Academic Laboratories Research Articles

Objetar Academic Laboratory, A Higher Education Model for Marketing and Advertising

El propósito de este trabajo es describir el proceso de diseño emprendido en la clase de Crítica del diseño de quinto semestre con los alumnos de la licenciatura en Mercadotecnia y publicidad en CENTRO, institución de educación superior afincada en la Ciudad de México. Como parte del modelo de trabajo se implementó un taller durante tres semestres (agosto–diciembre 2014, agosto–diciembre 2015 y agosto–diciembre 2016), experiencia en la cual participaron 49 estudiantes. Los participantes aplicaron el proceso de diseño para buscar y proyectar soluciones creativas concretadas en objetos conceptualmente críticos e ingeniosos.

Chlamydia muridarum infection causes bronchointerstitial pneumonia in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice.

The murine bacterial pathogen Chlamydia muridarum (Cm) has been used to study human Chlamydia infections in various mouse models. CD4+ T-cells, natural killer cells, and interferon-gamma (IFN-γ)-mediated immunity are important to control experimentally induced Cm infections. Despite its experimental use, natural infection by Cm has not been documented in laboratory mice since the 1940s. In 2022, the authors reported the discovery of natural Cm infections in numerous academic institutional laboratory mouse colonies around the globe. To evaluate the impact of Cm infection in severely immunocompromised mice, 19 NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice were cohoused with Cm shedding, naturally infected immunocompetent mice and/or their soiled bedding for 4 weeks and subsequently euthanized. Clinical disease, characterized by lethargy, dyspnea, and weight loss, was observed in 11/19 NSG mice, and 16/18 NSG mice had neutrophilia. All mice exhibited multifocal to coalescing histiocytic and neutrophilic bronchointerstitial pneumonia (17/19) or bronchiolitis (2/19) with intraepithelial chlamydial inclusions (CIs). Immunofluorescence showed CIs were often associated with bronchiolar epithelium. CIs were frequently detected by immunohistochemistry in tracheal and bronchiolar epithelium (19/19), as well as throughout the small and large intestinal epithelium without lesions (19/19). In a subset of cases, Cm colonized the surface epithelium in the nasopharynx (16/19), nasal cavity (7/19), and middle ear canal (5/19). Endometritis and salpingitis with intraepithelial CI were identified in a single mouse. These findings demonstrate that Cm infection acquired through direct contact or soiled bedding causes significant pulmonary pathology and widespread intestinal colonization in NSG mice.

Reactive Palladium-Ligand Complexes for 11C-Carbonylation at Ambient Pressure: A Breakthrough in Carbon-11 Chemistry.

The Pd-Xantphos-mediated 11C-carbonylation protocol (also known as the "Xantphos- method"), due to its simplistic and convenient nature, has facilitated researchers in meeting a longstanding need for preparing 11C-carbonyl-labeled radiopharmaceuticals at ambient pressure for positron emission tomography (PET) imaging and drug discovery. This development could be viewed as a breakthrough in carbon-11 chemistry, as evidenced by the rapid global adoption of the method by the pharmaceutical industry and academic laboratories worldwide. The method has been fully automated for the good manufacturing practice (GMP)-compliant production of novel radiopharmaceuticals for human use, and it has been adapted for "in-loop" reactions and microwave technology; an impressive number of 11C-labeled compounds (>100) have been synthesized. Given the simplicity and efficiency of the method, as well as the abundance of carbonyl groups in bioactive drug molecules, we expect that this methodology will be even more widely adopted in future PET radiopharmaceutical research and drug development.

The Genomics Organization for Academic Laboratories (GOAL): A vision for a genomics future for academic pathology

Innovative and self-sustaining clinical genomics laboratories specializing in cutting-edge oncology testing are critical to the success of academic pathology departments and resident and fellow education in molecular pathology. However, the pressures and challenges facing these laboratories are numerous, including the complexities of validating comprehensive cancer next-generation sequencing (NGS) panels, competition from commercial laboratories, and the reimbursement and regulatory hurdles inherent in high-complexity testing. Cross-institutional collaborations, including shared assay content and interpretative frameworks, are a valuable element to academic laboratory success. To address these and other needs, the Genomics Organization for Academic Laboratories (GOAL) was conceived in 2018, incorporated in 2020 and has grown to include 29 participating institutions in 2022. Here, we describe the mission of GOAL, its structure, and the outcomes and projects undertaken in its first years.

