Sampling complex social and behavioral phenomena.

We comment on the limits of relying on prior literature when constructing the design space for an integrative experiment; the adaptive nature of social and behavioral phenomena and the implications for the use of theory and modeling when constructing the design space; and on the challenges of measuring random errors and lab-related biases in measurement without replication.

Household air pollution and pneumococcal density related to nasopharyngeal inflammation in mothers and children in Ethiopia: A cross-sectional study.

BACKGROUND: Three billion people in low- and middle-income countries are exposed to household air pollution as they use biomass fuel for cooking. We investigated the associations between solid fuel use and nasopharyngeal (NP) inflammation, as well as the associations between high pneumococcal density and NP inflammation, in mothers and children in rural and urban Ethiopia. MATERIALS AND METHODS: Sixty pairs of mothers (median age, 30 years; range, 19-45 years) with a child (median age, 9 months; range, 1-24 months) were included from rural Butajira (n = 30) and urban Addis Ababa (n = 30) in Ethiopia. The cohort was randomly selected from a previous study of 545 mother/child pairs included 2016. Questionnaire-based data were collected which included fuel type used (solid: wood, charcoal, dung or crop waste; cleaner: electricity, liquefied petroleum gas). Nasopharyngeal (NP) samples were collected from all mothers and children and analyzed for the levels of 18 cytokines using a Luminex immunoassay. Pneumococcal DNA densities were measured by a real-time multiplex PCR and a high pneumococcal density was defined as a cyclic threshold (Ct) value ≤ 30. RESULTS: Mothers from rural areas had higher median CXCL8 levels in NP secretions than those from urban areas (8000 versus 1900 pg/mL; p < 0.01), while rural children had slightly higher IL-10 levels than those from the urban area (26 vs 13 pg/mL; p = 0.04). No associations between fuel type and cytokine levels were found. However, a high pneumococcal density was associated with higher levels of cytokines in both mothers (CCL4, CXCL8, IL-1ß, IL-6 and VEGF-A) and children (CCL4, CXCL8, IL-1ß, IL-6 and IL-18). CONCLUSIONS: No significant associations were found between solid fuel use and NP inflammation in Ethiopian mothers and children, but the inflammatory activity was higher in individuals living in the rural compared to the urban area. In addition, high cytokine levels were associated with high pneumococcal density in both mothers and children, indicating a significant impact of NP pathogens on inflammatory mediator levels in upper airways.

Cross-cultural adaption and inter-rater reliability of the Swedish version of the updated clinical frailty scale 2.0.

BACKGROUND: Worldwide, there is a large and growing group of older adults. Frailty is known as an important discriminatory factor for poor outcomes. The Clinical Frailty Scale (CFS) has become a frequently used frailty instrument in different clinical settings and health care sectors, and it has shown good predictive validity. The aims of this study were to describe and validate the translation and cultural adaptation of the CFS into Swedish (CFS-SWE), and to test the inter-rater reliability (IRR) for registered nurses using the CFS-SWE. METHODS: An observational study design was employed. The ISPOR principles were used for the translation, linguistic validation and cultural adaptation of the scale. To test the IRR, 12 participants were asked to rate 10 clinical case vignettes using the CFS-SWE. The IRR was assessed using intraclass correlation and Krippendorff's alpha agreement coefficient test. RESULTS: The Clinical Frailty Scale was translated and culturally adapted into Swedish and is presented in its final form. The IRR for all raters, measured by an intraclass correlation test, resulted in an absolute agreement value among the raters of 0.969 (95% CI: 0.929-0.991) and a consistency value of 0.979 (95% CI: 0.953-0.994), which indicates excellent reliability. Krippendorff's alpha agreement coefficient for all raters was 0.969 (95% CI: 0.917-0.988), indicating near-perfect agreement. The sensitivity of the reliability was examined by separately testing the IRR of the group of specialised registered nurses and non-specialised registered nurses respectively, with consistent and similar results. CONCLUSION: The Clinical Frailty Scale was translated, linguistically validated and culturally adapted into Swedish following a well-established standard technique. The IRR was excellent, judged by two established, separately used, reliability tests. The reliability test results did not differ between non-specialised and specialised registered nurses. However, the use of case vignettes might reduce the generalisability of the reliability findings to real-life settings. The CFS has the potential to be a common reference tool, especially when older adults are treated and rehabilitated in different care sectors.

