Automated machine learning for COVID-19 forecasting

In the context of the current COVID-19 pandemic, various sophisticated epidemic and machine learning models have been used for forecasting. These models, however, rely on carefully selected architectures and detailed data that is often only available for specific regions. Automated machine learning (AutoML) addresses these challenges by allowing to automatically create forecasting pipelines in a data-driven manner, resulting in high-quality predictions. In this paper, we study the role of open data along with AutoML systems in acquiring high-performance forecasting models for COVID-19. Here, we adapted the AutoML framework auto-sklearn to the time series forecasting task and introduced two variants for multi-step ahead COVID-19 forecasting, which we refer to as (a) multi-output and (b) repeated single output forecasting. We studied the usefulness of anonymised open mobility datasets (place visits and the use of different transportation modes) in addition to open mortality data. We evaluated three drift adaptation strategies to deal with concept drifts in data by (i) refitting our models on part of the data, (ii) the full data, or (iii) retraining the models completely. We compared the performance of our AutoML methods in terms of RMSE with five baselines on two testing periods (over 2020 and 2021). Our results show that combining mobility features and mortality data improves forecasting accuracy. Furthermore, we show that when faced with concept drifts, our method refitted on recent data using place visits mobility features outperforms all other approaches for 22 of the 26 countries considered in our study.Algorithms and the Foundations of Software technolog

Classification of Polarimetric SAR Data Using Dictionary Learning

End-user development (EUD) research has yielded a variety of novel environments and techniques, often accompanied by lab-based usability studies that test their effectiveness in the completion of representative real-world tasks. While lab studies play an important role in resolving frustrations and demonstrating the potential of novel tools, they are insufficient to accurately determine the acceptance of a technology in its intended context of use, which is highly dependent on the diverse and dynamic requirements of its users, as we show here. As such, usability in the lab is unlikely to represent usability in the field. To demonstrate this, we first describe the results of a think-aloud usability study of our EUD tool “Jeeves”, followed by two case studies where Jeeves was used by psychologists in their work practices. Common issues in the artificial setting were seldom encountered in the real context of use, which instead unearthed new usability issues through unanticipated user needs. We conclude with considerations for usability evaluation of EUD tools that enable development of software for other users, including planning for collaborative activities, supporting developers to evaluate their own tools, and incorporating longitudinal methods of evaluation.Postprin

Agreement between physical therapists and radiologists of stratifying patients with shoulder pain into new treatment related categories using ultrasound; an exploratory study

© 2019 Elsevier Ltd Study design: A systematic overview of the literature and an agreement study. Objectives: The aim of this study is to explore the inter-professional agreement of diagnostic musculoskeletal ultrasound (DMUS) between physical therapists (PT) and radiologists, using a new classification strategy based upon the therapeutic consequences in patients with shoulder pain. Background: DMUS is frequently used by PTs, although the agreement regarding traditional diagnostic labels between PTs and radiologists is only fair. Nevertheless, DMUS could be useful when used as a stratifying-tool. Methods: First, a systematic overview of current evidence was performed to assess which traditional diagnostic labels could be recoded into new treatment related categories (referral to secondary care, corticosteroid injections, physical therapy, watchful waiting). Next, kappa values were calculated for these categories between PTs and radiologists. Results: Only three categories were extracted, as none of the traditional diagnostic labels were classified into the ‘corticosteroid injection’ category. Overall, we found moderate agreement to stratify patients into treatment related categories and substantial agreement for the category ‘referral to secondary care’. Both categories ‘watchful waiting’ and ‘indication for physical therapy’ showed moderate agreement between the two professions. Conclusion: Our results indicate that the agreement between radiologists and PTs is moderate to substantial when labelling is based on treatment consequences. DMUS might be able to help the PT to guide treatment, especially for the category ‘referral to secondary care’ as this showed the highest agreement. However, as this is just an explorative study, more research is needed, to validate and assess the consequences of this stratification classification for clinical care

The GATA1s isoform is normally down-regulated during terminal haematopoietic differentiation and over-expression leads to failure to repress MYB, CCND2 and SKI during erythroid differentiation of K562 cells

