3D genomic mapping reveals multifocality of human pancreatic precancers.

Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.

Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions.

Pancreatic intraepithelial neoplasia (PanIN) is a precursor to pancreatic cancer and represents a critical opportunity for cancer interception. However, the number, size, shape, and connectivity of PanINs in human pancreatic tissue samples are largely unknown. In this study, we quantitatively assessed human PanINs using CODA, a novel machine-learning pipeline for 3D image analysis that generates quantifiable models of large pieces of human pancreas with single-cell resolution. Using a cohort of 38 large slabs of grossly normal human pancreas from surgical resection specimens, we identified striking multifocality of PanINs, with a mean burden of 13 spatially separate PanINs per cm3 of sampled tissue. Extrapolating this burden to the entire pancreas suggested a median of approximately 1000 PanINs in an entire pancreas. In order to better understand the clonal relationships within and between PanINs, we developed a pipeline for CODA-guided multi-region genomic analysis of PanINs, including targeted and whole exome sequencing. Multi-region assessment of 37 PanINs from eight additional human pancreatic tissue slabs revealed that almost all PanINs contained hotspot mutations in the oncogene KRAS, but no gene other than KRAS was altered in more than 20% of the analyzed PanINs. PanINs contained a mean of 13 somatic mutations per region when analyzed by whole exome sequencing. The majority of analyzed PanINs originated from independent clonal events, with distinct somatic mutation profiles between PanINs in the same tissue slab. A subset of the analyzed PanINs contained multiple KRAS mutations, suggesting a polyclonal origin even in PanINs that are contiguous by rigorous 3D assessment. This study leverages a novel 3D genomic mapping approach to describe, for the first time, the spatial and genetic multifocality of human PanINs, providing important insights into the initiation and progression of pancreatic neoplasia.

Determinantes do contexto familiar relacionados ao cuidado das crianças prematuras, segundo o modelo bioecológico / Determinants of the family context related to the care of premature children, according to the bioecological model

Resumo: Trata-se de um estudo qualitativo, descritivo, do tipo estudo de casos múltiplos, embasado no referencial metodológico de Yin, que teve como objetivo descrever os determinantes do contexto familiar relacionados ao cuidado de crianças prematuras, segundo o Modelo Bioecológico. Realizado em um município do Estado do Paraná, Brasil, entre setembro de 2021 e março de 2022, com famílias de crianças prematuras egressas da unidade neonatal, até um ano de idade corrigida, que realizaram o acompanhamento de crescimento e desenvolvimento no ambulatório de puericultura da instituição de saúde selecionada para este estudo. Obteve-se a participação de 18 famílias. A coleta de evidências ocorreu por meio de entrevistas on-line, e utilizou-se ferramentas como genogramas e ecomapas que ajudaram, de forma sistemática e organizada, a ampliar o conhecimento do contexto familiar, sua estrutura, forças e recursos. Na organização dos dados, utilizou -se o Software Web Qualitative Data Analysis, para posteriormente serem analisados à luz do marco teórico do Modelo Bioecológico de Urie Bronfenbrenner. Da análise, emergiram duas categorias temáticas que explicitam a influência bidirecional e sinergia entre a criança em desenvolvimento e o seu contexto. A categoria organização do sistema familiar, contempla a composição, características biopsicossociais, organização e funcionamento do sistema familiar. A segunda categoria, recursos do sistema familiar, compreende o acesso a serviços públicos, bens materiais e econômicos da família, além do estabelecimento da rede de apoio social como recurso para o cuidado da criança prematura. Ao estudar o contexto familiar no seu ambiente mais íntimo e próximo à criança, foi possível perceber o impacto da prematuridade como situação vital no curso de vida, na dinâmica da família e no processo de construção do papel parental; ao mesmo tempo, a exploração das interações com outros microssistemas e o núcleo familiar permitiu o reconhecimento dos múltiplos aspectos do contexto que se tornaram determinantes para facilitar ou dificultar o cuidado infantil, desde a gravidez, o nascimento e após a alta da unidade neonatal. Nessa perspectiva, esta abordagem disponibiliza uma visão ecologicamente válida que permite identificar aqueles determinantes potencialmente modificáveis, subsidiando informações relevantes para os profissionais da saúde priorizar e orientar os cuidados e suporte social, com vista a propor e manter contextos saudáveis e promotores do bem-estar da família, a saúde e o desenvolvimento integral das crianças prematuras.

