bluuebunny/crossref_metadata_2025_split huggingface dataset:
Batch equalization with a generative adversarial network
Authors: Qian Wesley Wei , Xia Cassandra , Venugopalan Subhashini , Narayanaswamy Arunachalam , Dimon Michelle , Ashdown George W , Baum Jake , Peng Jian , Ando D Michael 
Published: September 2020

Abstract

Motivation
Advances in automation and imaging have made it possible to capture a large image dataset that spans multiple experimental batches of data. However, accurate biological comparison across the batches is challenged by batch-to-batch variation (i.e. batch effect) due to uncontrollable experimental noise (e.g. varying stain intensity or cell density). Previous approaches to minimize the batch effect have commonly focused on normalizing the low-dimensional image measurements such as an embedding generated by a neural network. However, normalization of the embedding could suffer from over-correction and alter true biological features (e.g. cell size) due to our limited ability to interpret the effect of the normalization on the embedding space. Although techniques like flat-field correction can be applied to normalize the image values directly, they are limited transformations that handle only simple artifacts due to batch effect.

Results
We present a neural network-based batch equalization method that can transfer images from one batch to another while preserving the biological phenotype. The equalization method is trained as a generative adversarial network (GAN), using the StarGAN architecture that has shown considerable ability in style transfer. After incorporating new objectives that disentangle batch effect from biological features, we show that the equalized images have less batch information and preserve the biological information. We also demonstrate that the same model training parameters can generalize to two dramatically different types of cells, indicating this approach could be broadly applicable.

Availability and implementation
https://github.com/tensorflow/gan/tree/master/tensorflow_gan/examples/stargan

Supplementary information
Supplementary data are available at Bioinformatics online.
Status of adult inpatient burn rehabilitation in Europe: are we neglecting metabolic outcomes?
Authors: Schieffelers David R , van Breda Eric , Gebruers Nick , Meirte Jill , Van Daele Ulrike 
Published: September 2020

Abstract

Background
Hypermetabolism, muscle wasting and insulin resistance are challenging yet important rehabilitation targets in the management of burns. In the absence of concrete practice guidelines, however, it remains unclear how these metabolic targets are currently managed. This study aimed to describe the current practice of inpatient rehabilitation across Europe.

Methods
An electronic survey was distributed by the European Burn Association to burn centres throughout Europe, comprising generic and profession-specific questions directed at therapists, medical doctors and dieticians. Questions concerned exercise prescription, metabolic management and treatment priorities, motivation and knowledge of burn-induced metabolic sequelae. Odds ratios were computed to analyse associations between data derived from the responses of treatment priorities and knowledge of burn-induced metabolic sequelae.

Results
Fifty-nine clinicians with 12.3 ± 9 years of professional experience in burns, representing 18 out of 91 burn centres (response rate, 19.8%) across eight European countries responded. Resistance and aerobic exercises were only provided by 42% and 38% of therapists to intubated patients, 87% and 65% once out-of-bed mobility was possible and 97% and 83% once patients were able to leave their hospital room, respectively. The assessment of resting energy expenditure by indirect calorimetry, muscle wasting and insulin resistance was carried out by only 40.7%, 15.3% and 7.4% respondents, respectively, with large variability in employed frequency and methods. Not all clinicians changed their care in cases of hypermetabolism (59.3%), muscle wasting (70.4%) or insulin resistance (44.4%), and large variations in management strategies were reported. Significant interdisciplinary variation was present in treatment goal importance ratings, motivation and knowledge of burn-induced metabolic sequelae. The prevention of metabolic sequelae was regarded as the least important treatment goal, while the restoration of functional status was rated as the most important. Knowledge of burn-induced metabolic sequelae was linked to higher importance ratings of metabolic sequelae as a therapy goal (odds ratio, 4.63; 95% CI, 1.50–14.25; p &lt; 0.01).