Background: Although GATA1 is one of the most extensively studied haematopoietic transcription factors little is currently known about the physiological functions of its naturally occurring isoforms GATA1s and GATA1FL in humans—particularly whether the isoforms have distinct roles in different lineages and whether they have non-redundant roles in haematopoietic differentiation. As well as being of general interest to understanding of haematopoiesis, GATA1 isoform biology is important for children with Down syndrome associated acute megakaryoblastic leukaemia (DS-AMKL) where GATA1FL mutations are an essential driver for disease pathogenesis. <p/>Methods: Human primary cells and cell lines were analyzed using GATA1 isoform specific PCR. K562 cells expressing GATA1s or GATA1FL transgenes were used to model the effects of the two isoforms on in vitro haematopoietic differentiation. <p/>Results: We found no evidence for lineage specific use of GATA1 isoforms; however GATA1s transcripts, but not GATA1FL transcripts, are down-regulated during in vitro induction of terminal megakaryocytic and erythroid differentiation in the cell line K562. In addition, transgenic K562-GATA1s and K562-GATA1FL cells have distinct gene expression profiles both in steady state and during terminal erythroid differentiation, with GATA1s expression characterised by lack of repression of MYB, CCND2 and SKI. <p/>Conclusions: These findings support the theory that the GATA1s isoform plays a role in the maintenance of proliferative multipotent megakaryocyte-erythroid precursor cells and must be down-regulated prior to terminal differentiation. In addition our data suggest that SKI may be a potential therapeutic target for the treatment of children with DS-AMKL

Five-Year Follow-Up of a Slowly Resorbable Biosynthetic P4HB Mesh (Phasix) in VHWG Grade 3 Incisional Hernia Repair

OBJECTIVE: To assess the 5-year recurrence rate of incisional hernia repair in Ventral Hernia Working Group (VHWG) 3 hernia with a slowly resorbable mesh.SUMMARY BACKGROUND DATA: Incisional hernia recurs frequently after initial repair. In potentially contaminated hernia, recurrences rise to 40%. Recently, the biosynthetic Phasix mesh has been developed that is resorbed in 12-18 months. Resorbable meshes might be a solution for incisional hernia repair to decrease short- and long-term (mesh) complications. However, long-term outcomes after resorption are scarce.METHODS: Patients with VHWG grade 3 incisional midline hernia, who participated in the Phasix trial (Clinilcaltrials.gov: NCT02720042) were included by means of physical examination and computed tomography (CT). Primary outcome was hernia recurrence; secondary outcomes comprised of long-term mesh complications, reoperations, and abdominal wall pain [visual analogue score (VAS): 0-10].RESULTS: In total, 61/84 (72.6%) patients were seen. Median follow-up time was 60.0 [interquartile range (IQR): 55-64] months. CT scan was made in 39 patients (68.4%). A recurrence rate of 15.9% (95% confidence interval: 6.9-24.8) was calculated after 5 years. Four new recurrences (6.6%) were found between 2 and 5 years. Two were asymptomatic. In total, 13/84 recurrences were found. No long-term mesh complications and/or interventions occurred. VAS scores were 0 (IQR: 0-2).CONCLUSIONS: Hernia repair with Phasix mesh in high-risk patients (VHWG 3, body mass index &gt;28) demonstrated a recurrence rate of 15.9%, low pain scores, no mesh-related complications or reoperations for chronic pain between the 2- and 5-year follow-up. Four new recurrences occurred, 2 were asymptomatic. The poly-4-hydroxybutyrate mesh is a safe mesh for hernia repair in VHWG 3 patients, which avoids long-term mesh complications like pain and mesh infection.</p

Outcomes of a new slowly resorbable biosynthetic mesh (Phasix (TM)) in potentially contaminated incisional hernias : a prospective, multi-center, single-arm trial