Changes over time in papanicolaou cytology test and HPV test in a large women's academic center laboratory.

In the past 2 decades, cervical cancer screening guidelines in the United States have undergone numerous revisions with recent greater emphasis on primary high-risk human papillomavirus (hrHPV) testing. We examine the trends of Papanicolaou test and hrHPV testing at our large academic center across 4 years (2006, 2011, 2016, and 2021) over a 15-year period. The number of ThinPrep Papanicolaou and hrHPV tests, as well as the triggers for HPV testing, were retrospectively analyzed. A total of 308,355 Papanicolaou tests and 117,477 hrHPV tests were reported across the 4 years. The number of Papanicolaou tests performed decreased nearly 3-fold over the study period, with only 43,230 Papanicolaou tests performed in 2021. The HPV test to Papanicolaou test ratio increased: 17% of Papanicolaou tests had an associated HPV test in 2006, whereas 72% of Papanicolaou tests ordered in 2021 had a companion hrHPV. The use of co-testing also increased. Overall, 73% were co-tests and 27% were reflexively ordered in the 4 one-year time periods. Co-tests constituted only 46% of HPV tests in 2006, but this increased to 93% in 2021. The percentage of positive hrHPV results decreased; in 2006, 18.3% of cases were positive, dropping to 8.6% in 2021 due to the marked increase in co-testing. Stratifying by diagnostic category, hrHPV results have remained relatively constant. With the numerous recent revisions of cervical screening guidelines, screening strategies at our institution reflected these changes in clinical practice. Papanicolaou and HPV co-testing became the most common screening method for women 30 to 65 years of age in our cohort.

Scale-Up of Academic Mesenchymal Stromal Cell Production

Background: Many clinical trials have reported the use of mesenchymal stromal cells (MSCs) following the indication of severe SARS-CoV-2 infection. However, in the COVID19 pandemic context, academic laboratories had to adapt a production process to obtain MSCs in a very short time. Production processes, especially freezing/thawing cycles, or culture medium have impacts on MSC properties. We evaluated the impact of an intermediate cryopreservation state during MSC culture to increase production yields. Methods: Seven Wharton’s jelly (WJ)-MSC batches generated from seven different umbilical cords with only one cryopreservation step and 13 WJ-MSC batches produced with intermediate freezing were formed according to good manufacturing practices. The identity (phenotype and clonogenic capacities), safety (karyotype, telomerase activity, sterility, and donor qualification), and functionality (viability, mixed lymphocyte reaction) were analyzed. Results: No significant differences between MSC production processes were observed, except for the clonogenic capacity, which was decreased, although it always remained above our specifications. Conclusions: Intermediate cryopreservation allows an increase in the production yield and has little impact on the basic characteristics of MSCs.

Industry-Scale Orchestrated Federated Learning for Drug Discovery

To apply federated learning to drug discovery we developed a novel platform in the context of European Innovative Medicines Initiative (IMI) project MELLODDY (grant n°831472), which was comprised of 10 pharmaceutical companies, academic research labs, large industrial companies and startups. The MELLODDY platform was the first industry-scale platform to enable the creation of a global federated model for drug discovery without sharing the confidential data sets of the individual partners. The federated model was trained on the platform by aggregating the gradients of all contributing partners in a cryptographic, secure way following each training iteration. The platform was deployed on an Amazon Web Services (AWS) multi-account architecture running Kubernetes clusters in private subnets. Organisationally, the roles of the different partners were codified as different rights and permissions on the platform and administrated in a decentralized way. The MELLODDY platform generated new scientific discoveries which are described in a companion paper.

Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro.

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.

