bluuebunny/crossref_metadata_2025_split huggingface dataset:
The open abdomen in trauma, acute care, and vascular and endovascular surgery: comprehensive, expert, narrative review
Authors: Roberts Derek J , Leppäniemi Ari , Tolonen Matti , Mentula Panu , Björck Martin , Kirkpatrick Andrew W , Sugrue Michael , Pereira Bruno M , Petersson Ulf , Coccolini Federico , Latifi Rifat 
Published: October 2023

Abstract

Background
The open abdomen is an innovation that greatly improved surgical understanding of damage control, temporary abdominal closure, staged abdominal reconstruction, viscera and enteric fistula care, and abdominal wall reconstruction. This article provides an evidence-informed, expert, comprehensive narrative review of the open abdomen in trauma, acute care, and vascular and endovascular surgery.

Methods
A group of 12 international trauma, acute care, and vascular and endovascular surgery experts were invited to review current literature and important concepts surrounding the open abdomen.

Results
The open abdomen may be classified using validated systems developed by a working group in 2009 and modified by the World Society of the Abdominal Compartment Syndrome—The Abdominal Compartment Society in 2013. It may be indicated in major trauma, intra-abdominal sepsis, vascular surgical emergencies, and severe acute pancreatitis; to facilitate second look laparotomy or avoid or treat abdominal compartment syndrome; and when the abdominal wall cannot be safely closed. Temporary abdominal closure and staged abdominal reconstruction methods include a mesh/sheet, transabdominal wall dynamic fascial traction, negative pressure wound therapy, and hybrid negative pressure wound therapy and dynamic fascial traction. This last method likely has the highest primary fascial closure rates. Direct peritoneal resuscitation is currently an experimental strategy developed to improve primary fascial closure rates and reduce complications in those with an open abdomen. Primary fascial closure rates may be improved by early return to the operating room; limiting use of crystalloid fluids during the surgical interval; and preventing and/or treating intra-abdominal hypertension, enteric fistulae, and intra-abdominal collections after surgery. The majority of failures of primary fascial closure and enteroatmospheric fistula formation may be prevented using effective temporary abdominal closure techniques, providing appropriate resuscitation fluids and nutritional support, and closing the abdomen as early as possible.

Conclusion
Subsequent stages of the innovation of the open abdomen will likely involve the design and conduct of prospective studies to evaluate appropriate indications for its use and effectiveness and safety of the above components of open abdomen management.
Patient-reported outcome measures and surgery for Crohn’s disease: systematic review
Authors: Kim Whei J , Iskandarani Mohamad , Manzo Carlo A , Pellino Gianluca , Gallostra Marc Martí , Tekkis Paris P , Celentano Valerio , Kontovounisios Christos 
Published: October 2023

Abstract

Background/Aims
Crohn’s disease is an inflammatory bowel disease with up to 50 per cent of patients requiring surgery within 10 years of diagnosis. Patient-reported outcome measures (PROMs) are vital to monitor and assess patient health-related quality of life (HRQoL). This systematic review aims to evaluate PROMs within studies for perioperative Crohn's disease patients.

Methods
Articles from MEDLINE, Embase, Emcare and CINAHL databases were searched to find studies relating to the assessment of HRQoL in perioperative Crohn's disease patients using PROMs and patient-reported experience measures (PREMs) from 1st January 2015 to 22nd October 2023. Bias was assessed using the ROBINS-I tool was used for non-randomized interventional studies and the Cochrane RoB2 tool was used for randomized trials.

Results
1714 journal articles were filtered down to eight studies. Six studies focused on ileocaecal resection, one on perianal fistulas and one on the effects of cholecystectomy on patients with Crohn's disease. Within these articles, ten different PROM tools were identified (8 measures of HRQoL and 2 measures of functional outcome). Overall improvements in patient HRQoL pre- to postoperative for ileocaecal Crohn's disease were found in both paediatric and adult patients. Outcomes were comparable in patients in remission, with or without stoma, but were worse in patients with a stoma and active disease.

