of choice for biomarkers of brain disease but is limited by patient and clinician acceptability, and increasing attention is being paid to the search for blood-based biomarkers. The aim of this study was to use a novel in silico approach to discover a set of candidate biomarkers for AD. METHODS: We used an in silico literature mining approach to identify potential biomarkers by creating a summarized set of assertional metadata derived from relevant legacy information. We then assessed the validity of this approach using direct assays of the identified biomarkers in plasma by immunodetection methods. RESULTS: Using this in silico approach, we identified 25 biomarker candidates, at least three of which have subsequently been reported to be altered in blood or CSF from AD patients. Two further candidate biomarkers, indicated from the in silico approach, were choline acetyltransferase and urokinase-type plasminogen activator receptor. Using immunodetection, we showed that, in a large sample set, these markers are either altered in disease or correlate with MRI markers of atrophy. CONCLUSIONS: These data support as a proof of concept the use of data mining and in silico analyses to derive valid biomarker candidates for AD and, by extension, for other disorders.

Digital Approaches to Music-Making for People With Dementia in Response to the COVID-19 Pandemic: Current Practice and Recommendations.

Before COVID-19, dementia singing groups and choirs flourished, providing activity, cognitive stimulation, and social support for thousands of people with dementia in the UK. Interactive music provides one of the most effective psychosocial interventions for people with dementia; it can allay agitation and promote wellbeing. Since COVID-19 has halted the delivery of in-person musical activities, it is important for the welfare of people with dementia and their carers to investigate what alternatives to live music making exist, how these alternatives are delivered and how their accessibility can be expanded. This community case study examines recent practice in online music-making in response to COVID-19 restrictions for people with dementia and their supporters, focusing on a UK context. It documents current opportunities for digital music making, and assesses the barriers and facilitators to their delivery and accessibility. Online searches of video streaming sites and social media documented what music activities were available. Expert practitioners and providers collaborated on this study and supplied input about the sessions they had been delivering, the technological challenges and solutions they had found, and the responses of the participants. Recommendations for best practice were developed and refined in consultation with these collaborators. Over 50 examples of online music activities were identified. In addition to the challenges of digital inclusion and accessibility for some older people, delivering live music online has unique challenges due to audio latency and sound quality. It is necessary to adapt the session to the technology's limitations rather than expect to overcome these challenges. The recommendations highlight the importance of accessibility, digital safety and wellbeing of participants. They also suggest ways to optimize the quality of their musical experience. The pandemic has prompted innovative approaches to deliver activities and interventions in a digital format, and people with dementia and their carers have adapted rapidly. While online music is meeting a clear current need for social connection and cognitive stimulation, it also offers some advantages which remain relevant after COVID-19 restrictions are relaxed. The recommendations of this study are intended to be useful to musicians, dementia care practitioners, and researchers during the pandemic and beyond.

Cheminformatics analysis of assertions mined from literature that describe drug-induced liver injury in different species.

Drug-induced liver injury is one of the main causes of drug attrition. The ability to predict the liver effects of drug candidates from their chemical structures is critical to help guide experimental drug discovery projects toward safer medicines. In this study, we have compiled a data set of 951 compounds reported to produce a wide range of effects in the liver in different species, comprising humans, rodents, and nonrodents. The liver effects for this data set were obtained as assertional metadata, generated from MEDLINE abstracts using a unique combination of lexical and linguistic methods and ontological rules. We have analyzed this data set using conventional cheminformatics approaches and addressed several questions pertaining to cross-species concordance of liver effects, chemical determinants of liver effects in humans, and the prediction of whether a given compound is likely to cause a liver effect in humans. We found that the concordance of liver effects was relatively low (ca. 39-44%) between different species, raising the possibility that species specificity could depend on specific features of chemical structure. Compounds were clustered by their chemical similarity, and similar compounds were examined for the expected similarity of their species-dependent liver effect profiles. In most cases, similar profiles were observed for members of the same cluster, but some compounds appeared as outliers. The outliers were the subject of focused assertion regeneration from MEDLINE as well as other data sources. In some cases, additional biological assertions were identified, which were in line with expectations based on compounds' chemical similarities. The assertions were further converted to binary annotations of underlying chemicals (i.e., liver effect vs no liver effect), and binary quantitative structure-activity relationship (QSAR) models were generated to predict whether a compound would be expected to produce liver effects in humans. Despite the apparent heterogeneity of data, models have shown good predictive power assessed by external 5-fold cross-validation procedures. The external predictive power of binary QSAR models was further confirmed by their application to compounds that were retrieved or studied after the model was developed. To the best of our knowledge, this is the first study for chemical toxicity prediction that applied QSAR modeling and other cheminformatics techniques to observational data generated by the means of automated text mining with limited manual curation, opening up new opportunities for generating and modeling chemical toxicology data.

