The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA.

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.

Interobserver and Intraobserver Variability of Four Suprascapular Notch Classification Systems.

INTRODUCTION: Knowledge of the morphology of the suprascapular notch is clinically beneficial in patients with suspected suprascapular nerve compression or palsy. Several classification systems have been proposed for the morphological classification of the suprascapular notch and its several anatomical variations. The purpose of this study was to evaluate the inter- and intraobserver reliability of four different classification systems for suprascapular notch typing analysing shoulder computed tomography (CT) scans. METHODS: Shoulder CT scans from 109 subjects (71.5% males) were examined by three raters of various experience levels, one senior, one experienced, and one junior orthopaedic surgeon. The CT scans were evaluated quantitatively and qualitatively and the suprascapular notch was classified according to four classification systems at two separate timepoints, four weeks apart. To determine consistency among the same or different raters, the Kappa statistic was performed and intrarater reliability for each rater between the first and the second evaluation was assessed using Cohen's kappa. Reliability across all raters at each timepoint was assessed using the Fleiss kappa. RESULTS: Agreement was almost perfect for all the classification systems and amongst all raters, regardless of their experience level. There were no significant differences between the raters on any of the evaluations. The overall interobserver agreement for all classifications was almost perfect. CONCLUSION: The four suprascapular notch classification systems are reliable, and the rater's experience level has no impact on the evaluation.

Quantifying Bias in Hierarchical Category Systems.

Categorization is ubiquitous in human cognition and society, and shapes how we perceive and understand the world. Because categories reflect the needs and perspectives of their creators, no category system is entirely objective, and inbuilt biases can have harmful social consequences. Here we propose methods for measuring biases in hierarchical systems of categories, a common form of category organization with multiple levels of abstraction. We illustrate these methods by quantifying the extent to which library classification systems are biased in favour of western concepts and male authors. We analyze a large library data set including more than 3 million books organized into thousands of categories, and find that categories related to religion show greater western bias than do categories related to literature or history, and that books written by men are distributed more broadly across library classification systems than are books written by women. We also find that the Dewey Decimal Classification shows a greater level of bias than does the Library of Congress Classification. Although we focus on library classification as a case study, our methods are general, and can be used to measure biases in both natural and institutional category systems across a range of domains.

The Human Interference Scoring System (HISS): A New Tool for Quantifying Food Quality Based on Its Level of Processing.

The Human Interference Scoring System (HISS) is a novel food-based diet-quality-classification system based on the existing NOVA method. HISS involves food and fluid allocation into categories from digital imagery based on food processing levels, followed by meal plan analysis using food-servings quantification. The primary purpose of this work was to evaluate the reliability of HISS. Trained nutrition professionals analyzed digital photographs from five hypothetical 24 h food recalls and categorized foods into one of four HISS categories. A secondary purpose was to assess the nutrient composition of the food recalls and other selected foods from the HISS categories. Participants effectively categorized foods into HISS categories, with only minor discrepancies noted. High inter-rater reliability was observed in the outer HISS categories: unprocessed and ultra-processed foods. Ultra-processed items consistently displayed elevated energy, carbohydrates, and sugar compared to unprocessed foods, while unprocessed foods exhibited notably higher dietary fiber. This study introduces the HISS as a potentially useful tool for quantifying a food-quality-based system using digital-photography-based assessments. Its high inter-rater reliability and ability to capture relationships between food processing levels and nutrient composition make it a promising method for assessing dietary habits and food quality.

AIEgen-deep: Deep learning of single AIEgen-imaging pattern for cancer cell discrimination and preclinical diagnosis.

This study introduces AIEgen-Deep, an innovative classification program combining AIEgen fluorescent dyes, deep learning algorithms, and the Segment Anything Model (SAM) for accurate cancer cell identification. Our approach significantly reduces manual annotation efforts by 80%-90%. AIEgen-Deep demonstrates remarkable accuracy in recognizing cancer cell morphology, achieving a 75.9% accuracy rate across 26,693 images of eight different cell types. In binary classifications of healthy versus cancerous cells, it shows enhanced performance with an accuracy of 88.3% and a recall rate of 79.9%. The model effectively distinguishes between healthy cells (fibroblast and WBC) and various cancer cells (breast, bladder, and mesothelial), with accuracies of 89.0%, 88.6%, and 83.1%, respectively. Our method's broad applicability across different cancer types is anticipated to significantly contribute to early cancer detection and improve patient survival rates.