Conclusion
There are significant variations in how PROMs are used to evaluate perioperative Crohn's disease outcomes and a need for consensus on how tools are used. Routine assessments using an internationally accepted online platform can be used to monitor patients and support areas of treatment pathways that require further support to ensure high standards of care. They also enable future statistical comparisons in quantitative reviews and meta-analyses.
Lesion network mapping of eye-opening apraxia
Authors: Zarifkar Pardis , Shaff Nicholas A , Nersesjan Vardan , Mayer Andrew R , Ryman Sephira , Kondziella Daniel 
Published: October 2023

Abstract
Apraxia of eyelid opening (or eye-opening apraxia) is characterized by the inability to voluntarily open the eyes because of impaired supranuclear control. Here, we examined the neural substrates implicated in eye-opening apraxia through lesion network mapping. We analysed brain lesions from 27 eye-opening apraxia stroke patients and compared them with lesions from 20 aphasia and 45 hemiballismus patients serving as controls. Lesions were mapped onto a standard brain atlas using resting-state functional MRI data derived from 966 healthy adults in the Harvard Dataverse. Our analyses revealed that most eye-opening apraxia-associated lesions occurred in the right hemisphere, with subcortical or mixed cortical/subcortical involvement. Despite their anatomical heterogeneity, these lesions functionally converged on the bilateral dorsal anterior and posterior insula. The functional connectivity map for eye-opening apraxia was distinct from those for aphasia and hemiballismus. Hemiballismus lesions predominantly mapped onto the putamen, particularly the posterolateral region, while aphasia lesions were localized to language-processing regions, primarily within the frontal operculum. In summary, in patients with eye-opening apraxia, disruptions in the dorsal anterior and posterior insula may compromise their capacity to initiate the appropriate eyelid-opening response to relevant interoceptive and exteroceptive stimuli, implicating a complex interplay between salience detection and motor execution.
Molecular characteristics of circulating B cells and kidney cells at the single-cell level in special types of primary membranous nephropathy
Authors: Feng Xiaoqian , Chen Qilin , Zhong Jinjie , Yu Sijie , Wang Yue , Jiang Yaru , Wan Junli , Li Longfei , Jiang Huimin , Peng Liping , Wang Anshuo , Zhang Gaofu , Wang Mo , Yang Haiping , Li Qiu 
Published: October 2023

ABSTRACT

Background
Although primary membranous nephropathy (pMN) associated with podocyte autoantibodies (POS) is becoming well-known, the molecular characteristics of the specific type of pMN that is negative for podocyte autoantibodies (NEG) is still unclear.

Methods
We performed single-cell transcriptome sequencing and single-cell B cell receptor sequencing on circulating CD19+ cells and kidney cells of a NEG paediatric patient with pMN. The single-cell datasets of POS patients and healthy control individuals were included for integrative analysis.

Results
The gene expression characteristics and clonal expansion of naïve and memory B cells in the NEG patient changed significantly. We found that a group of CD38+ naïve B cells expanded in the NEG patient, which had the functional characteristics of cell activation. In addition, the conversion between immunoglobulin M (IgM)/IgD and IgG1 in the NEG patient was increased. Parietal epithelial cells (PECs) and podocytes shared similar signature genes (WT1, CLIC5), and new candidate marker genes for PECs, such as NID2, CAV1 and THY1, might contribute to the definition of cell subsets. PECs might have undergone significant changes in the disease, mainly manifested by changes in the expression of CCN2, PLAAT4 and SEPTIN2. The scores of gene sets related to extracellular matrix, cell adhesion and calcium channel in podocytes of the NEG patient was significantly increased. The gene expression of sodium transporter in a group of proximal tubule cells in the disease was significantly increased, especially SLC5A12, which might be related to the oedema of patients.

