Large-scale annotated dataset for cochlear hair cell detection and classification.

Our sense of hearing is mediated by cochlear hair cells, of which there are two types organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains 5-15 thousand terminally differentiated hair cells, and their survival is essential for hearing as they do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. Machine learning can be used to automate the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, rat, guinea pig, pig, primate, and human cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 107,000 hair cells which have been identified and annotated as either inner or outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair-cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to give other hearing research groups the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.

Large-scale annotated dataset for cochlear hair cell detection and classification.

Our sense of hearing is mediated by cochlear hair cells, localized within the sensory epithelium called the organ of Corti. There are two types of hair cells in the cochlea, which are organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains a few thousands of hair cells, and their survival is essential for our perception of sound because they are terminally differentiated and do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. However, the sheer number of cells along the cochlea makes manual quantification impractical. Machine learning can be used to overcome this challenge by automating the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, human, pig and guinea pig cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 90'000 hair cells, all of which have been manually identified and annotated as one of two cell types: inner hair cells and outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to supply other groups within the hearing research community with the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.

Dynamic Opposition of Histone Modifications.

Gene transcription does not only require writers of active histone modifications; on-site opposition by erasers is essential for many genes. Here, we propose the concept of dynamic opposition of histone modifications to explain this conundrum. We highlight the requirement of HDACs for acetylation balance at superenhancers, and the requirement of KDM5A for H4K3me3 recycling at highly active gene promoters. We propose that histone post-translational modifications regulate charge balance for biomolecular condensate formation and nucleosome turnover and form a short-term memory that informs lock-and-step checkpoints for chromatin engagement by RNA polymerase II.

Well-Defined Bifunctional Dendrimer Bearing 54 Nitric Oxide-Releasing Moieties and 54 Ursodeoxycholic Acid Groups Presenting High Anti-Inflammatory Activity.

Nitric oxide (NO) and ursodeoxycholic acid (UDCA) are endogenous molecules involved in physiological processes associated with inflammation. Since inflammatory processes are present in the mechanisms of many diseases, these molecules are important for the development of new drugs. Herein, we describe the synthesis of a well-defined bifunctional dendrimer with 108 termini bearing 54 NO-releasing groups and 54 UDCA units (Dendri-(NO/UDCA)54). For comparison, a lower-generation dendrimer bearing 18 NO-releasing groups and 18 UDCA units (Dendri-(NO/UDCA)18) was also synthesized. The anti-inflammatory activity of these dendrimers was evaluated, showing that the bifunctional dendrimers have an inverse correlation between concentration and anti-inflammatory activity, with an effect dramatically pronounced for Dendri-(NO/UDCA)54 20, which at just 0.25 nM inhibited 76.1% of IL-8 secretion. Data suggest that nanomolar concentrations of these dendrimers aid in releasing NO in a safe and controlled way. This bifunctional dendrimer has great potential as a drug against multifactorial diseases associated with inflammatory processes.

Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix.