Determination of Nursing Care Times Based on the Perroca Patient Classification Instrument in the Inpatient Oncology Unit: A Mixed Method Study.

OBJECTIVES: The aim of this study was to determine the daily nursing care times of hospitalized inpatient oncology unit patients according to degree of acuity using the Perroca Patient Classification tool. DATA SOURCES: This study used a mixed method sequential explanatory design. The "Nursing Activity Record Form" and "Perroca Patient Classification Instrument" were used for quantitative data collection, and direct observation was performed for 175 hours via time-motion study. Descriptive statistics, between-group comparison, and correlation analysis were used for data analysis. Using a semistructured questionnaire, qualitative data were collected from individual in-depth interviews with seven nurses who participated in the quantitative part of the study. Qualitative data were analyzed by thematic analysis. The reporting of this study followed GRAMMS checklist. CONCLUSIONS: As a result of the integration of quantitative and qualitative data, daily nursing care duration was determined as 2 to 2.5 hours for Type 1 patients, 2.6 to 3.5 hours for Type 2 patients, 3.6 to 4.75 hours for Type 3 patients, and 4.76 to 5.5 hours for Type 4 patients. The findings showed that in an inpatient oncology unit, nursing care hours increased as patients' Perroca Patient Classification Instrument acuity grade increased; thus, the instrument was discriminative in determining patients' degree of acuity. IMPLICATIONS FOR NURSING PRACTICE: Nurse managers can utilize this study's results to plan daily assignments that are sensitive to patient care needs. The results can also help nurse managers to identify relationships between nurse staffing and patient outcomes at the unit level, as well as to develop ways to analyze such relationships.

Interobserver variability in thyroid ultrasound.

PURPOSE: Ultrasound evaluation of thyroid nodules is the preferred technique, but it is dependent on operator interpretation, leading to inter-observer variability. The current study aimed to determine the inter-physician consensus on nodular characteristics, risk categorization in the classification systems, and the need for fine needle aspiration puncture. METHODS: Four endocrinologists from the same center blindly evaluated 100 ultrasound images of thyroid nodules from 100 different patients. The following ultrasound features were evaluated: composition, echogenicity, margins, calcifications, and microcalcifications. Nodules were also classified according to ATA, EU-TIRADS, K-TIRADS, and ACR-TIRADS classifications. Krippendorff's alpha test was used to assess interobserver agreement. RESULTS: The interobserver agreement for ultrasound features was: Krippendorff's coefficient 0.80 (0.71-0.89) for composition, 0.59 (0.47-0.72) for echogenicity, 0.73 (0.57-0.88) for margins, 0.55 (0.40-0.69) for calcifications, and 0.50 (0.34-0.67) for microcalcifications. The concordance for the classification systems was 0.7 (0.61-0.80) for ATA, 0.63 (0.54-0.73) for EU-TIRADS, 0.64 (0.55-0.73) for K-TIRADS, and 0.68 (0.60-0.77) for K-TIRADS. The concordance in the indication of fine needle aspiration puncture (FNA) was 0.86 (0.71-1), 0.80 (0.71-0.88), 0.77 0.67-0.87), and 0.73 (0.64-0.83) for systems previously described respectively. CONCLUSIONS: Interobserver agreement was acceptable for the identification of nodules requiring cytologic study using various classification systems. However, limited concordance was observed in risk stratification and many ultrasonographic characteristics of the nodules.

Assessment of ultra processed foods consumption in Senegal: validation of the Nova-UPF screener.