Beyond collective intelligence: Collective adaptation.

We develop a conceptual framework for studying collective adaptation in complex socio-cognitive systems, driven by dynamic interactions of social integration strategies, social environments and problem structures. Going beyond searching for 'intelligent' collectives, we integrate research from different disciplines and outline modelling approaches that can be used to begin answering questions such as why collectives sometimes fail to reach seemingly obvious solutions, how they change their strategies and network structures in response to different problems and how we can anticipate and perhaps change future harmful societal trajectories. We discuss the importance of considering path dependence, lack of optimization and collective myopia to understand the sometimes counterintuitive outcomes of collective adaptation. We call for a transdisciplinary, quantitative and societally useful social science that can help us to understand our rapidly changing and ever more complex societies, avoid collective disasters and reach the full potential of our ability to organize in adaptive collectives.

SAUNA QB - Array: The realization of a new concept in radioxenon detection.

We introduce a new concept in radioxenon detection - the radioxenon Array, defined as a system where air sampling and activity measurement is performed at multiple locations, using measurement units that are less sensitive, but on the other hand less costly, and easier to install and operate, compared to current state-of-the-art radioxenon systems. The inter-unit distance in the Array is typically hundreds of kilometres. Using synthetic nuclear explosions together with a parametrized measurement system model, we argue that, when such measurement units are combined into an Array, the aggregated verification performance (detection, location, and characterization) can be high. The concept has been realized by developing a measurement unit named SAUNA QB, and the world's first radioxenon Array is now operating in Sweden. The operational principles and performance of the SAUNA QB and the Array is described, and examples of first measured data are presented, indicating a measurement performance according to expectations.

Interobserver reproducibility of cribriform cancer in prostate needle biopsies and validation of International Society of Urological Pathology criteria.

AIMS: There is strong evidence that cribriform morphology indicates a worse prognosis of prostatic adenocarcinoma. Our aim was to investigate its interobserver reproducibility in prostate needle biopsies. METHODS AND RESULTS: A panel of nine prostate pathology experts from five continents independently reviewed 304 digitised biopsies for cribriform cancer according to recent International Society of Urological Pathology criteria. The biopsies were collected from a series of 702 biopsies that were reviewed by one of the panellists for enrichment of high-grade cancer and potentially cribriform structures. A 2/3 consensus diagnosis of cribriform and noncribriform cancer was reached in 90% (272/304) of the biopsies with a mean kappa value of 0.56 (95% confidence interval 0.52-0.61). The prevalence of consensus cribriform cancers was estimated to 4%, 12%, 21%, and 20% of Gleason scores 7 (3 + 4), 7 (4 + 3), 8, and 9-10, respectively. More than two cribriform structures per level or a largest cribriform mass with ≥9 lumina or a diameter of ≥0.5 mm predicted a consensus diagnosis of cribriform cancer in 88% (70/80), 84% (87/103), and 90% (56/62), respectively, and noncribriform cancer in 3% (2/80), 5% (5/103), and 2% (1/62), respectively (all P < 0.01). CONCLUSION: Cribriform prostate cancer was seen in a minority of needle biopsies with high-grade cancer. Stringent diagnostic criteria enabled the identification of cribriform patterns and the generation of a large set of consensus cases for standardisation.

Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction.