Conclusion
This survey reveals considerable non-uniformity around multiple aspects of inpatient rehabilitation across European burn care, including, most notably, a potential neglect of metabolic outcomes. The results contribute to the necessary groundwork to formulate practice guidelines for inpatient burn rehabilitation.
Clinical significance of a microRNA signature for the identification and predicting prognosis in colorectal cancers with mucinous differentiation
Authors: Ruiz-Bañobre Juan , Roy Roshni , Alustiza Fernández Miren , Murcia Óscar , Jover Rodrigo , Pera Miguel , Balaguer Francesc , López-López Rafael , Goel Ajay 
Published: September 2020

Abstract
Accumulating evidence supports the fact that the mere presence of mucinous differentiation in colorectal cancer (CRC), rather than its proportion, is a more accurate representative of a particular CRC subtype with distinct clinical and molecular features. In addition, the prognostic significance of the mucinous carcinoma (MC) subtype remains poorly understood and biomarkers have been barely explored in this disease. Herein, we have performed a systematic and comprehensive analysis in MCs and non-MCs and identified a panel of microRNAs (miRNAs) that are differentially expressed between these two subtypes of CRC. Next, we interrogated their clinical significance and demonstrated their robust diagnostic and prognostic clinical ability in CRCs with mucinous differentiation. Finally, we established an integrative risk-assessment model by combining the miRNA-based risk scores together with TNM staging, which was a superior predictor of prognosis in mucinous CRC patients. Collectively, we report a novel miRNA biomarker panel for the identification and predicting survival in CRC patients with mucinous differentiation.
Failure Mode Critical Effect Analysis and Design of Experiment-Based Robust Chromatographic Method for Simultaneous Estimation Lornoxicam and Eperisone Hydrochloride
Authors: Prajapati Pintu , Radadiya Vipul , Shah Shailesh 
Published: September 2020

Abstract
Failure mode critical effect analysis and design of experiment-based high performance thin layer chromatography (HPTLC) method has been developed for simultaneous estimation of lornoxicam (LOC) and eperisone hydrochloride (EPR). Failure modes were identified on the basis of prior knowledge and experimental data with the help of Ishikawa diagram for the development of method. The criticality of failure mode was assessed by giving risk priority number and criticality rank on the basis of preliminary experimental trials. The identified critical failure modes were analyzed for their effect by design of experiment (DoE)-based Plackett–Burman screening design. From 11 critical factors, the volume of methanol and modifier in mobile phase composition were found as critical failure modes. Critical failure mode was further analyzed by DoE based on central composite design for study of their relationship with resolution of both drugs. Quadratic model suggested by design was further used for failure mode risk control and navigation of design space for a resolution of both drugs more than 1.5. Failure mode risk control strategy was set for robust HPTLC method for simultaneous estimation of both drugs in laboratory mixture. Developed and validated HPTLC method was applied for assay of LOC and EPR in their laboratory mixture and assay values were found in good agreement with a spiked amount of drugs.
Burden of Ileal Perforations Among Surgical Patients Admitted in Tertiary Care Hospitals of Three Asian countries: Surveillance of Enteric Fever in Asia Project (SEAP), September 2016–September 2019
Authors: Qazi Saqib H , Yousafzai Mohammad T , Saddal Nasir S , Dehraj Irum F , Thobani Rozina S , Akhtar Afshan , Syed Jamal R , Kazi Abdul M , Hotwani Aneeta , Rahman Najeeb , Mehmood Junaid , Andrews Jason R , Luby Stephen P , Garrett Denise O , Qamar Farah N 
Published: September 2020

Abstract

Background
Typhoid fever is caused by Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) and can lead to systemic illness and complications. We aimed to characterize typhoid-related ileal perforation in the context of the population-based Surveillance of Enteric Fever in Asia Project (SEAP) in Bangladesh, Nepal and Pakistan.

Methods
Between September 2016 and September 2019, all cases of nontraumatic ileal perforation with a clinical diagnosis of typhoid were enrolled from 4 tertiary care hospitals in Karachi, 2 pediatric hospitals in Bangladesh, and 2 hospitals in Nepal. Sociodemographic data were collected from patients or their caregivers, and clinical and outcome data were retrieved from medical records. Tissue samples were collected for histopathology and blood cultures where available.