BACKGROUND: Ultra-processed foods (UPF), as proposed by the Nova food classification system, are linked to the development of obesity and several non-communicable chronic diseases and deaths from all causes. The Nova-UPF screener developed in Brazil is a simple and quick tool to assess and monitor the consumption of these food products. The aim of this study was to adapt and validate, against the 24-hour dietary recall, this short food-based screener to assess UPF consumption in the Senegalese context. METHODS: The tool adaptation was undertaken using DELPHI methodology with national experts and data from a food market survey. Following the adaptation, sub-categories were renamed, restructured and new ones introduced. The validation study was conducted in the urban area of Dakar in a convenience sample of 301 adults, using as a reference the dietary share of UPF on the day prior to the survey, expressed as a percentage of total energy intake obtained via 24-hour recall. Association between the Nova-UPF score and the dietary share of UPF was evaluated using linear regression models. The Pabak index was used to assess the agreement in participants' classification according to quintiles of Nova-UPF score and quintiles of the dietary share of UPF. RESULTS: The results show a linear and positive association (p-value < 0.001) between intervals of the Nova-UPF score and the average dietary share of UPF. There was a near perfect agreement in the distribution of individuals according to score's quintiles and UPF dietary share quintiles (Pabak index = 0.84). CONCLUSION: The study concluded that the score provided by the Nova-UPF screener adapted to the Senegalese context is a valid estimate of UPF consumption.

Documentation and classification of hospital pharmacist interventions: A scoping review.

The practice of documenting pharmacist interventions (PIs) has been endorsed by many hospital pharmacists' societies and organizations worldwide. Current systems for recording PIs have been developed to generate data on better patient and healthcare outcomes, but harmonization and transferability are apparently minimal. The present work aims to provide a descriptive and comprehensive overview of the currently utilized PI documentation and classification tools contributing to increased evidence systematization. A systematic literature search was conducted in PubMed, Scopus, Web of Science and the Cumulative Index to Nursing and Allied Health Literature. Studies from 2008, after the release of the Basel Statements, were included if interventions were made by hospital or clinical pharmacists in a global hospital setting. Publications quality assessment was accomplished using the Mixed Methods Appraisal Tool. A total of 26 studies were included. Three studies did not refer to the documentation/classification method, 10 used an in-house developed documentation/classification method, seven used externally developed documentation/classification tools and six described method validation or translation. Evidence confirmed that most documentation/classification systems are designed in-house, but external development and validation of PI systems to be used in hospital practice is gradually increasing. Reports on validated PI documentation/classification tools that are being used in hospital clinical practice are limited, including in countries with advanced hospital pharmacy practice. Needs and gaps in practice were identified. Further research should be conducted to understand why using validated documentation/classification methods is not a disseminated practice, knowing patients' and organizational advantages.

State Categories, Bureaucracies of Displacement, and Possibilities from the Margins.

In this presidential address, I argue for the importance of state-created categories and classification systems that determine eligibility for tangible and intangible resources. Through classification systems based on rules and regulations that reflect powerful interests and ideologies, bureaucracies maintain entrenched inequality systems that include, exclude, and neglect. I propose adopting a critical perspective when using formalized categories in our work, which would acknowledge the constructed nature of those categories, their naturalization through everyday practices, and their misalignments with lived experiences. This lens can reveal the systemic structures that engender both enduring patterns of inequality and state classification systems, and reframe questions about the people the state sorts into the categories we use. I end with a brief discussion of the benefits that can accrue from expanding our theoretical repertoires by including knowledge produced in the Global South.

Long-Term outcomes in adult patients with congenital heart disease considered for transplantation: A single center study.

BACKGROUND: Adult congenital heart disease (ACHD) patients pose unique challenges in identifying the time for transplantation and factors influencing outcomes. OBJECTIVE: To identify hemodynamic, functional, and laboratory parameters that correlate with 1- and 10-year outcomes in ACHD patients considered for transplantation. METHODS: A retrospective chart review of long-term outcomes in adult patients with congenital heart disease (CHD) evaluated for heart or heart + additional organ transplant between 2004 and 2014 at our center was performed. A machine learning decision tree model was used to evaluate multiple clinical parameters correlating with 1- and 10-year survival. RESULTS: We identified 58 patients meeting criteria. D-transposition of the great arteries (D-TGA) with atrial switch operation (20.7%), tetralogy of Fallot/pulmonary atresia (15.5%), and tricuspid atresia (13.8%) were the most common diagnosis for transplant. Single ventricle patients were most likely to be listed for transplantation (39.8% of evaluated patients). Among a comprehensive list of clinical factors, invasive hemodynamic parameters (pulmonary capillary wedge pressure (PCWP), systemic vascular pressure (SVP), and end diastolic pressures (EDP) most correlated with 1- and 10-year outcomes. Transplanted patients with SVP < 14 and non- transplanted patients with PCWP < 15 had 100% survival 1-year post-transplantation. CONCLUSION: For the first time, our study identifies that hemodynamic parameters most strongly correlate with 1- and 10-year outcomes in ACHD patients considered for transplantation, using a data-driven machine learning model.