Extracellular matrix (ECM) remodeling has emerged as a key feature of inflammatory bowel disease (IBD), and ECM fragments have been proposed as markers of clinical disease severity. Recent studies report increased protease activity in the gut microbiota of IBD patients. Nonetheless, the relationship between gut microbiota and ECM remodeling has remained unexplored. We hypothesized that members of the human gut microbiome could degrade the host ECM and that bacteria-driven remodeling, in turn, could enhance colonic inflammation. Through a variety of in vitro assays, we first confirmed that multiple bacterial species found in the human gut are capable of degrading specific ECM components. Clinical stool samples obtained from ulcerative colitis patients also exhibited higher levels of proteolytic activity in vitro, compared to those of their healthy counterparts. Furthermore, culture supernatants from bacteria species that are capable of degrading human ECM accelerated inflammation in dextran sodium sulfate (DSS)-induced colitis. Finally, we identified several of the bacterial proteases and carbohydrate degrading enzymes (CAZymes) that are potentially responsible for ECM degradation in vitro. Some of these protease families and CAZymes were also found in increased abundance in a metagenomic cohort of IBD. These results demonstrate that some commensal bacteria in the gut are indeed capable of degrading components of human ECM in vitro and suggest that this proteolytic activity may be involved in the progression of IBD. A better understanding of the relationship between nonpathogenic gut microbes, host ECM, and inflammation could be crucial to elucidating some of the mechanisms underlying host-bacteria interactions in IBD and beyond. IMPORTANCE Healthy gut epithelial cells form a barrier that keeps bacteria and other substances from entering the blood or tissues of the body. Those cells sit on scaffolding that maintains the structure of the gut and informs our immune system about the integrity of this barrier. In patients with inflammatory bowel disease (IBD), breaks are formed in this cellular barrier, and bacteria gain access to the underlying tissue and scaffolding. In our study, we discovered that bacteria that normally reside in the gut can modify and disassemble the underlying scaffolding. Additionally, we discovered that changes to this scaffolding affect the onset of IBD in mouse models of colitis as well as the abilities of these mice to recover. We propose that this new information will reveal how breaks in the gut wall lead to IBD and will open up new avenues by which to treat patients with IBD.

Public Engagement with Biotechnology Inside and Outside the Classroom: Community-Focused Approaches.

Biotechnology offers vast benefits to the environment, animals, and human health, and contributes to improving socioeconomic conditions for the public. However, biotechnology innovations continue to trigger public concern and opposition over their potential social, health, and ecological risks. There is an opportunity to increase knowledge and acceptance of biotechnology through engagement, education, and community participation. In this perspective, we highlight crucial factors that shape the public perception of biotechnology and present opportunities for scientists to effectively communicate their ideas while engaging with local and global communities. Initiatives that seek to involve communities in design, development, and adoption processes are crucial for the successful implementation of biotechnology-based solutions.

Engaging Scientific Diasporas in STEAM Education: The Case of Science Clubs Colombia.

Currently, there is limited insight on the role that scientific diasporas can play in STEAM education in Latin America. Here, we present the Science Clubs Colombia (Clubes de Ciencia Colombia-SCC) program, a pioneering STEAM capacity-building initiative led by volunteer scientists to engage youth and children from underserved communities in science. The program brings together researchers based in Colombia and abroad to lead intensive project-based learning workshops for young students in urban and rural areas. These projects focus on channeling the students' technical and cognitive scientific aptitudes to tackle challenges of both local and global relevance. The program provides high-quality STEAM education adapted to communities' needs and articulates long-lasting international collaborations using the mobility of the Colombian diaspora. The program's success is tangible via its sustained growth and adaptability. Since its first version in 2015, 722 volunteer scientists living abroad or in Colombia have collaborated to create 364 clubs with the participation of 9,295 students. We describe elements of the SCC program that lead to a scalable and reproducible outcome to engage science diasporas in STEAM education. Additionally, we discuss the involvement of multiple stakeholders and the generation of international networks as potential science diplomacy outcomes. The SCC program strengthens the involvement of Latin American youth in science, demonstrates the potential of engaging scientific diasporas in science education, and enriches connections between the Global South and the Global North.

Engineering the aortic valve extracellular matrix through stages of development, aging, and disease.

For such a thin tissue, the aortic valve possesses an exquisitely complex, multi-layered extracellular matrix (ECM), and disruptions to this structure constitute one of the earliest hallmarks of fibrocalcific aortic valve disease (CAVD). The native valve structure provides a challenging target for engineers to mimic, but the development of advanced, ECM-based scaffolds may enable mechanistic and therapeutic discoveries that are not feasible in other culture or in vivo platforms. This review first discusses the ECM changes that occur during heart valve development, normal aging, onset of early-stage disease, and progression to late-stage disease. We then provide an overview of the bottom-up tissue engineering strategies that have been used to mimic the valvular ECM, and opportunities for advancement in these areas.

Geographic differences in gut microbiota composition impact susceptibility to enteric infection.