Results
Of the 249 enrolled cases, 2 from Bangladesh, 5 from Nepal and 242 from Pakistan. In Pakistan, most of the cases were in the 0–15 (117/242; 48%) and 16–30 (89/242; 37%) age groups. In all countries, males were most affected: Pakistan 74.9% (180/242), Nepal 80% (4/5), and Bangladesh 100% (2/2). Blood culture was done on 76 cases; 8 (11%) were positive for S. Typhi, and all were extensively drug resistant (XDR) S. Typhi. Tissue cultures was done on 86 patients; 3 (3%) were positive for S. Typhi, and all were XDR S. Typhi, out of 86 samples tested for histopathology 4 (5%) revealed ileal perforation with necrosis. Culture or histopathology confirmed total 15 (11%) enteric fever cases with ileal perforation are similar to the clinically diagnosed cases. There were 16/242 (7%) deaths from Pakistan. Cases of ileal perforation who survived were more likely to have sought care before visiting the sentinel hospital (P = .009), visited any hospital for treatment (P = .013) compared to those who survived.

Conclusions
Although surveillance differed substantially by country, one reason for the higher number of ileal perforation cases in Pakistan could be the circulation of XDR strain of S. Typhi in Karachi.
Typhoid and Paratyphoid Cost of Illness in Bangladesh: Patient and Health Facility Costs From the Surveillance for Enteric Fever in Asia Project II
Authors: Mejia Nelly , Pallas Sarah W , Saha Samir , Udin Jamal , Sayeed K M Ishtiaque , Garrett Denise O , Date Kashmira , Abimbola Taiwo 
Published: September 2020

Abstract

Background
We conducted a cost of illness study to assess the economic burden of pediatric enteric fever (typhoid and paratyphoid) in Bangladesh. Results can inform public health policies to prevent enteric fever.

Methods
The study was conducted at 2 pediatric health facilities in Dhaka. For the patient and caregiver’s perspective, we administered questionnaires on costs incurred from illness onset until the survey dates to caregivers of patients with blood culture positive cases at enrollment and 6 weeks later to estimate the direct medical, direct nonmedical, and indirect costs. From the perspective of the health care provider, we collected data on quantities and prices of resources used by the 2 hospitals to estimate the direct medical economic costs to treat a case of enteric fever. We collected costs in Bangladeshi takas and converted them into 2018 US dollars. We multiplied the unit cost per procedure by the frequency of procedures in the surveillance case cohort to calculate the average cost per case.

Results
Among the 1772 patients from whom we collected information, the median cost of illness per case of enteric fever from the patient and caregiver perspective was US $64.03 (IQR: US $33.90 –$173.48). Median direct medical and nonmedical costs per case were 3% of annual labor income across the sample. From the perspective of the healthcare provider, the average direct medical cost per case was US $58.64 (range: US $37.25 at Hospital B, US $73.27 at Hospital A).

Conclusions
Our results show substantial economic burden of enteric fever in Bangladesh, with higher costs for patients receiving inpatient care. As antimicrobial resistance increases globally, the cost of illness could increase, due to more expensive and potent drugs required for treatment.
Staging Archaeology: Empire as Reality Effect at the 1906–07fêtes de Carthage
Authors: Sherman Daniel J. 
Published: September 2020

AbstractOrganized by a private association with the support of the French Protectorate, the 1906 and 1907 pageants or fêtes de Carthage, held at a recently excavated Roman theatre at an important site of ancient colonization, celebrated the achievements and the promise of archaeology in Tunisia. Inspired by open-air theatricals in the ancient theatres of Orange and Béziers, the elaborate stagings involved hundreds of actors, large volunteer crews, and sumptuous period costumes. After a program of excerpts from neoclassical drama and opera in 1906, the 1907 pageant featured two specially commissioned plays, one of them an encounter between a modern-day poet and a Carthaginian priestess on the very archaeological site where her tomb is discovered. The pageants drew on both specific archaeological findings and a pervasive visual culture that depicted French colonizers as preservers of the ancient culture of which they had found traces in North Africa. The violence of colonization was thus consigned to the realm of performance and archaeology cast as a valuable source of knowledge. Although the pageants operated in a nostalgic mode, they ultimately served a more historicist sense of time in which archaeology as an emerging science helped to police the boundary between past and present.
Efficacy and safety of endoscopic submucosal dissection versus endoscopic mucosal resection for superficial esophageal carcinoma: a systematic review and meta-analysis
Authors: Han Chunyao , Sun Yonghong 
Published: September 2020