Characterization and Classification of Spatial White Matter Tract Alteration Patterns in Glioma Patients Using Magnetic Resonance Tractography: A Systematic Review and Meta-Analysis.

INTRODUCTION: Magnetic resonance (MR) tractography can be used to study the spatial relations between gliomas and white matter (WM) tracts. Various spatial patterns of WM tract alterations have been described in the literature. We reviewed classification systems of these patterns, and investigated whether low-grade gliomas (LGGs) and high-grade gliomas (HGGs) demonstrate distinct spatial WM tract alteration patterns. METHODS: We conducted a systematic review and meta-analysis to summarize the evidence regarding MR tractography studies that investigated spatial WM tract alteration patterns in glioma patients. RESULTS: Eleven studies were included. Overall, four spatial WM tract alteration patterns were reported in the current literature: displacement, infiltration, disruption/destruction and edematous. There was a considerable heterogeneity in the operational definitions of these terms. In a subset of studies, sufficient homogeneity in the classification systems was found to analyze pooled results for the displacement and infiltration patterns. Our meta-analyses suggested that LGGs displaced WM tracts significantly more often than HGGs (n = 259 patients, RR: 1.79, 95% CI [1.14, 2.79], I2 = 51%). No significant differences between LGGs and HGGs were found for WM tract infiltration (n = 196 patients, RR: 1.19, 95% CI [0.95, 1.50], I2 = 4%). CONCLUSIONS: The low number of included studies and their considerable methodological heterogeneity emphasize the need for a more uniform classification system to study spatial WM tract alteration patterns using MR tractography. This review provides a first step towards such a classification system, by showing that the current literature is inconclusive and that the ability of fractional anisotropy (FA) to define spatial WM tract alteration patterns should be critically evaluated. We found variations in spatial WM tract alteration patterns between LGGs and HGGs, when specifically examining displacement and infiltration in a subset of the included studies.

Antiracist Structural Intervention at the Emory University Institutional Review Board.

Although racial and ethnic categories are social constructs without inherent biologic or genetic meaning, race and ethnicity impact health outcomes through racism. The use of racial categories in biomedical research often misattributes the cause of health inequities to genetic and inherent biological differences rather than to racism. Improving research practices around race and ethnicity is an urgent priority and requires education as well as structural change. We describe an evidence-based intervention for an institutional review board (IRB). Our IRB now requires all biomedical study protocols to define racial and ethnic classifications they plan to use, to state whether they are describing or explaining differences between groups, and to provide justification for any use of racial or ethnic group variables as covariates. This antiracist IRB intervention is an example of how research institutions can help ensure the scientific validity of studies and avoid the unscientific reification of race and ethnicity as inherently biological or genetic concepts.

BILE: A Literature Review Based Novel Clinical Classification and Treatment Algorithm of Iatrogenic Bile Duct Injuries.

PURPOSES: The management of patients with iatrogenic bile duct injuries (IBDI) is a challenging field, often with dismal medico legal projections. Attempts to classify IBDI have been made repeatedly and the final results were either analytical and extensive but not useful in everyday clinical practice systems, or simple and user friendly but with limited clinical correspondence approaches. The purpose of the present review is to propose a novel, clinical classification system of IBDI by reviewing the relevant literature. METHODS: A systematic literature review was conducted by performing bibliographic searches in the available electronic databases, including PubMed, Scopus, and the Cochrane Library. RESULTS: Based on the literature results, we propose a five (5) stage (A, B, C, D and E) classification system for IBDI (BILE Classification). Each stage is correlated with the recommended and most appropriate treatment. Although the proposed classification scheme is clinically oriented, the anatomical correspondence of each IBDI stage has been incorporated as well, using the Strasberg classification. CONCLUSIONS: BILE classification represents a novel, simple, and dynamic in nature classification system of IBDI. The proposed classification focuses on the clinical consequences of IBDI and provides an action map that can appropriately guide the treatment plan.