Large-scale studies of human gut microbiomes have revealed broad differences in composition across geographically distinct populations. Yet, studies examining impacts of microbiome composition on various health outcomes typically focus on single populations, posing the question of whether compositional differences between populations translate into differences in susceptibility. Using germ-free mice humanized with microbiome samples from 30 donors representing three countries, we observe robust differences in susceptibility to Citrobacter rodentium, a model for enteropathogenic Escherichia coli infections, according to geographic origin. We do not see similar responses to Listeria monocytogenes infections. We further find that cohousing the most susceptible and most resistant mice confers protection from C. rodentium infection. This work underscores the importance of increasing global participation in microbiome studies related to health outcomes. Diverse cohorts are needed to identify both population-specific responses to specific microbiome interventions and to achieve broader-reaching biological conclusions that generalize across populations.

A microfluidic chip carrier including temperature control and perfusion system for long-term cell imaging.

Microfluidic devices are widely used for biomedical applications but there is still a lack of affordable, reliable and user-friendly systems for transferring microfluidic chips from an incubator to a microscope while maintaining physiological conditions when performing microscopy. The presented carrier represents a cost-effective option for sustaining environmental conditions of microfluidic chips in combination with minimizing the device manipulation required for reagent injection, media exchange or sample collection. The carrier, which has the outer dimension of a standard well plate size, contains an integrated perfusion system that can recirculate the media using piezo pumps, operated in either continuous or intermittent modes (50-1000 µl/min). Furthermore, a film resistive heater made from 37 µm-thick copper wires, including temperature feedback control, was used to maintain the microfluidic chip temperature at 37 °C when outside the incubator. The heater characterisation showed a uniform temperature distribution along the chip channel for perfusion flow rates up to 10 µl/min. To demonstrate the feasibility of our platform for long term cell culture monitoring, mouse brain endothelial cells (bEnd.3) were repeatedly monitored for a period of 10 days, demonstrating a system with both the versatility and the potential for long imaging in microphysiological system cell cultures.

Gaining insight into the implementation of an e-learning smoking cessation course in Latin American countries.

Continuous medical education focused on health problems emerging in low- and middle-income countries (LMICs) is scarce. Although tobacco consumption is increasing in LMICs, there is a lack of tobacco cessation training programs in these countries. To promote smoking cessation interventions in Bolivia, Guatemala and Paraguay, we adapted an e-learning program developed in Catalonia (Spain). This process evaluation study reports on reach, dose and satisfaction of participants with the course, as well as the contextual factors of its application. We conducted a multiple method evaluation, which included a survey and several focus groups, each one specific to the same type of healthcare professional (nurses, doctors, other professionals). Two hundred and ninety-two participants registered into the online course. The motivation for undertaking the course was different between doctors and nurses. The main sources of difficulty in enrolling and finishing the course were the technical problems experienced when accessing the platform, and lack of acquaintance with computers and the Internet in general. Our results show that implementing e-learning education in hospitals from LMICs is feasible, especially when there are similarities between participating countries and the country in which the original program was developed. However, several elements such as strong organizational commitment, technical support and resources and adequate communication channels should be provided to facilitate enrollment and training completion. Efforts to improve Internet access should be made to avoid jeopardizing students' motivation to enroll and complete online training.

Building a virtual community to support and celebrate the success of Latinx scientists.

In February 2019, we co-founded LatinXinBME to build a diverse and welcoming virtual community of Latinx researchers in biomedical engineering (BME). We leverage digital tools and community mentoring approaches to support our members and to build safe spaces in academia, with the aim to diversify the academic workforce in STEM.

The internationalization of human microbiome research.

The human microbiome has now been linked with myriad diseases, yet most of this research has been conducted on American and European populations that make up only 1/6th of the world's population. With growing recognition that human microbiomes differ tremendously across global populations, it is especially important to understand how these compositional differences impact health outcomes. Recent advances in infectious disease and malnutrition research have demonstrated the potential for microbiome-based strategies to address the biggest challenges in global health. This review highlights major advances toward understanding microbiome diversity across the world and its contributions to disease, and outlines key questions, challenges, and opportunities to broaden the scope of and promote inclusivity within microbiome research.

