OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies.

The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

Costal cartilage or conchal cartilage for aesthetic and structural reconstruction of lower pole ear defects.

BACKGROUND: Lower pole defects of the ear involve loss of the ear lobule with a variable degree of cartilaginous helical rim and antihelix. OBJECTIVES: The authors describe a method of reconstructing lower pole ear defects with local skin flaps by incorporating conchal or costal cartilage grafts. METHODS: The authors retrospectively evaluated the charts of 13 patients who presented between 1998 and 2007 with lower pole auricular defects. For defects primarily involving the earlobe (seven cases), conchal cartilage was sandwiched between an anterior transposition flap and a posterior V-Y advancement flap. For defects extending into the inferior portions of the helical rim and antihelix (six cases), a costal cartilage framework was inserted into a skin pocket and released after six months. RESULTS: The mean follow-up for the 13 patients in this series was three years. Both techniques resulted in satisfactory long-term outcomes with excellent contour of the ear. All patients were satisfied with their reconstruction. Data showed that costal cartilage reconstructions required a minimum of two stages and that construction with conchal cartilage resulted in a softer lobule but was more likely to require minor aesthetic revision. CONCLUSIONS: With appropriate preoperative planning, these cartilage graft techniques produce excellent aesthetic outcomes in reconstructing complicated defects of the lower pole of the ear.

Treatment of unwanted hair in auricular reconstruction.

In many microtia patients, the hairline is lower than ideal. Despite this, it is essential to position the reconstructed ear in the correct place. Here is a series of tips and tricks to deal with unwanted hair on the skin that covers an autogenous tissue reconstruction. Replacement of the skin with a fascial flap and skin graft remains the mainstay of treatment for a very-low-hairline case. Surgical removal of hair on the helical rim during the release procedure is also described. Laser depilation, surgical electrolysis, and even shaving techniques are also discussed.

Bringing Open Data to Whole Slide Imaging.

Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.

Building bridges between cellular and molecular structural biology.

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

How does a populist government interpret and face a health crisis? Evidence from the Mexican populist response to COVID-19 / Como um governo populista interpreta e enfrenta uma crise na área de saúde? Evidências provenientes da resposta populista mexicana à COVID-19 / ¿Cómo interpreta y enfrenta un gobierno populista una crisis de salud? Evidencia de la respuesta populista mexicana a la COVID-19

Abstract In 2020, governments were faced with addressing the health crisis caused by the COVID-19 pandemic, without certainty about what would work best to reduce the health crisis without ruining the economy. Through all the uncertainty, national governments based their responses to COVID-19 on beliefs and political ideas, which was reflected on the diversity of the responses: liberal, authoritarian, centralized, decentralized, transparent, or opaque. In this article we focus on one of these responses, populism, and seek to understand how populist beliefs drive bureaucratic actions taken by a populist government to handle the health crisis. We conducted a comparative case study between the Mexican populist federal government and the non-populist Jalisco state government. Our findings suggest that the administrative actions chosen by the Mexican populist government were based on negative beliefs towards expert scientific knowledge from outside the government; a disinterest in searching for more information from distant or unfamiliar sources; and a strengthening of flagship programs as the main way to address the upcoming economic crisis. We also found that the Mexican government shows a peculiar manifestation of populism, which we refer as downsizing populism. Our article advances our understanding about how populism may affect the form and function of bureaucracies.

Resumo Em 2020, os governos foram confrontados com a necessidade de enfrentar a crise sanitária causada pela COVID-19, sem ter certeza sobre quais as melhores alternativas para lidar com a pandemia sem arruinar a economia. Em um marco de incerteza causada pelo novo vírus, os governos nacionais basearam suas respostas em crenças e ideias políticas, o que se refletiu na diversidade de respostas: liberais, autoritárias, centralizadas, descentralizadas, transparentes ou opacas. Nesse artigo, nos concentramos em um desses tipos de resposta, o populismo, e buscamos entender como as crenças populistas determinam as ações burocráticas adotadas por um governo para lidar com a crise sanitária. Com esse objetivo, fizemos um estudo de caso comparativo entre o governo federal mexicano (populista) e o governo do estado de Jalisco (não-populista). Nossos resultados sugerem que as ações administrativas adotadas pelo governo federal (populista) foram baseadas em crenças negativas com relação ao conhecimento científico especializado procedente de fora do governo; um desinteresse em buscar mais informações em fontes distantes ou pouco conhecidas; e o fortalecimento dos programas emblemáticos como a principal forma de enfrentar a crise econômica que se aproxima. Também descobrimos que o governo federal mexicano representa uma manifestação peculiar de populismo, que denominamos populismo downsizing (populismo que promove a redução do tamanho do estado). Nosso artigo permite avançar nosso entendimento sobre como o populismo pode afetar a forma e a função das burocracias.