Conclusions
Our research demonstrated the cell type–specific molecular features in the circulation and kidney of the NEG pMN patient.
Should we enlarge the indication for kidney biopsy in patients with diabetes? The pro part
Authors: Gesualdo Loreto , Fiorentino Marco , Conserva Francesca , Pontrelli Paola 
Published: October 2023

ABSTRACT
Diabetic nephropathy (DN) and non-diabetic renal diseases (NDRD) represent intricate challenges in diagnosis and treatment within the context of the global diabetes epidemic. As the prevalence of diabetes continues to escalate, effective management of renal complications becomes paramount. Recent advancements in comprehending the multifaceted nature of renal damage, fueled by insights from histopathological investigations, offer unprecedented prospects for refining diagnostic strategies and customizing therapeutic interventions. Renal biopsies have emerged as indispensable tools for unraveling the diverse phenotypes of renal damage in diabetes. The pioneering study by Mazzucco identified three classes of renal damage in type 2 diabetes patients: classical diabetic glomerulosclerosis (DN), vascular and ischemic glomerular changes (NDRD), and other glomerulonephritides in the presence (DN + NDRD, mixed forms) or absence of DN (NDRD). The prevalence of these classes varies widely in published studies, influenced by factors such as ethnicity, geography and selection criteria for renal biopsy. Moreover, the international Renal Pathology Society consensus classification system has stratified the classical diabetic nephropathy into progressive categories of renal impairment, a breakthrough that aids in prognostication. Histopathological scrutiny, particularly the intricate correlation between glomerular and tubulointerstitial lesions, contributes profoundly to enhancing our grasp of the phenotype's heterogeneity. This amplified comprehension holds the potential to steer personalized treatment strategies. Cutting-edge interventions, encompassing sodium-glucose cotransporter 2 inhibitors, mineralocorticoid receptor antagonists and anti-endothelin receptor agents, are broadening the arsenal against renal injury in diabetes. When combined with the profound insights garnered from histopathological, omics, imaging and clinical data, these therapeutic avenues promise a transformative shift towards precision-driven care paradigms. Collaborative efforts uniting researchers, clinicians and patients are indispensable for propelling our knowledge of diabetic renal damage and ameliorating patient outcomes. The fusion of histopathological, omics and imaging findings into clinical decision-making harbors the potential to customize interventions and optimize care for individuals grappling with diabetes-associated renal complications. Furthermore, groundbreaking initiatives like the iBeat Study within the BEAt-DKD (Biomarker Enterprise to Attack Diabetic Kidney Disease) project (https://www.beat-dkd.eu/), elucidating distinct phenotypes of renal damage within diabetes, underscore the imperative necessity of integrating histopathological data into the broader framework of diabetic renal management.
Thiopurine Exposure During Pregnancy is Not Associated With Anemia in Infants Born to Mothers With IBD
Authors: Yeaman Fiona , Stritzke Amelie , Kuret Verena , Sharifi Nastaran , Seow Cynthia H , Metcalfe Amy , Leung Yvette 
Published: October 2023

Abstract

Background
Thiopurines are commonly used to treat inflammatory bowel disease (IBD). Thiopurines are considered safe throughout pregnancy. However, a published study suggested the risk of neonatal anemia was increased if exposed to thiopurines in utero. This prospective cohort study aimed to determine if there is an increased risk of cytopenia among infants born to pregnant people with IBD, exposed or unexposed to thiopurines, compared to infants born to those without IBD.

Methods
Pregnant IBD patients, with and without thiopurine exposure, and one cohort of control individuals were recruited over a 5-year period. Consenting individuals completed a questionnaire and infants had a complete blood cell count at the newborn heel prick. Anemia was defined as hemoglobin (Hb) &lt; 140g/L. Descriptive statistics were used to characterize the study population. Fisher exact tests were used to examine differences in outcomes between groups, a P-value of &lt; 0.05 was deemed significant.

Results
Three cohorts were recruited: 19 IBD patients on thiopurines, 50 IBD patients not on thiopurines, and 37 controls (total of 106). Neonatal median Hb was not different with 177g/L (IQR 38g/L) for the IBD thiopurine group, 180.5g/L (IQR 40g/L) for the IBD non-thiopurine group, and 181g/L (IQR 37g/L) for the controls. Nineteen infants (18%) were cytopenic with 12 (11%) anemic, 6 (5.6%) thrombocytopenic, and 1 (0.94%) lymphopenic. Thiopurine exposure was only in one, mildly anemic, infant.