Classification and Diagnosis of Temporomandibular Disorders and Temporomandibular Disorder Pain.

Designing classification systems and developing diagnostic criteria for temporomandibular disorders is difficult. An appreciation of the utility and applicability of these entities requires an understanding of the importance of each, the differences between the two, and how they may be optimally operationalized for both clinical and research activities in light of their inherent advantages and limitations. In addition, consideration for adopting newer approaches, such as following ontological and precision-based medicine principles, accounting for genetics/epigenetic and neurobiological factors, and the inclusion of biomarkers will potentially result in more thorough and comprehensive classification systems and diagnostic criteria.

[Femoral neck fractures]. / Schenkelhalsfrakturen.

Femoral neck fractures (FNF) are the most frequent fractures in the older population and are also of high socioeconomic importance due to the high risk of mortality. The diagnostics are based on the clinical examination and imaging procedures. The classification systems used in the routine clinical practice are oriented towards the prognosis and are therefore a valuable aid in making decisions for the selection of the treatment procedure. Early surgery is decisive for the success of treatment. Older patients (> 60 years) with arthritically damaged hips and a high degree of fracture dislocation benefit from prompt hip replacement (bipolar systems, total hip arthroplasty, dual mobility systems). In contrast, joint-preserving surgery by osteosynthesis is indicated in younger patients with a low degree of dislocation. This article summarizes the clinically relevant aspects of FNF and gives an overview of current treatment strategies with inclusion of the scientific literature.

Comparison of Interobserver Agreement of Four Classification Systems for Lateral Clavicle Fractures between Two Groups of Surgeons: A Multicenter Study.

OBJECTIVE: Distal clavicle fracture classification directly affects the treatment decisions. It is unclear whether the classification systems implemented differ depending on surgeons' backgrounds. This study aimed to compare the interobserver agreement of four classification systems used for lateral clavicle fractures by shoulder specialists and general trauma surgeons. METHODS: Radiographs of 20 lateral clavicle fractures representing a full spectrum of adult fracture patterns were analyzed by eight experienced shoulder specialists and eight general trauma surgeons from 10 different hospitals. All cases were graded according to the Orthopedic Trauma Association (OTA), Neer, Jäger/Breitner, and Gongji classification systems. To measure observer agreement, Fleiss' kappa coefficient (κ) was applied and assessed. RESULTS: When only X-ray films were presented, both groups achieved fair agreement. However, when the 3D-CT scan images were provided, improved interobserver agreement was found in the specialist group when the OTA, Jäger/Breitner, and Gongji classification systems were used. In the generalist groups, improved agreement was found when using the Gongji classification system. In terms of interobserver reliability, the OTA, Neer, and Jäger/Breitner classification systems showed better agreement among shoulder specialists, while a slightly lower level of agreement was found using the Gongji classification system. For the OTA classification system, interobserver agreement had a mean kappa value of 0.418, ranging from 0.446 (specialist group) to 0.402 (generalist group). For the Neer classification system, interobserver agreement had a mean kappa value of 0.368, ranging from 0.402 (specialist group) to 0.390 (generalist group). For the Jäger/Breitner classification system, the inter-observer agreement had a mean kappa value of 0.380, ranging from 0.413 (specialist group) to 0.404 (generalist group). For the Gongji classification system, interobserver agreement had a mean kappa value of 0.455, ranging from 0.480 (specialist group) to 0.485 (generalist group). CONCLUSION: Generally speaking, 3D-CT scans provide a richer experience that can lead to better results in most classification systems of lateral clavicle fractures, highlighting the value of digitization and specialization in diagnosis and treatment. Competitive interobserver agreement was exhibited in the generalist group using the Gongji classification system, suggesting that the Gongji classification is suitable for general trauma surgeons who are not highly experienced in the shoulder field.