Summary
Endoscopic submucosal dissection (ESD) has been developed to overcome the limitations of endoscopic mucosal resection (EMR). Yet, the potential for EMR should not be ignored. This study aimed to compare the efficacy and safety of ESD and EMR in the treatment of superficial esophageal carcinoma (SEC). All relevant articles were retrieved from electronic databases. The primary outcomes included en bloc resection, curative resection, R0 resection, and local recurrence rates. Secondary outcomes included procedure time, rates of perforation, bleeding, and postoperative stricture. Subgroup analyses based on histologic types and lesion sizes were conducted. Twenty-two studies were enrolled. Overall results showed higher en bloc, curative, and R0 resection rate, and lower recurrence rate in ESD compared with EMR. ESD was significantly more time-consuming and induced more perforations than EMR procedure. In subgroup analyses of squamous cell carcinoma (SCC) and Barrett’s esophagus (BE)-associated neoplasia and esophageal adenocarcinoma (EAC) subtypes, ESD also excelled in en bloc, curative, R0 resection and local recurrence rates. However, in subgroup analysis stratifying outcomes according to lesion sizes, the superior effect of ESD in en bloc resection, curative resection, and local recurrence rate only manifested when lesion size &gt;20 mm. Overall, ESD seemed to have superior efficacy and similar safety profiles compared to EMR in treating SCC, BE-associated neoplasia and EAC. Nevertheless, the selection of ESD or EMR should take lesion size into consideration. EMR is appropriate when lesion size ≤10 mm, EMR and ESD are both applicable for lesion between 11 and 20 mm, and ESD is preferable for lesions &gt;20 mm. More evidences are needed to confirm the current findings.
Fate of a coronary artery intramural haematoma complicating aortic root surgery: a case report
Authors: Folino Giulio , Scaffa Raffaele , Salica Andrea , De Paulis Ruggero 
Published: September 2020

Abstract

Background
Coronary intramural haematoma (CIH) is an uncommon but potentially life-threatening complication during aortic root surgery (such as Bentall procedure). Depending on its extension it can lead to cardiogenic shock. Documented reports of this complication are lacking in literature.

Case summary
In the report we present a case of CIH and its management and we show a stepwise imaging of the healing process that gives an insight of the fate of CIHs.

Discussion
This case raises awareness of CIH as differential diagnosis for myocardial ischaemia during aortic root surgery. It underlines the effectiveness of immediate surgical revascularization, highlights the potential temporary role of coronary artery bypass graft that can stabilize the acute coronary syndrome and may give time to the CIH to reabsorb and native coronary circulation to re-establish.
Similar cardiovascular outcomes in patients with diabetes and established or high risk for coronary vascular disease treated with dulaglutide with and without baseline metformin
Authors: Ferrannini Giulia , Gerstein Hertzel , Colhoun Helen Martina , Dagenais Gilles R , Diaz Rafael , Dyal Leanne , Lakshmanan Mark , Mellbin Linda , Probstfield Jeffrey , Riddle Matthew Casey , Shaw Jonathan Edward , Avezum Alvaro , Basile Jan Neil , Cushman William C , Jansky Petr , Keltai Mátyás , Lanas Fernando , Leiter Lawrence Alan , Lopez-Jaramillo Patricio , Pais Prem , Pīrāgs Valdis , Pogosova Nana , Raubenheimer Peter Johann , Sheu Wayne Huey-Herng , Rydén Lars 
Published: September 2020

Abstract

Objective
Recent European Guidelines for Diabetes, Prediabetes and Cardiovascular Diseases introduced a shift in managing patients with type 2 diabetes at high risk for or established cardiovascular (CV) disease by recommending GLP-1 receptor agonists and SGLT-2 inhibitors as initial glucose-lowering therapy. This is questioned since outcome trials of these drug classes had metformin as background therapy. In this post hoc analysis, the effect of dulaglutide on CV events was investigated according to the baseline metformin therapy by means of a subgroup analysis of the Researching Cardiovascular Events with a Weekly Incretin in Diabetes (REWIND) trial.