Conclusions
These findings further support physicians and IBD patients contemplating pregnancy that current guidelines recommending thiopurine adherence do not lead to increased perinatal risk of anemia or cytopenia.
Automatic measurements of left ventricular volumes and ejection fraction by artificial intelligence: clinical validation in real time and large databases
Authors: Olaisen Sindre , Smistad Erik , Espeland Torvald , Hu Jieyu , Pasdeloup David , Østvik Andreas , Aakhus Svend , Rösner Assami , Malm Siri , Stylidis Michael , Holte Espen , Grenne Bjørnar , Løvstakken Lasse , Dalen Havard 
Published: October 2023

Abstract

Aims
Echocardiography is a cornerstone in cardiac imaging, and left ventricular (LV) ejection fraction (EF) is a key parameter for patient management. Recent advances in artificial intelligence (AI) have enabled fully automatic measurements of LV volumes and EF both during scanning and in stored recordings. The aim of this study was to evaluate the impact of implementing AI measurements on acquisition and processing time and test–retest reproducibility compared with standard clinical workflow, as well as to study the agreement with reference in large internal and external databases.

Methods and results
Fully automatic measurements of LV volumes and EF by a novel AI software were compared with manual measurements in the following clinical scenarios: (i) in real time use during scanning of 50 consecutive patients, (ii) in 40 subjects with repeated echocardiographic examinations and manual measurements by 4 readers, and (iii) in large internal and external research databases of 1881 and 849 subjects, respectively. Real-time AI measurements significantly reduced the total acquisition and processing time by 77% (median 5.3 min, P &lt; 0.001) compared with standard clinical workflow. Test–retest reproducibility of AI measurements was superior in inter-observer scenarios and non-inferior in intra-observer scenarios. AI measurements showed good agreement with reference measurements both in real time and in large research databases.

Conclusion
The software reduced the time taken to perform and volumetrically analyse routine echocardiograms without a decrease in accuracy compared with experts.
Non-steroidal anti-inflammatory drugs and risk of pulmonary embolism in patients with inflammatory joint disease—results from the nationwide Norwegian Cardio-rheuma registry
Authors: Ikdahl Eirik , Rollefstad Silvia , Kazemi Amirhossein , Provan Sella A , Larsen Trine-Lise , Semb Anne Grete 
Published: October 2023

Abstract

Aims
Patients with inflammatory joint diseases (IJD), including rheumatoid arthritis (RA), psoriatic arthritis (PsA), and axial spondyloarthritis (axSpA) have increased rates of pulmonary embolism (PE). Non-steroidal anti-inflammatory drugs (NSAIDs) use is associated with PE in the general population. Our aim was to evaluate the association between NSAIDs use and PE in IJD patients.

Methods and results
Using individual-level registry data from the whole Norwegian population, including data from the Norwegian Patient Registry and the Norwegian Prescription Database, we: (1) evaluated PE risk in IJD compared to non-IJD individuals, (2) applied the self-controlled case series method to evaluate if PE risks were associated with use of traditional NSAIDs (tNSAIDs) and selective cox-2 inhibitors (coxibs). After a one-year wash-out period, we followed 4 660 475 adults, including 74 001 with IJD (RA: 39 050, PsA: 20 803, and axSpA: 18 591) for a median of 9.0 years. Crude PE incidence rates per 1000 patient years were 2.02 in IJD and 1.01 in non-IJD individuals. Age and sex adjusted hazard ratios for PE events were 1.57 for IJD patients compared to non-IJD. Incidence rate ratios (IRR) [95% confidence interval (CI)] for PE during tNSAIDs use were 0.78 (0.64–0.94, P = 0.010) in IJD and 1.68 (1.61–1.76, P &lt; 0.001) in non-IJD. IRR (95% CI) for PE during coxibs use was 1.75 (1.10–2.79, P = 0.018) in IJD and 2.80 (2.47–3.18, P &lt; 0.001) for non-IJD.