Butenafine and analogues: An expeditious synthesis and cytotoxicity and antifungal activities.

The incidence of fungal infections is considered a serious public health problem worldwide. The limited number of antimycotic drugs available to treat human and animal mycosis, the undesirable side effects and toxicities of the currently available drugs, and the emergence of fungal resistance emphasizes the urgent need for more effective antimycotic medicines. In this paper, we describe a rapid, simple, and efficient synthetic route for preparation of the antifungal agent butenafine on a multigram scale. This novel synthetic route also facilitated the preparation of 17 butenafine analogues using Schiff bases as precursors in three steps or less. All the synthesized compounds were evaluated against the yeast, Cryptococcus neoformans/C. gattii species complexes and the filamentous fungi Trichophyton rubrum and Microsporum gypseum. Amine 4bd, a demethylated analogue of butenafine, and its corresponding hydrochloride salt showed low toxicity in vitro and in vivo while maintaining inhibitory activity against filamentous fungi.

Creation of disease-inspired biomaterial environments to mimic pathological events in early calcific aortic valve disease.

An insufficient understanding of calcific aortic valve disease (CAVD) pathogenesis remains a major obstacle in developing treatment strategies for this disease. The aim of the present study was to create engineered environments that mimic the earliest known features of CAVD and apply this in vitro platform to decipher relationships relevant to early valve lesion pathobiology. Glycosaminoglycan (GAG) enrichment is a dominant hallmark of early CAVD, but culture of valvular interstitial cells (VICs) in biomaterial environments containing pathological amounts of hyaluronic acid (HA) or chondroitin sulfate (CS) did not directly increase indicators of disease progression such as VIC activation or inflammatory cytokine production. However, HA-enriched matrices increased production of vascular endothelial growth factor (VEGF), while matrices displaying pathological levels of CS were effective at retaining lipoproteins, whose deposition is also found in early CAVD. Retained oxidized low-density lipoprotein (oxLDL), in turn, stimulated myofibroblastic VIC differentiation and secretion of numerous inflammatory cytokines. OxLDL also increased VIC deposition of GAGs, thereby creating a positive feedback loop to further enrich GAG content and promote disease progression. Using this disease-inspired in vitro platform, we were able to model a complex, multistep pathological sequence, with our findings suggesting distinct roles for individual GAGs in outcomes related to valve lesion progression, as well as key differences in cell-lipoprotein interactions compared with atherosclerosis. We propose a pathogenesis cascade that may be relevant to understanding early CAVD and envision the extension of such models to investigate other tissue pathologies or test pharmacological treatments.

Patient-centered boundary mechanisms to foster intercultural partnerships in health care: a case study in Guatemala.

BACKGROUND: Up to one half of the population in Africa, Asia and Latin America has little access to high-quality biomedical services and relies on traditional health systems. Medical pluralism is thus in many developing countries the rule rather than the exception, which is why the World Health Organization is calling for intercultural partnerships to improve health care in these regions. They are, however, challenging due to disparate knowledge systems and lack of trust that hamper understanding and collaboration. We developed a collaborative, patient-centered boundary mechanism to overcome these challenges and to foster intercultural partnerships in health care. To assess its impact on the quality of intercultural patient care in a medically pluralistic developing country, we conducted and evaluated a case study. METHODS: The case study took place in Guatemala, since previous efforts to initiate intercultural medical partnerships in this country were hampered by intense historical and societal conflicts. It was designed by a team from ETH Zurich's Transdisciplinarity Lab, the National Cancer Institute of Guatemala, two traditional Councils of Elders and 25 Mayan healers from the Kaqchikel and Q'eqchi' linguistic groups. It was implemented from January 2014 to July 2015. Scientists and traditional political authorities collaborated to facilitate workshops, comparative diagnoses and patient referrals, which were conducted jointly by biomedical and traditional practitioners. The traditional medical practices were thoroughly documented, as were the health-seeking pathways of patients, and the overall impact was evaluated. RESULTS: The boundary mechanism was successful in discerning barriers of access for indigenous patients in the biomedical health system, and in building trust between doctors and healers. Learning outcomes included a reduction of stereotypical attitudes towards traditional healers, improved biomedical procedures due to enhanced self-reflection of doctors, and improved traditional health care due to refined diagnoses and adapted treatment strategies. In individual cases, the beneficial effects of traditional treatments were remarkable, and the doctors continued to collaborate with healers after the study was completed. Comparison of the two linguistic groups illustrated that the outcomes are highly context-dependent. CONCLUSIONS: If well adapted to local context, patient-centered boundary mechanisms can enable intercultural partnerships by creating access, building trust and fostering mutual learning, even in circumstances as complex as those in Guatemala. Creating multilateral patient-centered boundary mechanisms is thus a promising approach to improve health care in medically pluralistic developing countries.