Research design and methods
Patients in REWIND (n = 9901; women: 46.3%; mean age: 66.2 years) had type 2 diabetes and either a previous CV event (31%) or high CV risk (69%). They were randomized (1:1) to sc. dulaglutide (1.5 mg/weekly) or placebo in addition to standard of care. The primary outcome was the first of a composite of nonfatal myocardial infarction, nonfatal stroke, and death from cardiovascular or unknown causes. Key secondary outcomes included a microvascular composite endpoint, all-cause death, and heart failure. The effect of dulaglutide in patients with and without baseline metformin was evaluated by a Cox regression hazard model with baseline metformin, dulaglutide assignment, and their interaction as independent variables. Adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated by a Cox regression model with adjustments for factors differing at baseline between people with vs. without metformin, identified using the backward selection.

Results
Compared to patients with metformin at baseline (n = 8037; 81%), those without metformin (n = 1864; 19%) were older and slightly less obese and had higher proportions of women, prior CV events, heart failure, and renal disease. The primary outcome occurred in 976 (12%) participants with baseline metformin and in 281 (15%) without. There was no significant difference in the effect of dulaglutide on the primary outcome in patients with vs. without metformin at baseline [HR 0.92 (CI 0.81–1.05) vs. 0.78 (CI 0.61–0.99); interaction P = 0.18]. Findings for key secondary outcomes were similar in patients with and without baseline metformin.

Conclusion
This analysis suggests that the cardioprotective effect of dulaglutide is unaffected by the baseline use of metformin therapy.
Impact of electroanatomical mapping-guided lead implantation on procedural outcome of His bundle pacing
Authors: Richter Sergio , Ebert Micaela , Bertagnolli Livio , Gebauer Roman , Lucas Johannes , Scheller Dominik , Paetsch Ingo , Hindricks Gerhard , Döring Michael 
Published: September 2020

Abstract

Aims
Conventional His bundle pacing (HBP) can be technically challenging and fluoroscopy-intense, particularly in patients with His-Purkinje conduction disease (HPCD). Three-dimensional electroanatomical mapping (EAM) facilitates non-fluoroscopic lead navigation and HB electrogram mapping. We sought to assess the procedural outcome of routine EAM-guided HBP compared with conventional HBP in a real-world population and evaluate the feasibility and safety of EAM-guided HBP in patients with HPCD.

Methods and results
We included 58 consecutive patients (72 ± 13 years; 71% male) who underwent an attempt to conventional (EAM− group; n = 29) or EAM-guided (EAM+ group; n = 29) HBP between June 2019 and April 2020. The centre’s learning curve was initially determined (n = 40 cases) to define the conventional control group and minimize outcome bias favouring EAM-guided HBP. His bundle pacing was successful in 26 patients (90%) in the EAM+ and 27 patients (93%) in the EAM− group (P = 0.64). The procedure time was 90 (73–135) and 110 (70–130) min, respectively (P = 0.89). The total fluoroscopy time [0.7 (0.5–1.4) vs. 3.3 (1.4–6.5) min; P &lt; 0.001] and fluoroscopy dose [21.9 (9.1–47.7) vs. 78.6 (27.2–144.9) cGycm2; P = 0.001] were significantly lower in the EAM+ than EAM− group. There were no significant differences between groups in His capture threshold (1.2 ± 0.6 vs. 1.4 ± 1.0 V/1.0 ms; P = 0.33) and paced QRS duration (113 ± 15 vs. 113 ± 17 ms; P = 0.89). In patients with HPCD, paced QRS duration was similar in both groups (121 ± 15 vs. 123 ± 12 ms; P = 0.77). The bundle branch-block recruitment threshold tended to be lower in the EAM+ than EAM− group (1.3 ± 0.7 vs. 1.8 ± 1.2 V/1.0 ms; P = 0.31). No immediate procedure-related complications occurred. One patient (2%) experienced lead dislodgement during 4-week follow-up.

Conclusion
Implementation of routine EAM-guided HBP lead implantation is feasible and safe in a real-world cohort of patients with and without HPCD and results in a tremendous reduction in radiation exposure without prolonging procedure time or increasing procedure-related complications.