Conclusion
Pulmonary embolism rates appeared to be higher in IJD than among non-IJD subjects in our study. Traditional NSAIDs may protect against PE in IJD patients, while coxibs may associated with increased PE risk.
Absence of long-term structural and functional cardiac abnormalities on multimodality imaging in a multi-ethnic group of COVID-19 survivors from the early stage of the pandemic
Authors: Sewanan Lorenzo R , Di Tullio Marco R , Laine Andrew F , D’Souza Belinda , Leb Jay , Mironov Alexander , Khan Ahsan , Stanger Dylan E , Konofagou Elisa E , Goldsmith Rochelle L , Jambawalikar Sachin R , Hirschfeld Cole B , Castillo Michelle , Durkin Kathleen J , Dashnaw Stephen , Thomas Vaughan J , Einstein Andrew J 
Published: October 2023

Abstract

Aims
Many patients with coronavirus disease-2019 (COVID-19), particularly from the pandemic’s early phase, have been reported to have evidence of cardiac injury such as cardiac symptoms, troponinaemia, or imaging or ECG abnormalities during their acute course. Cardiac magnetic resonance (CMR) and transthoracic echocardiography (TTE) have been widely used to assess cardiac function and structure and characterize myocardial tissue during COVID-19 with report of numerous abnormalities. Overall, findings have varied, and long-term impact of COVID-19 on the heart needs further elucidation.

Methods and results
We performed TTE and 3 T CMR in survivors of the initial stage of the pandemic without pre-existing cardiac disease and matched controls at long-term follow-up a median of 308 days after initial infection. Study population consisted of 40 COVID-19 survivors (50% female, 28% Black, and 48% Hispanic) and 12 controls of similar age, sex, and race-ethnicity distribution; 35% had been hospitalized with 28% intubated. We found no difference in echocardiographic characteristics including measures of left and right ventricular structure and systolic function, valvular abnormalities, or diastolic function. Using CMR, we also found no differences in measures of left and right ventricular structure and function and additionally found no significant differences in parameters of tissue structure including T1, T2, extracellular volume mapping, and late gadolinium enhancement. With analysis stratified by patient hospitalization status as an indicator of COVID-19 severity, no differences were uncovered.

Conclusion
Multimodal imaging of a diverse cohort of COVID-19 survivors indicated no long-lasting damage or inflammation of the myocardium.
Machine learning–based feature selection to search stable microbial biomarkers: application to inflammatory bowel disease
Authors: Lee Youngro , Cappellato Marco , Di Camillo Barbara 
Published: October 2023

Abstract

Background
Biomarker discovery exploiting feature importance of machine learning has risen recently in the microbiome landscape with its high predictive performance in several disease states. To have a concrete selection among a high number of features, recursive feature elimination (RFE) has been widely used in the bioinformatics field. However, machine learning–based RFE has factors that decrease the stability of feature selection. In this article, we suggested methods to improve stability while sustaining performance.

Results
We exploited the abundance matrices of the gut microbiome (283 taxa at species level and 220 at genus level) to classify between patients with inflammatory bowel disease (IBD) and healthy control (1,569 samples). We found that applying an already published data transformation before RFE improves feature stability significantly. Moreover, we performed an in-depth evaluation of different variants of the data transformation and identify those that demonstrate better improvement in stability while not sacrificing classification performance. To ensure a robust comparison, we evaluated stability using various similarity metrics, distances, the common number of features, and the ability to filter out noise features. We were able to confirm that the mapping by the Bray–Curtis similarity matrix before RFE consistently improves the stability while maintaining good performance. Multilayer perceptron algorithm exhibited the highest performance among 8 different machine learning algorithms when a large number of features (a few hundred) were considered based on the best performance across 100 bootstrapped internal test sets. Conversely, when utilizing only a limited number of biomarkers as a trade-off between optimal performance and method generalizability, the random forest algorithm demonstrated the best performance. Using the optimal pipeline we developed, we identified 14 biomarkers for IBD at the species level and analyzed their roles using Shapley additive explanations.

Conclusion
Taken together, our work not only showed how to improve biomarker discovery in the metataxonomic field without sacrificing classification performance but also provided useful insights for future comparative studies.