Unreliable predictions can occur when an artificial intelligence (AI) system is presented with data it has not been exposed to during training. We demonstrate the use of conformal prediction to detect unreliable predictions, using histopathological diagnosis and grading of prostate biopsies as example. We digitized 7788 prostate biopsies from 1192 men in the STHLM3 diagnostic study, used for training, and 3059 biopsies from 676 men used for testing. With conformal prediction, 1 in 794 (0.1%) predictions is incorrect for cancer diagnosis (compared to 14 errors [2%] without conformal prediction) while 175 (22%) of the predictions are flagged as unreliable when the AI-system is presented with new data from the same lab and scanner that it was trained on. Conformal prediction could with small samples (N = 49 for external scanner, N = 10 for external lab and scanner, and N = 12 for external lab, scanner and pathology assessment) detect systematic differences in external data leading to worse predictive performance. The AI-system with conformal prediction commits 3 (2%) errors for cancer detection in cases of atypical prostate tissue compared to 44 (25%) without conformal prediction, while the system flags 143 (80%) unreliable predictions. We conclude that conformal prediction can increase patient safety of AI-systems.

Microbial community development during syngas methanation in a trickle bed reactor with various nutrient sources.

Microbial community development within an anaerobic trickle bed reactor (TBR) during methanation of syngas (56% H2, 30% CO, 14% CO2) was investigated using three different nutrient media: defined nutrient medium (241 days), diluted digestate from a thermophilic co-digestion plant operating with food waste (200 days) and reject water from dewatered digested sewage sludge at a wastewater treatment plant (220 days). Different TBR operating periods showed slightly different performance that was not clearly linked to the nutrient medium, as all proved suitable for the methanation process. During operation, maximum syngas load was 5.33 L per L packed bed volume (pbv) & day and methane (CH4) production was 1.26 L CH4/Lpbv/d. Microbial community analysis with Illumina Miseq targeting 16S rDNA revealed high relative abundance (20-40%) of several potential syngas and acetate consumers within the genera Sporomusa, Spirochaetaceae, Rikenellaceae and Acetobacterium during the process. These were the dominant taxa except in a period with high flow rate of digestate from the food waste plant. The dominant methanogen in all periods was a member of the genus Methanobacterium, while Methanosarcina was also observed in the carrier community. As in reactor effluent, the dominant bacterial genus in the carrier was Sporomusa. These results show that syngas methanation in TBR can proceed well with different nutrient sources, including undefined medium of different origins. Moreover, the dominant syngas community remained the same over time even when non-sterilised digestates were used as nutrient medium. KEY POINTS: • Independent of nutrient source, syngas methanation above 1 L/Lpbv/D was achieved. • Methanobacterium and Sporomusa were dominant genera throughout the process. • Acetate conversion proceeded via both methanogenesis and syntrophic acetate oxidation.

Mortality in men with castration-resistant prostate cancer-A long-term follow-up of a population-based real-world cohort.

Objectives: The objective of this study is to find clinical variables that predict the prognosis for men with castration-resistant prostate cancer (CRPC) in a Swedish real-life CRPC cohort, including a risk group classification to clarify the risk of succumbing to prostate cancer. This is a natural history cohort representing the premodern drug era before the introduction of novel hormonal drug therapies. Methods: PSA tests from the clinical chemistry laboratories serving health care in six regions of Sweden were retrieved and cross-linked to the National Prostate Cancer Registry (NPCR) to identify men with a prostate cancer diagnosis. Through further cross-linking with data sources at the Swedish Board of Health and Welfare, we retrieved other relevant information such as prescribed drugs, hospitalizations, and cause of death. Men entered the CRPC cohort at the first date of doubling of their PSA nadir value with the last value being >2 ng/ml, or an absolute increase of >5 ng/ml or more, whilst on 3 months of medical castration or if they had been surgically castrated (n = 4098). By combining the two variables with the largest C-statistics, "PSA at time of CRPC" and "PSA doubling time," a risk group classification was created. Results: PSA-DT and PSA at date of CRPC are the strongest variables associated with PC specific survival. At the end of follow-up, the proportion of men who died due to PC was 57%, 71%, 81%, 86%, and 89% for risk categories one through five, respectively. The median overall survival in our cohort of men with CRPC was 1.86 years (95% CI: 1.79-1.97). Conclusion: For a man with castration-resistant prostate cancer, there is a high probability that this will be the main cause contributing to his death. However, there is a significant difference in mortality that varies in relation to tumor burden assessed as PSA doubling time and PSA at time of CRCP. This information could be used in a clinical setting when deciding when to treat more or less aggressively once entering the CRPC phase of the disease.

