Giant hiatal hernia with intrathoracic spleen: A case report.

Hiatal hernia is a frequent pathology in the population; however, the most frequent hiatal hernia is type I, which accounts for up to 95% incidence, types II, III, and IV being less frequent and representing between 5% and 15%, and even less common are giant hernias. The definition of the giant hernia is still not exact in the literature; some authors define giant or massive hiatal hernia as one in which the hernia occupies more than 30% of the stomach and/or passes from other abdominal structures to the thorax. We describe the case of a patient with gastrointestinal symptomology without response to a proton pump inhibitor, with base exacerbation that required imaging studies, showing a large hernia defect passing to the thorax from abdominal organs (stomach, spleen, mesenteric fat), as well as alteration of the gastric and spleen axis with ascent in pancreatic body and tail, which corresponds to a giant hiatal hernia. Said pathology is very infrequent, with recurrences and postoperative complications. Our patient recovered from the surgical procedure with therapeutic success.

Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia

The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. To provide a better understanding of the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia, and performed Bayesian phylodynamic analyses to estimate the time of variants introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. We detected a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the start of the pandemic. We showed that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions towards the emergence and circulation of novel SARS-CoV-2 variants.

A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole viral genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY(R) SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA as well as in Bogota, Colombia (September 2, 2020 - March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls ({kappa} [≥] 0.856) and 25 of 30 targets ({kappa} [≥] 0.820) tested on the panel. The assay had a high diagnostic sensitivity ([≥]93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants ([≥]96.15%) and all 30 targets ([≥]94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. ImportanceThe continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 - March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.

Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica.

Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were collected from five 2000 m2 permanent plots in Lowland, Upland and Riparian primary forests in Costa Rica 3 months before and 7 months after Hurricane Otto damaged the forests. The soil Water, inorganic N and Biomass C increased and total organic C decreased Post-Hurricane, all of which best predicted the changes in the Post-Hurricane soil microbial communities. Post-Hurricane soils from all forest types showed significant changes in community composition of total bacteria, total fungi, and five functional groups of microbes (i.e., degrading/lignin degrading, NH4+-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi), along with a decrease in richness in genera of all groups. As well, the mean proportion of DNA sequences (MPS) of all five functional groups increased. There were also significant changes in the MPS values of 7 different fungal and 7 different bacterial genera that were part of these functional groups. This is the first evidence that hurricane-induced deposition of canopy material is stimulating changes in the soil microbial communities after the hurricane, involving changes in specific taxonomic and functional group genera, and reduction in the community richness while selecting for dominant genera possibly better suited to process the canopy material. These changes may represent examples of taxonomic switching of functionally redundant microbial genera in response to dramatic changes in resource input. It is possible that differences in these microbial communities and genera may serve as indicators of disturbed and recovering regional soil ecosystems, and should be evaluated in the future.

Reporte de caso: Carcinoma escamocelular de próstata tratado con radioterapia externa técnica IMRT / Case report: Prostate squamous cell carcinoma managed with an external intensity-modulated radiotherapy technique

Resumen La incidencia de carcinoma escamocelular de próstata es del 0,5 al 1% de todas las lesiones neoplásicas de esta glándula. Por su rareza, no existen recomendaciones protocolizadas sobre el manejo de estos pacientes. Se reporta el caso de un paciente tratado en el Instituto con este diagnóstico, así como su desenlace a dos años de seguimiento y la revisión del tema. Reporte de caso: Paciente masculino de 79 anos de edad, con diagnóstico de carcinoma escamocelular infiltrante de próstata estadificado como T4NxMx. PSA de 2,64 y Gleason no determinable. Se descartó posible primario de órgano aledaño a la próstata y los estudios de extensión fueron negativos. Fue tratado con radioterapia externa como monoterapia y se utilizó técnica IMRT. Recibió una dosis en pelvis de 46 Gy en fracciones de 2 Gy día (PTV 1), posteriormente refuerzo en próstata y vesículas hasta 56 Gy (PTV 1,1) y en próstata hasta 76 Gy (PTV 1,1,1). A los dos años de seguimiento se documentaron lesiones pulmonares a las cuales se les practicó biopsia y el estudio anatomopatológico fue compatible con carcinoma escamocelular invasivo.

Abstract The incidence of squamous cell carcinoma of prostate is between 0.5-1% of all neoplastic lesions of this gland. Due to their rarity, there are no protocolised recommendations on the management of these patients. A report is presented on a patient with this diagnosis treated at our institution, its outcome at two years of follow-up, and a review of the subject. Case report: Male patient, 79 years old, diagnosed with invasive squamous cell carcinoma of the prostate. Staged as T4NxMx/IPSA 2.64/Gleason undeterminable. Work up studies were negative, and primaries from nearby organs were ruled out. He was treated with radiotherapy as monotherapy and was scheduled for an intensity-modulated radiotherapy (IMRT) technique, initially to the pelvis at a radiotherapy dose of 46 Gy 2Gy daily (PTV 1), further reinforcing prostate and vesicles up to 56 Gy (1.1 PTV), and finally to 76 Gy to prostate (PTV 1,1,1). With a follow-up of two years, lung lesions were found, which were biopsied and positive for squamous cell carcinoma.