The 14q32 maternally imprinted locus is a major source of longitudinally stable circulating microRNAs as measured by small RNA sequencing.

Understanding the normal temporal variation of serum molecules is a critical factor for identifying useful candidate biomarkers for the diagnosis and prognosis of chronic disease. Using small RNA sequencing in a longitudinal study of 66 women with no history of cancer, we determined the distribution and dynamics (via intraclass correlation coefficients, ICCs) of the miRNA profile over 3 time points sampled across 2-5 years in the course of the screening trial, UKCTOCS. We were able to define a subset of longitudinally stable miRNAs (ICC >0.75) that were individually discriminating of women who had no cancer over the study period. These miRNAs were dominated by those originating from the C14MC cluster that is subject to maternal imprinting. This assessment was not significantly affected by common confounders such as age, BMI or time to centrifugation nor alternative methods to data normalisation. Our analysis provides important benchmark data supporting the development of miRNA biomarkers for the impact of life-course exposure as well as diagnosis and prognostication of chronic disease.

Colorectal cancer ascertainment through cancer registries, hospital episode statistics, and self-reporting compared to confirmation by clinician: A cohort study nested within the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS).

BACKGROUND: Electronic health records are frequently used for cancer epidemiology. We report on their quality for ascertaining colorectal cancer (CRC) in UK women. METHODS: Population-based, retrospective cohort study nested within the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS). Postmenopausal women aged 50-74 who were diagnosed with CRC during 2001-11 following randomisation to the UKCTOCS were identified and their diagnosis confirmed with their treating clinician. The sensitivity and positive predictive value (PPV) of cancer and death registries, hospital episode statistics, and self-reporting were calculated by pairwise comparisons to the treating clinician's confirmation, while specificity and negative predictive value were estimated relative to expected cases. RESULTS: Notification of CRC events were received for 1,085 women as of 24 May 2011. Responses were received from 61% (660/1,085) of clinicians contacted. Nineteen women were excluded (18 no diagnosis date, one diagnosed after cut-off). Of the 641 eligible, 514 had CRC, 24 had a benign polyp, and 103 had neither diagnosis. The sensitivity of cancer registrations at one- and six-years post-diagnosis was 92 (95% CI 90-94) and 99% (97-100), respectively, with a PPV of 95% (95% CI 92/93-97). The sensitivity & PPV of cancer registrations (at one-year post-diagnosis) & hospital episode statistics combined were 98 (96-99) and 92% (89-94), respectively. CONCLUSIONS: Cancer and death registrations in the UK are a reliable resource for CRC ascertainment in women. Hospital episode statistics can supplement delays in cancer registration. Self-reporting seems less reliable.

Development of a pharmacy resident rotation to expand decentralized clinical pharmacy services.