Preparedness for Fire Emergency in the Nutrition Laboratory at University X in Semarang: as a Safety Education for University Students

The Occupational Safety and Health Administration (OSHA) indicates that academic laboratories are 11 times more dangerous than the industrial sectors. The nutrition laboratory is a place that has a high potential to cause fire because there are cooking activities, where these activities are very risky because they deal directly with fire and gas cylinders there. If the gas cylinder has a leak, it can cause a fire risk. This study aims to look at the preparedness of fire disaster management in the Nutrition Laboratory at University X in Semarang city. The research design used in this research was a descriptive qualitative. There were 3 informants, namely the person in charge of the nutrition laboratory and 2 students of the Nutrition Study Program. Data collection techniques used in this research was in-depth interviews. The results showed that the nutrition laboratory at University X in Semarang city already had management related to fire prevention such as the availability of fire extinguishers, evacuation routes, and assembly points. It is recommended that related parties complete active and passive protection systems, improve fire prevention teams, train and socialize, and conduct regular testing of active protection facilities in the Nutrition Laboratory.

Old Drugs and New Challenges: A Narrative Review of Nitazenes.

Nitazenes are a group of compounds developed in the 1950s as opioid analgesics, but they were never approved to market. As such, they are not well known outside of academic research laboratories. A characteristic of nitazenes is their high potency (e.g., hundreds to thousands fold more potent than morphine and other opioids and tenfold more potent than fentanyl). In the past few years, several nitazenes, including "designer analogs," have been detected in the illicit drug supply and have been implicated in overdose mortality, primarily due to their exceptionally high potency. In the street drug supply, nitazenes are often found mixed with fentanyl or other agents but their presence is not always disclosed to drug buyers, who may not even be familiar with nitazenes. These drugs pose a particular challenge since there is little experience in how to reverse a nitazene overdose or potential drug-drug or drug-alcohol interactions. Public health efforts are needed to better inform street drug consumers, first responders, healthcare professionals, and the general public about these "new old drugs" that are infiltrating the recreational drug supply.

A review Recent Advanced of Fabrication Techniques and Application of Micro-Needle

Micro-needles are micron-scaled medical devices used to administer vaccines, drugs, and other therapeutic agents. Micro-needles typically measure 0.1–1 mm in length. A variety of materials such as silicon, ceramic, stainless steel and polymers have been used for fabrication. Micro-needles devices are compatible with the delivery of both Small and macromolecular therapeutics. Micro-needles (MNs) are currently being utilized to enhance transdermal delivery of small and large molecules. With the emergence of micro fabrication manufacturing technology over the past several decades, (MNs) have been developed by academic laboratories and pharmaceutical companies. Micro-needle has useful in application in diseases such as type 2 Diabetes, cancer treatment, Glaucoma, and also useful application in cosmetic, vaccine therapy. The present article provides an overview of micro-needle, fabrication technique, general properties, Material and methods of fabrication techniques, application and advantages and disadvantages of micro-needle drug delivery system. Micro-needles (MNs) are currently being utilized to enhance trans-dermal delivery of small and large molecules. With the emergence of micro fabrication manufacturing technology over the past several decades, have been developed by academic laboratories and pharmaceutical companies.

Uncovering Manufacturing Challenges Behind Cell and Gene Therapy

Uncovering Manufacturing Challenges Behind Cell and Gene Therapy

See[ing] elegance in sensory biology: an interview with Piali Sengupta.

See[ing] elegance in sensory biology: an interview with Piali Sengupta.

CONFIDENT-trial protocol: a pragmatic template for clinical implementation of artificial intelligence assistance in pathology

IntroductionArtificial intelligence (AI) has been on the rise in the field of pathology. Despite promising results in retrospective studies, and several CE-IVD certified algorithms on the market, prospective clinical implementation...