Background: Resorbable biomaterials have been developed to reduce the amount of foreign material remaining in the body after hernia repair over the long-term. However, on the short-term, these resorbable materials should render acceptable results with regard to complications, infections, and reoperations to be considered for repair. Additionally, the rate of resorption should not be any faster than collagen deposition and maturation; leading to early hernia recurrence. Therefore, the objective of this study was to collect data on the short-term performance of a new resorbable biosynthetic mesh (Phasix (TM)) in patients requiring Ventral Hernia Working Group (VHWG) Grade 3 midline incisional hernia repair. Materials and methods: A prospective, multi-center, single-arm trial was conducted at surgical departments in 15 hospitals across Europe. Patients aged >= 18, scheduled to undergo elective Ventral Hernia Working Group Grade 3 hernia repair of a hernia larger than 10 cm(2) were included. Hernia repair was performed with Phasix (TM) Mesh in sublay position when achievable. The primary outcome was the rate of surgical site occurrence (SSO), including infections, that required intervention until 3 months after repair. Results: In total, 84 patients were treated with Phasix (TM) Mesh. Twenty-two patients (26.2%) developed 32 surgical site occurrences. These included 11 surgical site infections, 9 wound dehiscences, 7 seromas, 2 hematomas, 2 skin necroses, and 1 fistula. No significant differences in surgical site occurrence development were found between groups repaired with or without component separation technique, and between clean-contaminated or contaminated wound sites. At three months, there were no hernia recurrences. Conclusion: Phasix (TM) Mesh demonstrated acceptable postoperative surgical site occurrence rates in patients with a Ventral Hernia Working Group Grade 3 hernia. Longer follow-up is needed to evaluate the recurrence rate and the effects on quality of life. This study is ongoing through 24 months of follow-up

Human Bile Contains Cholangiocyte Organoid-Initiating Cells Which Expand as Functional Cholangiocytes in Non-canonical Wnt Stimulating Conditions

Diseases of the bile duct (cholangiopathies) remain a common indication for liver transplantation, while little progress has been made over the last decade in understanding the underlying pathophysiology. This is largely due to lack of proper in vitro model systems to study cholangiopathies. Recently, a culture method has been developed that allows for expansion of human bile duct epithelial cells grown as extrahepatic cholangiocyte organoids (ncECOs) in non-canonical Wnt-stimulating conditions. These ncECOs closely resemble cholangiocytes in culture and have shown to efficiently repopulate collagen scaffolds that could act as functional biliary tissue in mice. Thus far, initiation of ncECOs required tissue samples, thereby limiting broad patient-specific applications. Here, we report that bile fluid, which can be less invasively obtained and with low risk for the patients, is an alternative source for culturing ncECOs. Further characterization showed that bile-derived cholangiocyte organoids (ncBCOs) are highly similar to ncECOs obtained from bile duct tissue biopsies. Compared to the previously reported bile-cholangiocyte organoids cultured in canonical Wnt-stimulation conditions, ncBCOs have superior function of cholangiocyte ion channels and are able to respond to secretin and somatostatin. In conclusion, bile is a new, less invasive, source for patient-derived cholangiocyte organoids and makes their regenerative medicine applications more safe and feasible

A Population-based Study on Lymph Node Retrieval in Patients with Esophageal Cancer: Results from the Dutch Upper Gastrointestinal Cancer Audit