Resumen En 2020, los gobiernos se enfrentaron a la necesidad de abordar la crisis de salud causada por la COVID-19, sin estar seguros de qué funcionaría mejor para abordar esta crisis de salud sin arruinar la economía. En un marco de incertidumbre provocado por el nuevo virus, los gobiernos nacionales basaron sus respuestas en creencias e ideas políticas, lo que se reflejó en la diversidad de respuestas: liberales, autoritarias, centralizadas, descentralizadas, transparentes o veladas. En este artículo, nos enfocamos en uno de esos tipos de respuestas, el populismo, y buscamos entender cómo las creencias populistas determinan las acciones burocráticas tomadas por un gobierno para enfrentar la crisis de salud. Para ello, realizamos un estudio de caso comparativo entre el gobierno federal mexicano (populista) y el gobierno del estado de Jalisco (no populista). Nuestros resultados sugieren que las acciones administrativas tomadas por el gobierno federal se basaron en creencias negativas con respecto al conocimiento científico especializado proveniente de fuera del gobierno; falta de interés en buscar más información de fuentes lejanas o poco conocidas; y el fortalecimiento de programas emblemáticos como principal forma de enfrentar la crisis económica que se avecina. También encontramos que el gobierno federal mexicano representa una manifestación peculiar del populismo, al que denominamos "populismo reductor" (populismo que promueve la reducción del tamaño del estado). Nuestro artículo nos permite avanzar en nuestra comprensión de cómo el populismo puede afectar la forma y función de las burocracias.

Laser depilation of the natal cleft--an aid to healing the pilonidal sinus.

BACKGROUND: Pilonidal disease is common. Excessive hair growth in the natal cleft is thought to be a factor in initiating these sinuses. It is chronic and intermittent in nature and treatment can be difficult. Hair removal by shaving or use of creams is often advised as a compliment to surgical treatments. However, access to the natal cleft can be difficult. Laser removal of hair in the natal cleft is considered as an aid to healing the pilonidal sinus. PATIENTS AND METHODS: Over a 5-year period, 14 patients with recurrent pilonidal disease were treated in our unit with laser depilation. They were all contacted by postal questionnaire, and those with ongoing disease were asked to return to the clinic for evaluation and possible further treatment. RESULTS: All patients returned the postal questionnaire. Of the 14 patients, 4 had on-going disease and received further depilation with the Alexandrite laser. All are now healed with no reported complications. All patients found the procedure painful and received local anaesthetic. CONCLUSIONS: Laser depilation in the natal cleft is by no means a cure for pilonidal disease. Removal of hair by this method represents an alternative and effective method of hair removal and, although long lasting, is only temporary. However, it allows the sinuses to heal rapidly. It is relatively safe, and simple to teach, with few complications. It should thus be considered as an aid to healing the problem pilonidal sinus.

The bacteriology of children prior to 1st stage autologous ear reconstruction.

In virtually all surgical specialities the use of peri-operative antibiotic prophylaxis to minimise wound site infection is routine practice. Antibiotic selection is targeted towards the pathogens most commonly encountered at the surgical site. The surgical management of microtia is by autologous rib cartilage reconstruction, a process that involves at least two surgical stages. The pits and recesses of the microtia ear are difficult to clean and may shelter unusual pathogens not routinely found as skin commensals, requiring modified prophylaxis. This retrospective review of 37 patients undergoing 1st stage ear reconstruction, examines the pre-operative ear site, nose and throat swabs to determine the common pre-operative bacteria encountered in children prior to ear reconstruction, to aid in appropriate antibiotic selection.