Sticky Solutions

This article explores the agency of animal materiality, class, and context in shaping social values within wood research and manufacturing communities in mid-twentieth-century Japan, with a focus on animal glues (nikawa 膠) in relation to other adhesives. It relates the materiality and affordances of adhesives to their value within multiple technosocial contexts, in which glues made from mammalian skin, bones, and hooves remained the predominant adhesive within wood product manufacturing microenterprises but were being replaced by casein-, soybean-, and carbon-based adhesives in academic and corporate laboratories. Working primarily from research reports and consultation records compiled by industrial research institutes embedded within small-scale manufacturing communities, the article proposes that the materiality of animal glues and the larger assemblage of materials-energy-environment-tools-skill-knowledge present in, between, and around labs and workshops both rendered that materiality highly evident to human users and prompted them to value nikawa in highly divergent ways, depending on class and context. The affordances of animal-based glues, alongside those of plant- and carbon-based glues and other substances used with them in manufacturing, led different social groups to value them differently. The result was a bifurcation of value between adjacent but separate social groups, with workshop owners preferring to use animal glues, even as technical advisors labored to dissolve small workshop owners’ attachment or adherence to animal glues, and to prompt them to adopt newer, more “modern” adhesives as part of industrial rationalization and modernization. This paper is part of a special issue entitled “Making Animal Materials in Time,” edited by Laurence Douny and Lisa Onaga.

A Fast and Cost-Effective Genotyping Method for CRISPR-Cas9-Generated Mutant Rice Lines.

With increasing throughput in both the generation and phenotyping of mutant lines in plants, it is important to have an efficient and reliable genotyping method. Traditional workflows, still commonly used in many labs, have time-consuming and expensive steps, such as DNA purification, cloning and growing E. coli cultures. We propose an alternative workflow where these steps are bypassed, using Phire polymerase on fresh plant tissue, and ExoProStar treatment as preparation for sequencing. We generated CRISPR-Cas9 mutants for ZAS (ZAXINONE SYNTHASE) in rice with two guide RNAs. Using both a traditional workflow and our proposed workflow, we genotyped nine T1 plants. To interpret the sequencing output, which is often complex in CRISPR-generated mutants, we used free online automatic analysis systems and compared the results. Our proposed workflow produces results of the same quality as the old workflow, but in 1 day instead of 3 days and about 35 times cheaper. This workflow also consists of fewer steps and reduces the risk of cross contamination and mistakes. Furthermore, the automated sequence analysis packages are mostly accurate and could easily be used for bulk analysis. Based on these advantages, we encourage academic and commercial labs conducting genotyping to consider switching over to our proposed workflow.

Current clinical practices and challenges in molecular testing: a GOAL Consortium Hematopathology Working Group report

AbstractWhile molecular testing of hematologic malignancies is now standard of care, there is variability in practice and testing capabilities between different academic laboratories, with common questions arising on how to best meet clinical expectations. A survey was sent to hematopathology subgroup members of the Genomics Organization for Academic Laboratories consortium to assess current and future practice and potentially establish a reference for peer institutions. Responses were received from 18 academic tertiary-care laboratories regarding next-generation sequencing (NGS) panel design, sequencing protocols and metrics, assay characteristics, laboratory operations, case reimbursement, and development plans. Differences in NGS panel size, use, and gene content were reported. Gene content for myeloid processes was reported to be generally excellent, while genes for lymphoid processes were less well covered. The turnaround time (TAT) for acute cases, including acute myeloid leukemia, was reported to range from 2 to 7 calendar days to 15 to 21 calendar days, with different approaches to achieving rapid TAT described. To help guide NGS panel design and standardize gene content, consensus gene lists based on current and future NGS panels in development were generated. Most survey respondents expected molecular testing at academic laboratories to continue to be viable in the future, with rapid TAT for acute cases likely to remain an important factor. Molecular testing reimbursement was reported to be a major concern. The results of this survey and subsequent discussions improve the shared understanding of differences in testing practices for hematologic malignancies between institutions and will help provide a more consistent level of patient care.