Evaluation of SARS-CoV-2 rapid antigen diagnostic tests for saliva samples.

Using saliva samples would facilitate sample collection, diagnostic feasibility, and mass screening of SARS-CoV-2. We tested two rapid antigen (RAD) immunochromatographic tests designed for detection of SARS-CoV-2 in saliva: Rapid Response™ COVID-19 Antigen Rapid Test Cassette for oral fluids and DIAGNOS™ COVID-19 Antigen Saliva Test. Evaluation of detection limit was performed with purified SARS-CoV-2 nucleocapsid protein and live SARS-CoV-2 virus. Sensitivity and specificity were further evaluated with reverse transcription quantitative PCR (RT-qPCR) positive and negative saliva samples from hospitalized individuals with COVID-19 (n = 39) and healthcare workers (n = 20). DIAGNOS showed higher sensitivity than Rapid Response for both nucleocapsid protein and live virus. The limit of detection of the saliva test from DIAGNOS was further comparable with the Abbott Panbio™ COVID-19 Ag Rapid Test designed for nasopharyngeal samples. DIAGNOS and Rapid Response detected nine (50.0%) and seven (38.9%), respectively, of the 18 RT-qPCR positive saliva samples. All RT-qPCR negative saliva (n = 41) were negative with both tests. Only one of the RT-qPCR positive saliva samples contained infectious virus as determined by cell culture and was also positive using the saliva RADs. The results show that the DIAGNOS may be an important and easy-to-use saliva RAD complement to detect SARS-CoV-2 positive individuals, but validation with a larger sample set is warranted.

Predictors of short- and long-term mortality in critically ill, older adults admitted to the emergency department: an observational study.

BACKGROUND: In the future, we can expect an increase in older patients in emergency departments (ED) and acute wards. The main purpose of this study was to identify predictors of short- and long-term mortality in the ED and at hospital discharge. METHODS: This is a retrospective, observational, single-center, cohort study, involving critically ill older adults, recruited consecutively in an ED. The primary outcome was mortality. All patients were followed for 6.5-7.5 years. The Cox proportional hazards model was used. RESULTS: Regarding all critically ill patients aged ≥ 70 years and identified in the ED (n = 402), there was a significant association between mortality at 30 days after ED admission and unconsciousness on admission (HR 3.14, 95% CI 2.09-4.74), hypoxia on admission (HR 2.51, 95% CI 1.69-3.74) and age (HR 1.06 per year, 95% CI 1.03-1.09), (all p < 0.001). Of 402 critically ill patients aged ≥ 70 years and identified in the ED, 303 were discharged alive from hospital. There was a significant association between long-term mortality and the Charlson Comorbidity Index (CCI) > 2 (HR 1.90, 95% CI 1.46-2.48), length of stay (LOS) > 7 days (HR 1.72, 95% CI 1.32-2.23), discharge diagnosis of pneumonia (HR 1.65, 95% CI 1.24-2.21) and age (HR 1.08 per year, 95% CI 1.05-1.10), (all p < 0.001). The only symptom or vital sign associated with long-term mortality was hypoxia on admission (HR 1.70, 05% CI 1.30-2.22). CONCLUSIONS: Among critically ill older adults admitted to an ED and discharged alive the following factors were predictive of long-term mortality: CCI > 2, LOS > 7 days, hypoxia on admission, discharge diagnosis of pneumonia and age. The following factors were predictive of mortality at 30 days after ED admission: unconsciousness on admission, hypoxia and age. These data might be clinically relevant when it comes to individualized care planning, which should take account of risk prediction and estimated prognosis.

Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies-Current Status and Next Steps.