Patient satisfaction and aesthetic outcomes after ear reconstruction with a Branemark-type, bone-anchored, ear prosthesis: a 16 year review.

INTRODUCTION: Reconstruction of the human ear with a bone-anchored prosthesis is a widely accepted alternative when autologous reconstruction is technically impossible or declined by the individual. However, there are relatively few data in the literature documenting patient satisfaction with this form of reconstruction. METHODS: This study examines different aspects of patient satisfaction using an eighteen-point postal questionnaire to measure patient outcomes against a Likert rating scale. The questionnaire was sent to 33 patients who completed prosthetic ear reconstruction over a 16 year period at a specialist plastic surgery unit in the United Kingdom. Medical case notes for these cases were also reviewed. Twenty completed questionnaires were returned. RESULTS: The response rate was 61%. The majority of patients were satisfied with the aesthetics, ease of handling and comfort of the bone-anchored implant and prosthesis. However, the majority of patients was only moderately satisfied or was dissatisfied with this method of reconstruction. Specifically, 15 of the respondents reported skin problems around the abutments of the bone-anchored implant with 10 patients reporting ongoing skin complications. Granulation tissue was the most common skin problem (12 cases) followed by local infection (10 cases). Interestingly, despite the chronic skin problems, most patients indicated that they would undergo the same procedure again or would recommend it to others. DISCUSSION: Our survey shows that patients fitted with a Branemark-type bone-anchored implant for ear reconstruction are pleased with the aesthetic appearance but experience multiple, chronic, skin complications and other implant related problems. These affect their satisfaction with this method of reconstruction. Our findings may have significant implications for patients and surgeons considering this form of reconstruction and for the institutions making decisions about funding this treatment.

Massive bilateral breast reduction in an 11-year-old girl: 24% ablation of body weight.

An 11-year-old girl with massive virginal breast hypertrophy is presented. The breasts had begun to grow rapidly at puberty and had reached an enormous size within a year, to the point of causing physical impairment and respiratory compromise. Routine blood chemistry and endocrine investigation was normal, as was an MRI scan of the pituitary fossa. A bilateral reduction mammaplasty with free nipple grafts was performed, removing 12.5 kg of tissue in all (24% of the total body weight). There was no recurrence at a 2 year follow up, and no requirement for additional surgery. A review of the literature reveals that breast regrowth is less frequent when free nipple grafting is used, and this technique is recommended for these extraordinary cases.

Post traumatic ear reconstruction.

This is a review of 249 patients who have suffered ear trauma and who have presented for reconstruction over the last eighteen years. All were born with normal ears and had lost one or both ears or a major segment of the ear. Congenital ear problems including microtia are not included.

Donor-site morbidity after autologous costal cartilage harvest in ear reconstruction and approaches to reducing donor-site contour deformity.

BACKGROUND: Harvesting of rib as a source of cartilage can result in significant donor-site morbidity. In experienced hands, excellent results from using autologous rib cartilage are achievable for ear reconstruction, rhinoplasty, and otolaryngology. The authors report the morbidity associated with the harvest of costal cartilage in 42 patients who underwent ear reconstruction. METHODS: The notes were examined retrospectively and further data were collected with a questionnaire. Patients noted their experience of pain, clicking, and satisfaction with the donor site. Fifteen patients underwent additional clinical assessments of their donor scar and contour deformity using a standardized scale. Five donor sites were reconstructed with spare cartilage left over from carving the ear framework. RESULTS: The results showed that pain and clicking of the chest wall represented the commonest complaints. These peaked in the first week after surgery and diminished slowly over 3 months. The donor-site scar and deformity were acceptable to most patients. There was an improvement in the contour deformity of the chest wall harvest site in the five patients who underwent reconstruction of their donor site. CONCLUSIONS: To improve the outcome for patients undergoing cartilage harvest, efforts must be made to further reduce pain and donor-site morbidity. Reconstruction of the donor site with spare cartilage should be attempted where possible to improve the contour defect of the donor site. Refinements in the methods of cartilage harvest or donor-site reconstruction may achieve this in the future.

Pinnaplasty: reshaping ears to improve hearing aid retention.