PURPOSE: The development of a pharmacy resident rotation to expand decentralized clinical pharmacy services is described. SUMMARY: In an effort to align with the initiatives proposed within the ASHP Practice Advancement Initiative, the department of pharmacy at Cleveland Clinic, a 1,400-bed academic, tertiary acute care medical center in Cleveland, Ohio, established a goal to provide decentralized clinical pharmacy services for 100% of patient care units within the hospital. Patient care units that previously had no decentralized pharmacy services were evaluated to identify opportunities for expansion. Metrics analyzed included number of medication orders verified per hour, number of pharmacy dosing consultations, and number of patient discharge counseling sessions. A pilot study was conducted to assess the feasibility of this service and potential resident learning opportunities. A learning experience description was drafted, and feedback was solicited regarding the development of educational components utilized throughout the rotation. Pharmacists who were providing services to similar patient populations were identified to serve as preceptors. Staff pharmacists were deployed to previously uncovered patient care units, with pharmacy residents providing decentralized services on previously covered areas. A rotating preceptor schedule was developed based on geographic proximity and clinical expertise. An initial postimplementation assessment of this resident-driven service revealed that pharmacy residents provided a comparable level of pharmacy services to that of staff pharmacists. Feedback collected from nurses, physicians, and pharmacy staff also supported residents' ability to operate sufficiently in this role to optimize patient care. CONCLUSION: A learning experience developed for pharmacy residents in a large medical center enabled the expansion of decentralized clinical services without requiring additional pharmacist full-time equivalents.

Renal Transplant Acute Rejection with Lower Mycophenolate Mofetil Dosing and Proton Pump Inhibitors or Histamine-2 Receptor Antagonists.

BACKGROUND: Pharmacokinetic data show reduced mycophenolic acid levels in renal transplant recipients taking mycophenolate mofetil (MMF) and proton pump inhibitors (PPIs) concomitantly. This reduced exposure could increase rejection risk. The typical initial MMF dose post renal transplantation is 2 g/day, which often requires dose reduction secondary to side effects. Existing studies have not shown significant acute rejection differences for patients taking MMF-PPI versus patients taking MMF-ranitidine. OBJECTIVE: The purpose of this study was to evaluate clinical outcomes in renal transplant recipients receiving a lower MMF dose than previously studied (1.5 g/day) and either a PPI or histamine-2 receptor antagonist (H2RA). METHODS: This retrospective cohort study included adult subjects receiving a renal transplant between January 1, 2009, and June 30, 2013. Comparison groups were defined based on acid-suppressing therapy class prescribed at discharge from transplantation. The primary outcome was acute rejection incidence within 1 year posttransplantation. RESULTS: Of 728 renal transplant recipients screened, 522 were included: 183 taking a PPI and 339 taking an H2RA. There was no significant difference in acute rejection within 1 year (H2RA 19% versus PPI 14%, p=0.12) or 3 months (4% vs 5%, p=0.44, respectively) posttransplantation. Maintenance immunosuppression (MMF dose and tacrolimus troughs) was similar between groups at 3 months and 1 year. Graft and patient survivals were favorable (> 95%), and graft function at 1 year was stable and similar between groups. CONCLUSION: Despite taking lower MMF doses than previously studied, subjects on a PPI compared to an H2RA were not at increased risk of acute rejection within 1 year posttransplantation.

Phylogenetic characterization of a novel herpesvirus found in the liver and lungs of a Chilean flamingo (Phoenicopterus chilensis).

A novel herpesvirus was detected in a 17-day-old Chilean flamingo (Phoenicopterus chilensis) with pneumonia, hepatopathy, and severe anemia that was housed in California. Postmortem examination identified a pale, enlarged liver, mildly increased fluid in the lungs, and red foci in the spleen. Histologic examination revealed marked hepatic necrosis with syncytia, splenic necrosis, and interstitial pneumonia with eosinophilic intranuclear inclusions within hepatocytes and in unidentified cells of the lung. Transmission electron microscopy identified virions consistent with a herpesvirus in the nucleus and cytoplasm of degenerative hepatocytes. Nested consensus PCR, sequencing, and phylogenetic analysis identified a novel herpesvirus within the genus Iltovirus in the subfamily Alphaherpesvirinae.