Abstract: This is, a qualitative, a descriptive multiple-case study grounded in Yin's methodological framework, which aimed to describe the family context determinants related to the care of preterm babies, according to the Bioecological Model. It was conducted in a municipality of Parana State, Brazil, between september 2021 and march 2022, with families of infant preterm, whose were discharged from a neonatal unit, children until one year of corrected age and, whose growth and development were followed up at the childcare outpatient unit of the healthcare institution selected for this study. 18 families participated in the study. Data collection was carried out by means of online interviews, and some tools were used, such as genograms and ecomaps, which helped, in a systematic and organized way, to expand knowledge of the family context, its structure, strengths and resources. For data organization, the Web Qualitative Data Analysis, Software, was used for further data analysis in light of the Bioecological Model by Urie Bronfenbrenner. From the analysis, two thematic categories emerged, which clarified the bidirectional influence and synergy between the developing child and his/her context. The family system organization category, contemplates the composition, biopsychosocial characteristics, organization and functioning of the family system. The second category, family system resources, comprises the access to public services, family's material and economic resources, apart from the establishment of a social support network as a resource to take care of the premature child. By studying the family context in its inner and closest environment to the child, it was possible to perceived the impact of prematurity as a vital situation in the course of life, in the dynamics of the family and in the process of building the parental role; at the same time, the exploration of interaction with other microsystems and the nuclear family enabled the recognition of the multiple aspects of the context that became determinants to facilitate or hinder child care, from pregnancy, birth and after discharge from the neonatal unit. In this perspective, this approach provides an ecologically valid view, that allows to identify those potentially modifiable determinants, underpinning relevant information for health care professionals to be able to prioritize and guide care and social support, in order to propose and keep healthy contexts, which promote the well-being of the family, health and integral development of premature children.

The Association of Gender and Mortality in Geriatric Trauma Patients.

The association of gender with mortality in trauma remains a subject of debate. Geriatric trauma patients have a higher risk of mortality compared to younger patients. We sought to evaluate the association of gender with mortality in a group of geriatric trauma patients presenting to an academic level 1 trauma center (trauma center designated by New York State capable of handling the most severe injuries and most complex cases). METHODS: We performed a retrospective review of geriatric trauma patients who were admitted to our trauma center between January 2018 and December 2020. Data collected included vital signs, demographics, injury, and clinical characteristics, laboratory data and outcome measures. The study controlled for co-morbidities, injury severity score (ISS), and systolic blood pressure (SBP) in the ED. Multivariable logistic regression analysis was performed to evaluate the association of gender and mortality. RESULTS: 4432 geriatric patients were admitted during the study period, there were 1635 (36.9%) men and 3859 (87.2%) were White with an average age of 81 ± 8.5 years. The mean ISS was 6.7 ± 5.4 and average length of stay was 6 ± 6.3 days. There were 165 deaths. Male gender (OR 1.94, 95% CI 1.38 to 2.73), ISS (OR 1.12, 95% CI 1.09 to 1.14), Emergency Department SBP less than 90 mmHg (OR 6.17, 95% CI 3.17 to 12.01), and having more than one co-morbidity (OR 2.28, 95% CI 1.55 to 3.35) were independently predictive of death on multivariable logistic regression analysis. CONCLUSION: Male gender, Emergency Department systolic blood pressure less than 90 mmHg, having more than one co-morbidity, and injury severity are independent predictors of mortality among geriatric trauma patients.

Exhaled VOCs can discriminate subjects with COVID-19 from healthy controls.