Deep Neuro-Fuzzy System application trends, challenges, and future perspectives: a systematic survey.

Deep neural networks (DNN) have remarkably progressed in applications involving large and complex datasets but have been criticized as a black-box. This downside has recently become a motivation for the research community to pursue the ideas of hybrid approaches, resulting in novel hybrid systems classified as deep neuro-fuzzy systems (DNFS). Studies regarding the implementation of DNFS have rapidly increased in the domains of computing, healthcare, transportation, and finance with high interpretability and reasonable accuracy. However, relatively few survey studies have been found in the literature to provide a comprehensive insight into this domain. Therefore, this study aims to perform a systematic review to evaluate the current progress, trends, arising issues, research gaps, challenges, and future scope related to DNFS studies. A study mapping process was prepared to guide a systematic search for publications related to DNFS published between 2015 and 2020 using five established scientific directories. As a result, a total of 105 studies were identified and critically analyzed to address research questions with the objectives: (i) to understand the concept of DNFS; (ii) to find out DNFS optimization methods; (iii) to visualize the intensity of work carried out in DNFS domain; and (iv) to highlight DNFS application subjects and domains. We believe that this study provides up-to-date guidance for future research in the DNFS domain, allowing for more effective advancement in techniques and processes. The analysis made in this review proves that DNFS-based research is actively growing with a substantial implementation and application scope in the future.

Validation of the Thumbs food classification system as a tool to accurately identify the healthiness of foods.

The Thumbs food classification system was developed to assist remote Australian communities to identify food healthiness. This study aimed to assess: (1) the Thumbs system's alignment to two other food classification systems, the Health Star Rating (HSR) and the Northern Territory School Canteens Guidelines (NTSCG); (2) its accuracy in classifying 'unhealthy' (contributing to discretionary energy and added sugars) and 'healthy' products against HSR and NTSCG; (3) areas for optimisation. Food and beverage products sold between 05/2018 and 05/2019 in fifty-one remote stores were classified in each system. System alignment was assessed by cross-tabulating percentages of products, discretionary energy and added sugars sold assigned to the same healthiness levels across the systems. The system/s capturing the highest percentage of discretionary energy and added sugars sold in 'unhealthy' products and the lowest levels in 'healthy' products were considered the best performing. Cohen's κ was used to assess agreement between the Thumbs system and the NTSCG for classifying products as healthy. The Thumbs system classified product healthiness in line with the HSR and NTSCG, with Cohen's κ showing moderate agreement between the Thumbs system and the NTSCG (κ = 0·60). The Thumbs system captured the most discretionary energy sold (92·2 %) and added sugar sold (90·6 %) in unhealthy products and the least discretionary energy sold (0 %) in healthy products. Modifications to optimise the Thumbs system include aligning several food categories to the NTSCG criteria and addressing core/discretionary classification discrepancies of fruit juice/drinks. The Thumbs system offers a classification algorithm that could strengthen the HSR system.

How should we describe complications and stratify error in the treatment of facial fractures? A systematic review of the literature.

Oral and maxillofacial (OMFS) facial fractures account for approximately 5%-10% of presentations to emergency departments in the UK. Although most trauma is treated operatively, different methods of surgery exist for the same clinical presentation and non- surgical management is in some cases appropriate. Analysis of patient morbidity is an essential component of clinical governance in surgery. OMFS units in the UK should hold regular morbidity and mortality (M&M) meetings, but no consensus exists for which cases should be discussed. For example, most units focus only on cases treated surgically, primarily unexpected returns to theatre. Finally, there is no agreed structure for describing how complications occur and a focus on terms such as error. The aim of this review is to help inform which patients should be discussed in M&M meetings based on existing scoring systems. A systematic review of the literature has been undertaken using the Preferred Reporting in Systematic Reviews and Meta-Analysis methodology. Databases searched were PubMed and Science Direct. Eleven unique papers and a companion article met the criteria and were analysed. Many M&M classification systems exist, but these systems are unsuited for maxillofacial purposes. There is a need for a novel system which is tailored to the specialty.