Bilateral phacofragmentation in a New Zealand fur seal (Arctocephalus forsteri).

Ophthalmic examination under anesthesia of a 5-yr-old, captive, male New Zealand fur seal (Arctocephalus forsteri) with reduced visual capacity revealed bilateral cataracts. Surgical extraction of the lenses was performed by phacofragmentation. Preoperative mydriasis was unsuccessful using common topical mydriatic agents. Intraoperative intracameral epinephrine 1:10,000 produced minimal pupillary dilation, but excellent dilation was achieved with intracameral epinephrine at 1:1,000. Postoperative uveitis was controlled with oral prednisolone. Postoperative complications included generalized corneal edema persisting for approximately 1 wk and corneal ulceration caused by the lateral canthotomy sutures. Vision was restored in both eyes.

Ontology-based interactive information extraction from scientific abstracts.

Over recent years, there has been a growing interest in extracting information automatically or semi-automatically from the scientific literature. This paper describes a novel ontology-based interactive information extraction (OBIIE) framework and a specific OBIIE system. We describe how this system enables life scientists to make ad hoc queries similar to using a standard search engine, but where the results are obtained in a database format similar to a pre-programmed information extraction engine. We present a case study in which the system was evaluated for extracting co-factors from EMBASE and MEDLINE.

Body temperature in captive long-beaked echidnas (Zaglossus bartoni).

The routine occurrence of both short-term (daily) and long-term torpor (hibernation) in short-beaked echidnas, but not platypus, raises questions about the third monotreme genus, New Guinea's Zaglossus. We measured body temperatures (T(b)) with implanted data loggers over three and a half years in two captive Zaglossus bartoni at Taronga Zoo, Sydney. The modal T(b) of both long-beaks was 31 degrees C, similar to non-hibernating short-beaked echidnas, Tachyglossus aculeatus, in the wild (30-32 degrees C) and to platypus (32 degrees C), suggesting that this is characteristic of normothermic monotremes. T(b) cycled daily, usually over 2-4 degrees C. There were some departures from this pattern to suggest periods of inactivity but nothing to indicate the occurrence of long-term torpor. In contrast, two short-beaked echidnas monitored concurrently in the same pen showed extended periods of low T(b) in the cooler months (hibernation) and short periods of torpor at any time of the year, as they do in the wild. Whether torpor or hibernation occurs in Zaglossus in the wild or in juveniles remains unknown. However, given that the environment in this study was conducive to hibernation in short-beaks, which do not easily enter torpor in captivity, and their large size, we think that torpor in wild adult Zaglossus is unlikely.

Stability of furosemide in human albumin solution.

OBJECTIVE: To determine the chemical stability of furosemide in human albumin solution over a 28-day period and to assess admixtures for microbiologic contamination. METHODS: Samples were prepared by mixing furosemide injectable solution and 25% human albumin solution in a 1:1 molar ratio. Six bulk containers were prepared and stored in the dark: 3 under refrigeration (approximately 4 degrees C) and 3 at room temperature (approximately 25 degrees C). Study samples were withdrawn from each bulk solution immediately after preparation and at predetermined intervals over the subsequent 28 days. Containers were observed for color change and precipitation against a light and dark background at each sampling interval. Total furosemide concentration was determined using HPLC. Additional vials were prepared and assessed for microbiologic growth at time points corresponding with chemical stability results. RESULTS: A mean of 94.5%+/-1.33% of the initial furosemide concentration remained after 48 hours at room temperature. Under refrigeration, 100.6%+/-1.02% of the initial concentration remained at 14 days. Beyond these respective time points, <90% of the initial furosemide concentration remained. No bacterial or fungal growth was observed. CONCLUSIONS: When combined with 25% human albumin solution and stored under darkness, furosemide is chemically stable and free of microbiologic contamination for 48 hours at room temperature and 14 days under refrigeration.