Background: For esophageal cancer, the number of retrieved lymph nodes (LNs) is often used as a quality indicator. The aim of this study is to analyze the number of retrieved LNs in The Netherlands, assess factors associated with LN yield, and explore the association with short-term outcomes. This is a population-based study on lymph node retrieval in patients with esophageal cancer, presenting results from the Dutch Upper Gastrointestinal Cancer Audit. Study Design: For this retrospective national cohort study, patients with esophageal carcinoma who underwent esophagectomy between 2011 and 2016 were included. The primary outcome was the number of retrieved LNs. Univariable and multivariable regression analyses were used to test for association with ≥ 15 LNs. Patients and Results: 3970 patients were included. Between 2011 and 2016, the median number of LNs increased from 15 to 20. Factors independently associated with ≥ 15 LNs were: 0–10 kg preoperative weight loss (versus: unknown weight loss, odds ratio [95% confidence interval]: 0.71 [0.57–0.88]), Charlson score 0 (versus: Charlson score 2: 0.76 [0.63–0.92]), cN2 category (reference: cN0, 1.32 [1.05–1.65]), no neoadjuvant therapy and neoadjuvant chemotherapy (reference: neoadjuvant chemoradiotherapy, 1.73 [1.29–2.32] and 2.15 [1.54–3.01]), minimally invasive transthoracic (reference: open transthoracic, 1.46 [1.15–1.85]), open transthoracic (versus open and minimally invasive transhiatal, 0.29 [0.23–0.36] and 0.43 [0.32–0.59]), hospital volume of 26–50 or > 50 resections/year (reference: 0–25, 1.94 [1.55–2.42] and 3.01 [2.36–3.83]), and year of surgery [reference: 2011, odds ratios (ORs) 1.48, 1.53, 2.28, 2.44, 2.54]. There was no association of ≥ 15 LNs with short-term outcomes. Conclusions: The number of LNs retrieved increased between 2011 and 2016. Weight loss, Charlson score, cN category, neoadjuvant therapy, surgical approach, year of resection, and hospital volume were all associated with increased LN yield. Retrieval of ≥ 15 LNs was not associated with increased postoperative morbidity/mortality

High tie versus low tie in rectal surgery: comparison of anastomotic perfusion

Item does not contain fulltextPURPOSE: Both "high tie" (HT) and "low tie" (LT) are well-known strategies in rectal surgery. The aim of this study was to compare colonic perfusion after HT to colonic perfusion after LT. METHODS: Patients undergoing rectal resection for malignancy were included. Colonic perfusion was measured with laser Doppler flowmetry, immediately after laparotomy on the antimesenterial side of the colon segment that was to become the afferent loop (measurement A). This measurement was repeated after rectal resection (measurement B). The blood flow ratios (B/A) were compared between the HT group and the LT group. RESULTS: Blood flow was measured in 33 patients, 16 undergoing HT and 17 undergoing LT. Colonic blood flow slightly decreased in the HT group whereas the flow increased in the LT group. The blood flow ratio was significantly higher in the LT group (1.48 vs. 0.91; p = 0.04), independent of the blood pressure. CONCLUSION: This study shows the blood flow ratio to be higher in the LT group. This suggests that anastomoses may benefit from better perfusion when LT is performed

Harmonic long shears further reduce operation time in transanal endoscopic microsurgery

Background: Previous research indicates that application of 5-mm harmonic shears rather than diathermia significantly reduces operation time in transanal endoscopic microsurgery (TEM). Frequently, however, additional instruments were required to complete resection. We investigated whether the new 5-mm harmonic long shears (H-LS) are better equipped for TEM compared with regular harmonic shears (HS). Methods: Between 2001 and 2006, 162 tumors (117 adenomas, 42 carcinomas, and 3 other tumors; mean distance 6.6 cm, mean area 40 cm2) were excised in 161 patients (82 men, 79 women; mean age 66 years). Results: Eighty-eight resections were performed with HS and 74 with H-LS. Tumor and patient characteristics were similar except for specimen area. Tumors resected by H-LS were on average smaller than those resected by HS (34.4 versus 44.1 cm2; Mann-Whitney U-test: p = 0.027). Mean operation time was 48 min and proportional to area in both groups (univariate analysis of variance p<0.001). Mean operation time was 54 min using HS and 41 min using H-LS (t-test: p<0.001). After correction for area, operation time for H-LS was reduced by 14% compared with HS (t-test: p<0.001). H-LS is singly capable of completing resection in 88% compared with 26% for HS (Mann- Whitney U-test: p<0.001). Mean blood loss was 16 cc for HS and 3 cc for H-LS (p<0.001). Morbidity (11%) and mortality (0.6%) were not different between the two groups (Fisher's exact test). Conclusion: Performing transanal endoscopic microsurgery with 5-mm harmonic long shears reduces operation time compared with regular shears, and completing resection seldom requires other instruments