COVID-19 detection currently relies on testing by reverse transcription polymerase chain reaction (RT-PCR) or antigen testing. However, SARS-CoV-2 is expected to cause significant metabolic changes in infected subjects due to both metabolic requirements for rapid viral replication and host immune responses. Analysis of volatile organic compounds (VOCs) from human breath can detect these metabolic changes and is therefore an alternative to RT-PCR or antigen assays. To identify VOC biomarkers of COVID-19, exhaled breath samples were collected from two sample groups into Tedlar bags: negative COVID-19 (n= 12) and positive COVID-19 symptomatic (n= 14). Next, VOCs were analyzed by headspace solid phase microextraction coupled to gas chromatography-mass spectrometry. Subjects with COVID-19 displayed a larger number of VOCs as well as overall higher total concentration of VOCs (p< 0.05). Univariate analyses of qualified endogenous VOCs showed approximately 18% of the VOCs were significantly differentially expressed between the two classes (p< 0.05), with most VOCs upregulated. Machine learning multivariate classification algorithms distinguished COVID-19 subjects with over 95% accuracy. The COVID-19 positive subjects could be differentiated into two distinct subgroups by machine learning classification, but these did not correspond with significant differences in number of symptoms. Next, samples were collected from subjects who had previously donated breath bags while experiencing COVID-19, and subsequently recovered (COVID Recovered subjects (n= 11)). Univariate and multivariate results showed >90% accuracy at identifying these new samples as Control (COVID-19 negative), thereby validating the classification model and demonstrating VOCs dysregulated by COVID are restored to baseline levels upon recovery.

Lived Experiences of Hospitalized COVID-19 Patients: A Qualitative Study.

The COVID-19 pandemic has resulted in many hospitalized patients and deaths worldwide. Coronavirus patients were isolated from their relatives and visits were banned to prevent contagion. This has brought about a significant change in deeply rooted care habits in Mediterranean and Latin American countries where the family normally accompanies vulnerable hospitalized patients. The aim of this qualitative study was to examine the hospitalization experience of COVID-19 patients and their family members. A phenomenological qualitative approach was used. Data collection included inductive, in-depth interviews with 11 COVID-19 hospitalized patients. The mean age of patients was 55.4 years and 45% were female. Nearly 50% required Intensive Care Unit (ICU) admission. Ten meaningful statements were identified and grouped in three themes: Positive and negative aspects of the care provided, the patient's perspective, and perception of the experience of the disease. In conclusion, COVID-19 patients, aware of the severity of the pandemic, were very adaptable to the situation and had full confidence in health professionals. Patient isolation was perceived as necessary. Technology has helped to maintain communication between patients and relatives.

Experiences of nursing students as healthcare aid during the COVID-19 pandemic in Spain: A phemonenological research study.

BACKGROUND: The coronavirus disease (COVID-19) pandemic has caused a worldwide health and social crisis directly impacting the healthcare system. Hospitals had to rearrange its structure to meet clinical needs. Spain has been experiencing a shortage of working nurses. Student nurses in their last year at university were employed to help the National Health System respond to the COVID-19 crisis. AIM: The aim of this study was to explore and understand the experience of nursing students' roles as healthcare aid in responding to the COVID-19 crisis. METHODS: A qualitative phenomenology design was used to explore undergraduate nursing students' perceptions of their experiences as HAs during the COVID-19 outbreak. Open face-to-face interviews were conducted to nursing students (n = 10) in May 2020. Data was analyzed using the hermeneutic interpretative approach. RESULTS: All participants were women aged between 21 and 25 years. Seven main themes emerged: learning, ambivalent emotions and adaptation were classified at a personal level; teamwork, patient communication, and unclear care processes were categorized under hospital structure; and coping mechanisms were part of external factors. CONCLUSIONS: Orientation, follow-up, and emotional support in crisis situations are key to unexperienced healthcare workers overcoming stressful emotions. Previous academic education and training may help novice future nurses feel more confident about their tasks and responsibilities as well as improve patient outcomes, resource management, and staff safety.

Detection of Volatile Organic Compounds (VOCs) in Urine via Gas Chromatography-Mass Spectrometry QTOF to Differentiate Between Localized and Metastatic Models of Breast Cancer.