Perfil clínico e hemodinâmico de pacientes consecutivos com estenose aórtica valvar estudados na era pré-implante transcateter valvar aórtico em instituição acadêmica. Análise comparativa da avaliação invasiva com a ecocardiográfica

Background: In view of the better understanding of the pathophysiology of aortic valve stenosis, the complexity of assessing its severity has simultaneously grown, with relevant uncertainty persisting as to the applicability of invasive methods by cardiac catheterization and non-invasive methods based on echocardiography. The objective of this study was to analyze the hemodynamic patterns of evaluation with echocardiography compared to the estimation of severity of aortic stenosis with catheterization in consecutive patients referred for diagnostic evaluation by the laboratory of a tertiary academic hospital in the 2016 to 2018 triennium. Methods: An observational, descriptive and retrospective study of clinical characteristics and results of assessments of severity of aortic valve stenosis obtained in 96 consecutive patients, through catheterization and echocardiography. Results: A population sample of 49 men and 47 women, with a median age of 66.5 (56.5 to 72.8) years, degenerative aortic valve stenosis in 49%, and rheumatic aortic stenosis in 40%, in addition to several comorbidities, including coronary disease (37%). Using catheterization, based on the peak gradient of 48 (20 to 68), aortic valve stenosis was assessed as severe in 56%, with ventricular end-diastolic pressure of 20mmHg (16 to 30mmHg). Using echocardiography, the valve area was 0.9cm2 (0.7 to 1.2cm2), indexed valve area was 0.5cm2/m2 (0.43 to 0.5cm2/m2), with peak gradient of 62±26mmHg. Aortic valve stenosis was considered severe in 69.2%. There was disagreement between the methods regarding severity of aortic valve stenosis in 30% of exams, with a Spearman coefficient between the valve area on the echocardiogram and the peak gradient on catheterization of -0.7 (p<0.001). Conclusion: In a representative sample of various hemodynamic patterns, the assessment of severity of aortic valve stenosis, as routinely practiced in an academic laboratory, was limited to measuring the peak transvalvular gradient. The estimation of the valve area using the echocardiographic method was indirect and also subject to criticism, and contributed to the discrepancies found, rendering it justifiable to seek the improvement of both methods, in view of the clinical and hemodynamic complexity detected.

Liver-Humanized NSG-PiZ Mice Support the Study of Chronic Hepatitis B Virus Infection and Antiviral Therapies.

Hepatitis B virus (HBV) is a pathogen of major public health importance that is largely incurable once a chronic infection is established. Only humans and great apes are fully permissive to HBV infection, and this species restriction has impacted HBV research by limiting the utility of small animal models. To combat HBV species restrictions and enable more in vivo studies, liver-humanized mouse models have been developed that are permissive to HBV infection and replication. Unfortunately, these models can be difficult to establish and are expensive commercially, which has limited their academic use. As an alternative mouse model to study HBV, we evaluated liver-humanized NSG-PiZ mice and showed that they are fully permissive to HBV. HBV selectively replicates in human hepatocytes within chimeric livers, and HBV-positive (HBV+) mice secrete infectious virions and hepatitis B surface antigen (HBsAg) into blood while also harboring covalently closed circular DNA (cccDNA). HBV+ mice develop chronic infections lasting at least 169 days, which should enable the study of new curative therapies targeting chronic HBV, and respond to entecavir therapy. Furthermore, HBV+ human hepatocytes in NSG-PiZ mice can be transduced by AAV3b and AAV.LK03 vectors, which should enable the study of gene therapies that target HBV. In summary, our data demonstrate that liver-humanized NSG-PiZ mice can be used as a robust and cost-effective alternative to existing chronic hepatitis B (CHB) models and may enable more academic research labs to study HBV disease pathogenesis and antiviral therapy. IMPORTANCE Liver-humanized mouse models have become the gold standard for the in vivo study of hepatitis B virus (HBV), yet their complexity and cost have prohibited widespread use of existing models in research. Here, we show that the NSG-PiZ liver-humanized mouse model, which is relatively inexpensive and simple to establish, can support chronic HBV infection. Infected mice are fully permissive to hepatitis B, supporting both active replication and spread, and can be used to study novel antiviral therapies. This model is a viable and cost-effective alternative to other liver-humanized mouse models that are used to study HBV.

The IVG ‘relatedness paradox’: researchers should mind speculation

Companies and academic laboratories are pursuing the production of gametes from stem cells. Researchers should be active participants in discussions about speculative scenarios, to avoid this endeavor to accommodate genetic parenthood undermines the value it is meant to serve, because of either unrealistic or insufficient ethical reflection.