Robust Generation of Quiescent Porcine Valvular Interstitial Cell Cultures.

BACKGROUND: Valvular interstitial cells (VICs) in the healthy aortic valve leaflet exhibit a quiescent phenotype, with <5% of VICs exhibiting an activated phenotype. Yet, in vitro culture of VICs on tissue culture polystyrene surfaces in standard growth medium results in rapid transformation to an activated phenotype in >90% of cells. The inability to preserve a healthy VIC phenotype during in vitro studies has hampered the elucidation of mechanisms involved in calcific aortic valve disease. This study describes the generation of quiescent populations of porcine VICs in 2-dimensional in vitro culture and their utility in studying valve pathobiology. METHODS AND RESULTS: Within 4 days of isolation from fresh porcine hearts, VICs cultured in standard growth conditions were predominantly myofibroblastic (activated VICs). This myofibroblastic phenotype was partially reversed within 4 days, and fully reversed within 9 days, following application of a combination of a fibroblast media formulation with culture on collagen coatings. Specifically, culture in this combination significantly reduced several markers of VIC activation, including proliferation, apoptosis, α-smooth muscle actin expression, and matrix production, relative to standard growth conditions. Moreover, VICs raised in a fibroblast media formulation with culture on collagen coatings exhibited dramatically increased sensitivity to treatment with transforming growth factor ß1, a known pathological stimulus, compared with VICs raised in either standard culture or medium with a fibroblast media formulation. CONCLUSIONS: The approach using a fibroblast media formulation with culture on collagen coatings generates quiescent VICs that more accurately mimic a healthy VIC population and thus has the potential to transform the study of the mechanisms of VIC activation and dysfunction involved in the early stages of calcific aortic valve disease.

Intraoral lipomas: Review of literature and report of two clinical cases.

BACKGROUND: Lipomas are benign mesenchymal tumors composed of mature adipocytes. They are classified according to their histological pattern and their etiology remains unclear. Objectives: To present two cases and review the literature. MATERIAL AND METHODS: A search was conducted in the Medline / PubMed and Scielo data bases of the last 10 years (2004-2014) with the keywords " intraoral lipoma OR oral cavity lipoma". RESULTS: 46 articles with 95 cases (56 women and 39 men) were reviewed. The average age was found to be 52.28 years (52.28 ± 18.55); and most of them occurred between the 4th and 6th decade of life. Lipomas occur mostly in the buccal mucosa (n = 36, 37.9%), followed by the tongue (n = 23, 24.2%) and other locations (n = 36, 37.9%). The most common histologic pattern was simple lipomas (n = 40, 42%), followed by fibrolipomas (n = 18, 18.9%) and other types (n = 37, 39.1%). The average tumor size was 19.77 ± 16.26mm. CONCLUSIONS: Lipomas are a relatively rare finding in the oral cavity. Surgical excision is the treatment of choice and recurrence is not expected. Key words:Benign oral tumor, oral lipoma, lipoma, oral cavity.