Breast cancer is the most common cancer detected in women and current screening methods for the disease are not sensitive. Volatile organic compounds (VOCs) include endogenous metabolites that provide information about health and disease which might be useful to develop a better screening method for breast cancer. The goal of this study was to classify mice with and without tumors and compare tumors localized to the mammary pad and tumor cells injected into the iliac artery by differences in VOCs in urine. After 4T1.2 tumor cells were injected into BALB/c mice either in the mammary pad or into the iliac artery, urine was collected, VOCs from urine headspace were concentrated by solid phase microextraction and results were analyzed by gas chromatography-mass spectrometry quadrupole time-of-flight. Multivariate and univariate statistical analyses were employed to find potential biomarkers for breast cancer and metastatic breast cancer in mice models. A set of six VOCs classified mice with and without tumors with an area under the receiver operator characteristic (ROC AUC) of 0.98 (95% confidence interval [0.85, 1.00]) via five-fold cross validation. Classification of mice with tumors in the mammary pad and iliac artery was executed utilizing a different set of six VOCs, with a ROC AUC of 0.96 (95% confidence interval [0.75, 1.00]).

Adverse events in critical care: Search and active detection through the Trigger Tool.

AIM: To investigate the incidence of disadvantageous events by using the Global Trigger Tool in an intensive care unit (ICU). METHODS: A retrospective descriptive study was performed in a 12-bed university ICU in the city of Medellin, Colombia. Clinical charts of hospitalized patients were reviewed, between January 1 and December 31, 2016, with the following inclusion criteria: subjects aged over 18 years, with at least 24 h of hospitalization and who had a complete medical history that could be accessed. Interventions: Trained reviewers conducted a retrospective examination of medical charts searching for clue events that elicit investigation, in order to detect an unfavorable event. Measurements: Information was processed through SPSS software version 21; for numerical variables, the mean was reported with standard deviation (SD). Percentages were calculated for qualitative variables. RESULTS: Two hundred and forty-four triggers occurred, with 82.4% of subjects having presented with at least one and an average of 3.37 (SD 3.47). A total of 178 adverse events (AEs) took place in 48 individuals, with an incidence of 52.1%. On average, four events per patient were recorded, and for each unfortunate event, 1.98 triggers were presented. The most frequent displeasing issues were: pressure ulcers (17.6%), followed by complications or reactions to medical devices (4.3%), and lacerations or skin defects (3.7%); the least frequent was delayed diagnosis or treatment (0.56%). Thirty-eight point four percent of mishap events caused temporary damage that required intervention, and 48.9% of AEs were preventable. Comparison between AEs and admission diagnoses found that hypertension and sepsis were the only diagnoses that had statistical significance (P = 0.042 and 0.022, respectively). CONCLUSION: Almost half of the unfavorable issues were classified as avoidable, which leaves a very wide field of work in terms of preventative activities.

Preferential host switching and its relation with Hantavirus diversification in South America.

In recent years, the notion of co-speciation between Hantavirus species and their hosts was discarded in favour of a more likely explanation: preferential host switching. However, the relative importance of this last process in shaping the evolutionary history of hantaviruses remains uncertain, given the present limited knowledge not only of virus-host relationships but also of the pathogen and reservoir phylogenies. In South America, more than 25 hantavirus genotypes were detected; several of them act as aetiological agents of hantavirus pulmonary syndrome (HPS). An understanding of the diversity of hantaviruses and of the processes underlying host switching is critical since human cases of HPS are almost exclusively the result of human-host interactions. In this study, we tested if preferential host switching is the main process driving hantavirus diversification in South America, by performing a co-phylogenetic analysis of the viruses and their primary hosts. We also suggest a new level of amino acid divergence to define virus species in the group. Our results indicate that preferential host switching would not be the main process driving virus diversification. The historical geographical proximity among rodent hosts emerges as an alternative hypothesis to be tested.

Species delimitation in the continental forms of the genus Epicrates (Serpentes, Boidae) integrating phylogenetics and environmental niche models.