Diagnosis and Gleason grading of prostate cancer in biopsies are critical for the clinical management of men with prostate cancer. Despite this, the high grading variability among pathologists leads to the potential for under- and overtreatment. Artificial intelligence (AI) systems have shown promise in assisting pathologists to perform Gleason grading, which could help address this problem. In this mini-review, we highlight studies reporting on the development of AI systems for cancer detection and Gleason grading, and discuss the progress needed for widespread clinical implementation, as well as anticipated future developments. PATIENT SUMMARY: This mini-review summarizes the evidence relating to the validation of artificial intelligence (AI)-assisted cancer detection and Gleason grading of prostate cancer in biopsies, and highlights the remaining steps required prior to its widespread clinical implementation. We found that, although there is strong evidence to show that AI is able to perform Gleason grading on par with experienced uropathologists, more work is needed to ensure the accuracy of results from AI systems in diverse settings across different patient populations, digitization platforms, and pathology laboratories.

OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology.

SUMMARY: Digital pathology enables applying computational methods, such as deep learning, in pathology for improved diagnostics and prognostics, but lack of interoperability between whole slide image formats of different scanner vendors is a challenge for algorithm developers. We present OpenPhi-Open PatHology Interface, an Application Programming Interface for seamless access to the iSyntax format used by the Philips Ultra Fast Scanner, the first digital pathology scanner approved by the United States Food and Drug Administration. OpenPhi is extensible and easily interfaced with existing vendor-neutral applications. AVAILABILITY AND IMPLEMENTATION: OpenPhi is implemented in Python and is available as open-source under the MIT license at: https://gitlab.com/BioimageInformaticsGroup/openphi. The Philips Software Development Kit is required and available at: https://www.openpathology.philips.com. OpenPhi version 1.1.1 is additionally provided as Supplementary Data. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Human social sensing is an untapped resource for computational social science.

The ability to 'sense' the social environment and thereby to understand the thoughts and actions of others allows humans to fit into their social worlds, communicate and cooperate, and learn from others' experiences. Here we argue that, through the lens of computational social science, this ability can be used to advance research into human sociality. When strategically selected to represent a specific population of interest, human social sensors can help to describe and predict societal trends. In addition, their reports of how they experience their social worlds can help to build models of social dynamics that are constrained by the empirical reality of human social systems.

SARS-CoV-2 rapid antigen test: High sensitivity to detect infectious virus.

BACKGROUND: The COVID-19 pandemic has highlighted the need for rapid, cost effective and easy-to-use diagnostic tools for SARS-CoV-2 infections that can be used in point of care settings to limit disease transmission. OBJECTIVE: We evaluated two rapid antigen immunochromatographic tests, Abbott Panbio™ COVID-19 Ag Rapid Test (Panbio) and Zhejiang Orient Gene/Healgen Biotech Coronavirus Ag rapid test cassette (Orient gene) for detection of infectious SARS-CoV-2. RESULTS: The tests were evaluated on nasopharyngeal samples taken from individuals having respiratory and/or COVID-19 related symptoms, which had been analyzed for SARS-CoV-2 RNA using real-time PCR. In total 156 PCR-positive, and 130 (Panbio) and 176 (Orient Gene) PCR-negative samples were analyzed. Overall sensitivity and specificity were 71.8% and 100% for Panbio and 79.5% and 74.4% for the Orient Gene test respectively. The false positives by the Orient Gene test were verified as SARS-CoV-2 negative by in-house real-time PCR assay and were negative for the four seasonal coronaviruses. Subgroup analysis revealed that the antigen tests had high sensitivity for samples with Ct-values <25 (>88%) and for samples containing infectious viruses as determined by cultivation on Vero cells, 94.1% and 97.1% for the Panbio and Orient gene tests, respectively. Furthermore, both tests had a sensitivity of <50 picogram for nucleocapsid protein. No sample with a Ct-value >27 was shown to contain infectious virus. CONCLUSION: The results indicate that the rapid antigen tests, especially the Panbio tests may be a valuable tool to detect contagious persons during the ongoing pandemic.

Integrating social and cognitive aspects of belief dynamics: towards a unifying framework.

Belief change and spread have been studied in many disciplines-from psychology, sociology, economics and philosophy, to biology, computer science and statistical physics-but we still do not have a firm grasp on why some beliefs change more easily and spread faster than others. To fully capture the complex social-cognitive system that gives rise to belief dynamics, we first review insights about structural components and processes of belief dynamics studied within different disciplines. We then outline a unifying quantitative framework that enables theoretical and empirical comparisons of different belief dynamic models. This framework uses a statistical physics formalism, grounded in cognitive and social theory, as well as empirical observations. We show how this framework can be used to integrate extant knowledge and develop a more comprehensive understanding of belief dynamics.