The hearing aid is extremely important to the deaf. A small number have difficulty in retaining the device because the ear is prominent or cup-shaped. This report describes 11 children whose ear shape was modified to improve hearing aid retention and one adult in whom an over set back ear was released to allow fitment of a postaural device. In eight of the 11 children treated, conservative measures such as double-sided tape and retention bands (Huggies) had been tried previously without success. The creation of an antihelical fold in a misshapen ear lacking such a fold provides a reinforcing strut which is useful to support a hearing aid. In patients whose ear had been excessively tethered by previous surgery, projection was restored by inserting a cartilage block behind the ear. In one child with ears tethered by previous surgery, costal cartilage was used not only to release both ears, but also to reconstruct a new helical rim on one side. Surgery enabled a normal postaural hearing aid to be worn in 17 of the 19 ears treated. The two failures deserve special mention. In one patient with a unilateral deformity and severe mental retardation, the dressings were pulled off immediately after surgery. In another patient with a bilateral problem, the appearance and hearing aid retention was improved, but there was not enough room in the postauricular sulcus on one side for the battery component to fit comfortably and an in-the-ear device is now used on that side. Pinnaplasty is a helpful strategy to improve hearing aid retention. Care must be taken not to overdo the set back so that enough room is left to retain the hearing device.

Facial acne and fine lines: transforming patient outcomes with plasma skin regeneration.

BACKGROUND: A novel device for skin rejuvenation has been developed and tested. The device converts a stream of nitrogen into a plasma of ionized gas, which ablates surface tissue in a controlled manner. METHODS: Eleven patients were followed up for 6 months. The results were assessed objectively using skin molds to measure skin irregularity, as well subjectively using patient- and doctor-assessed parameters. RESULTS: Plasma skin regeneration was shown to reduce fine line wrinkles by an average of 24% at 6 months (P = 0.005, Mann-Whitney rank sum test) and to improve acne scarring by 23% at 6 months (P = 0.001, Mann-Whitney rank sum test). CONCLUSIONS: The main benefit of this system was that the patients had minimal erythema lasting only 1-6 days and no pigmentary changes. This is therefore a device with proven efficacy and limited morbidity.

Intra-lesional injections of collagenase are ineffective in the treatment of keloid and hypertrophic scars.

The treatment of keloid and hypertrophic scars remains difficult. Enzymatic digestion of keloid scars has been previously proposed as an effective treatment strategy for reducing the volume of keloid scars. To test this, we administered intra-lesional injections of pure collagenase (between 600 and 4500 units for each scar) into the keloid and hypertrophic scars of seven human volunteers (five keloid and two hypertrophic scars). Five patients (three keloid and two hypertrophic) received more than one injection of collagenase. The treatment resulted in a temporary reduction in scar volume for three of the patients with keloid scars. However, scar volumes for these three patients returned to the same (or greater) levels after 6 months of follow-up. Treatment with collagenase produced no change in scar volume for the two patients with hypertrophic scar. Side effects were numerous and severe including; pain, swelling, blistering, ulceration and ecchymosis at the site of injection. One patient required admission to hospital for 48 h after the first injection. Maximum length of follow-up was 6 months. None of the seven patients completed the study and returned for final follow-up at 2 years. This pilot study suggests that treatment of keloid and hypertrophic scars with intra-lesional injections of collagenase is ineffective.

Mirror ear: a reconstructive technique for substantial tragal anomalies or polyotia.

Polyotia (mirror ear) is an extremely rarely reported congenital anomaly of the external ear. The aetiology of this condition is unclear, and there are few descriptions of surgical techniques used. We aimed to review our experience with this condition by performing a retrospective review of the cases treated in our unit. Eight cases of polyotia treated at a referral centre for ear reconstruction in a 12 year period (1992-2004) were reviewed. Patient demographic data and associated syndromes were recorded. Operative techniques used in the cases were studied. There was an equal number of males and females. Four patients had abnormal contralateral ears and two patients were formally diagnosed as suffering from a congenital developmental syndrome. Five main components of surgical technique were found to be particularly relevant to these cases. These relate to deconstruction of the defect, management of extra cartilage, management of skin, proximity of the facial nerve and the timing of surgery. The authors conclude that a structured surgical approach can lead to successful reconstruction of these difficult abnormalities.