Until recently, the genus Epicrates (Boidae) presented only one continental species, Epicrates cenchria, distributed in Central and South America, but after a taxonomic revision using morphologic characters five species were recognized: E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi. We analyzed two independent data sets, environmental niche models and phylogeny based on molecular information, to explore species delimitation in the continental species of this genus. Our results indicated that the environmental requirements of the species are different; therefore there are not evidences of ecological interchangeability among them. There is a clear correlation between species distributions and the major biogeographic regions of Central and South America. Their overall distribution reveals that allopatry or parapatry is the general pattern. These evidences suggest that habitat isolation prevents or limits gene exchange among them. The phylogenetic reconstruction showed that the continental Epicrates are monophyletic, being E. alvarezi the sister species for the remaining two clades: E. crassus-E. assisi, and E. maurus-E. cenchria. The clade grouping the continental Epicrates is the sister taxon of the genus Eunectes and not of the Caribbean Epicrates clade, indicating that the genus is paraphyletic. There is a non-consistent pattern in niche evolution among continental Epicrates. On the contrary, a high variation and abrupt shifts in environmental variables are shown when ancestral character states were reconstructed on the sequence-based tree. The degree of genetic and ecological divergence among continental Epicrates and the phylogenetic analyses support the elevation to full species of E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi.

Isolation of Helicobacter pylori in gastric mucosa and susceptibility to five antimicrobial drugs in Southern Chile

Helicobacter pylori colonizes more than 50 percent of the world population thus, it is considered an important cause of gastric cancer. The aim of this study was to determine the isolation frequency of H. pylori in Southern Chile from patients with symptomatology compatible with gastritis or gastric ulcer and to correlate these findings with demographic parameters of infected patients and the susceptibility profiles of the isolated strains to the antimicrobial drugs used in the eradication treatments. A total of 240 patients were enrolled in the study. Each gastric biopsy was homogenized and seeded onto blood agar plates containing a selective antibiotics mixture (DENT supplement). Plates were incubated at 37° C in a microaerophilic environment for five days. The susceptibility profiles to amoxicillin, ciprofloxacin, clarithromycin, tetracycline and metronidazole were determined using the E-test method. H. pylori was isolated from 99 patients (41.3 percent) with slightly higher frequency in female (42 percent positive cultures) than male (40.2 percent positive cultures). With regard to age and educational level, the highest isolation frequencies were obtained in patients between 21-30 (55 percent) and 41-50 (52.6 percent) years old, and patients with secondary (43.9 percent) and university (46.2 percent) educational levels. Nineteen (21.6 percent) strains showed resistance to at least one antimicrobial drug. Tetracycline was the most active antimicrobial in vitro, whereas metronidazole was the less active. One strain (5.3 percent) showed resistance to amoxicillin, clarithomycin and metronidazole, simultaneously.

Isolation of Helicobacter pylori in gastric mucosa and susceptibility to five antimicrobial drugs in Southern chile.

Helicobacter pylori colonizes more than 50% of the world population thus, it is considered an important cause of gastric cancer. The aim of this study was to determine the isolation frequency of H. pylori in Southern Chile from patients with symptomatology compatible with gastritis or gastric ulcer and to correlate these findings with demographic parameters of infected patients and the susceptibility profiles of the isolated strains to the antimicrobial drugs used in the eradication treatments. A total of 240 patients were enrolled in the study. Each gastric biopsy was homogenized and seeded onto blood agar plates containing a selective antibiotics mixture (DENT supplement). Plates were incubated at 37° C in a microaerophilic environment for five days. The susceptibility profiles to amoxicillin, ciprofloxacin, clarithromycin, tetracycline and metronidazole were determined using the E-test method. H. pylori was isolated from 99 patients (41.3%) with slightly higher frequency in female (42% positive cultures) than male (40.2% positive cultures). With regard to age and educational level, the highest isolation frequencies were obtained in patients between 21-30 (55%) and 41-50 (52.6%) years old, and patients with secondary (43.9%) and university (46.2%) educational levels. Nineteen (21.6%) strains showed resistance to at least one antimicrobial drug. Tetracycline was the most active antimicrobial in vitro, whereas metronidazole was the less active. One strain (5.3%) showed resistance to amoxicillin, clarithomycin and metronidazole, simultaneously.