Falling through the cracks: Modeling the formation of social category boundaries.

Social categorizations divide people into "us" and "them", often along continuous attributes such as political ideology or skin color. This division results in both positive consequences, such as a sense of community, and negative ones, such as group conflict. Further, individuals in the middle of the spectrum can fall through the cracks of this categorization process and are seen as out-group by individuals on either side of the spectrum, becoming inbetweeners. Here, we propose a quantitative, dynamical-system model that studies the joint influence of cognitive and social processes. We model where two social groups draw the boundaries between "us" and 'them" on a continuous attribute. Our model predicts that both groups tend to draw a more restrictive boundary than the middle of the spectrum. As a result, each group sees the individuals in the middle of the attribute space as an out-group. We test this prediction using U.S. political survey data on how political independents are perceived by registered party members as well as existing experiments on the perception of racially ambiguous faces, and find support.

Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies.

Numerous studies have shown a correlation between perineural invasion (PNI) in prostate biopsies and outcome. The reporting of PNI varies widely in the literature. While the interobserver variability of prostate cancer grading has been studied extensively, less is known regarding the reproducibility of PNI. A total of 212 biopsy cores from a population-based screening trial were included in this study (106 with and 106 without PNI according to the original pathology reports). The glass slides were scanned and circulated among four pathologists with a special interest in urological pathology for assessment of PNI. Discordant cases were stained by immunohistochemistry for S-100 protein. PNI was diagnosed by all four observers in 34.0% of cases, while 41.5% were considered to be negative for PNI. In 24.5% of cases, there was a disagreement between the observers. The kappa for interobserver variability was 0.67-0.75 (mean 0.73). The observations from one participant were compared with data from the original reports, and a kappa for intraobserver variability of 0.87 was achieved. Based on immunohistochemical findings among discordant cases, 88.6% had PNI while 11.4% did not. The most common diagnostic pitfall was the presence of bundles of stroma or smooth muscle. It was noted in a few cases that collagenous micronodules could be mistaken for a nerve. The distance between cancer and nerve was another cause of disagreement. Although the results suggest that the reproducibility of PNI may be greater than that of prostate cancer grading, there is still a need for improvement and standardization.

Predictors of adverse pathology on radical prostatectomy specimen in men initially enrolled in active surveillance for low-risk prostate cancer.

PURPOSE: To evaluate clinical variables, including magnetic resonance imaging (MRI) predictive of adverse pathology (AP) at radical prostatectomy (RP) in men initially enrolled in active surveillance (AS). METHODS: A population-based cohort study of men diagnosed with low-risk prostate cancer (PCa), in Stockholm County, Sweden, during 2008-2017 enrolled in AS their intended primary treatment followed by RP. AP was defined as ISUP grade group ≥ 3 and/or pT-stage ≥ T3. Association between clinical variables at diagnosis and time to AP was evaluated using Cox regression and multivariate logistic regression to evaluate the association between AP and clinical variables at last biopsy before RP. RESULTS: In a cohort of 6021 patients with low-risk PCa, 3116 were selected for AS and 216 underwent RP. Follow-up was 10 years, with a median time on AS of 23 months. 37.7% of patients had AP at RP. Clinical T-stage [Hazard ratio (HR): 1.81, 95% confidence interval (CI) 1.04-3.18] and PSA (HR: 1.31, 95% CI 1.17-1.46) at diagnosis and age [Odds Ratio (OR): 1.09, 95% CI 1.02-1.18), PSA (OR: 1.22, 95% CI 1.07-1.41), and PI-RADS (OR 1.66, 95% CI 1.11-2.55)] at last re-biopsy were significantly associated with AP. CONCLUSION: PI-RADS score is significantly associated with AP at RP and support current guidelines recommending MRI before enrollment in AS. Furthermore, age, cT-stage, and PSA are significantly associated with AP.