bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular prognostication in Ph-negative MPNs in 2022
Authors: Vannucchi Alessandro Maria , Guglielmelli Paola 
Published: December 2022

Abstract
The application of genomic techniques, including cytogenetics and DNA sequencing, to decipher the molecular landscape of patients with myeloproliferative neoplasms (MPNs) has radically modified diagnostic approach and management through improved risk stratification. Three driver mutated genes (JAK2, MPL, CALR) are variably harbored by &gt;80% of patients and associated with clinical characteristics, as well as major disease-related complications and different survival outcomes. Therefore, JAK2 V617F mutation is included in the revised International Prognosis Score of Thrombosis for Essential Thrombocythemia score for prediction of thrombosis in patients with essential thrombocythemia and prefibrotic primary myelofibrosis, while a CALR type 1 mutated genotype constitutes a favorable variable for survival in patients with myelofibrosis (MF). Novel, integrated clinical and cytogenetic/mutation scores (Mutation-Enhanced International Prognostic Score System for Transplantation-Age Patients with Primary Myelofibrosis [MIPSS70/v2], genetically inspired prognostic scoring system [GIPSS], Myelofibrosis Secondary to PV and ET- Prognostic Model [MYSEC-PM]) have been devised that guide selection of stem cell transplantation candidates with MF or help predict the risk associated with the transplant procedure (Myelofibrosis Transplant Scoring System), with greater performance compared with conventional scores based on hematologic and clinical variables only. On the other hand, several clinical needs remain unmet despite the great amount of molecular information available nowadays. These include the prediction of evolution to acute leukemia in a clinically actionable time frame, the identification of patients most likely to derive durable benefits from target agents, in primis JAK inhibitors, and, conversely, the significance of molecular responses that develop in patients receiving interferon or some novel agents. Here, we discuss briefly the significance and the role of genomic analysis for prognostication in patients with MPNs from a clinician's point of view, with the intent to provide how-to-use hints.
Treatment of Richter's syndrome
Authors: Thompson Philip A. , Siddiqi Tanya 
Published: December 2022

Abstract
Richter's syndrome (RS) is an aggressive histologic transformation of chronic lymphocytic leukemia (CLL), most commonly to diffuse large B-cell lymphoma (DLBCL). Outcomes are generally poor, with complete remission (CR) rates of only about 20% and less than 20% long-term survival with chemoimmunotherapy (CIT). RS is biologically heterogeneous, and in 80% of patients with CLL who develop DLBCL, the disease is clonally related to the CLL. Clonally unrelated cases are genetically and immunologically distinct from clonally related DLBCL-RS, have more favorable responses to CIT, and are best treated as de novo DLBCL. Relatively favorable outcomes with CIT are also seen in patients who have never previously received treatment for CLL and who lack TP53 mutation or deletion. For the remaining patients, treatment on a clinical trial is optimal. Fortunately, numerous agents are now in clinical development that show encouraging results. Here we review clinical data for some of the most promising approaches. DLBCL-RS tumor cells frequently express programmed cell death 1 protein (PD-1), and several studies have demonstrated activity for PD-1 inhibitors, especially in combination with ibrutinib. The BCL2 inhibitor venetoclax in combination with R-EPOCH CIT achieved CR in 50% of patients, and a study of venetoclax–R-CHOP is ongoing. The noncovalent Bruton's tyrosine kinase inhibitor pirtobrutinib has achieved responses in approximately two-thirds of heavily pretreated patients and, given its favorable toxicity profile, appears ideally suited to combining with other active agents. Finally, we review available data for bispecific antibodies, antibody-drug conjugates, and chimeric antigen receptor T-cell therapy, which, after revolutionizing the treatment of DLBCL, are now being evaluated in RS.
Individualized patient care in nodular lymphocyte-predominant Hodgkin lymphoma
Authors: Borchmann Sven 
Published: December 2022

Abstract
Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) is a rare lymphoma that has traditionally been considered a subgroup of Hodgkin lymphoma. However, morphology, surface marker expression, genetics, and clinical course are different from classic Hodgkin lymphoma. While most patients experience indolent disease with slow progression, some patients can also have more aggressive disease. Nevertheless, outcomes are excellent, and excess mortality due to NLPHL is at most very low. The treatment of newly diagnosed NLPHL has historically mirrored that of classic Hodgkin lymphoma. However, evidence for deviations from that approach has emerged over time and is discussed herein. Less evidence is available for the optimal management of relapsed patients. So-called variant histology has recently emerged as a biological risk factor, providing at least a partial explanation for the observed heterogeneity of NLPHL. Considering variant histology together with other risk factors and careful observation of the clinical course of the disease in each patient can help to assess individual disease aggressiveness. Also important in this mostly indolent disease are the preferences of the patient and host factors, such as individual susceptibility to specific treatment side effects. Considering all this together can guide individualized treatment recommendations, which are paramount in this rare disease.
Cold AIHA and the best treatment strategies
Authors: Despotovic Jenny McDade , Kim Taylor Olmsted 
Published: December 2022

Abstract
Cold-reactive autoimmune hemolytic anemia (AIHA) is rare among the hemolytic anemias. It results when 1 of a variety of processes causes the generation of immunoglobulin M (IgM) autoantibodies against endogenous erythrocytes, resulting in complement activation and predominantly intravascular hemolysis. Cold AIHA is typically a primary lymphoproliferative disorder with marrow B-cell clones producing pathogenic IgM. More rarely, secondary cold AIHA (cAIHA) can develop from malignancy, infection, or other autoimmune disorders. However, in children cAIHA is typically post infection, mild, and self-limited. Symptoms include a sequelae of anemia, fatigue, and acrocyanosis. The severity of disease is variable and highly dependent on the thermal binding range of the autoantibody. In adults, treatment has most commonly focused on reducing antibody production with rituximab-based regimens. The addition of cytotoxic agents to rituximab improves response rates, but at the expense of tolerability. Recent insights into the cause of cold agglutinin disease as a clonal disorder driven by complement form the basis of newer therapeutic options. While rituximab-based regimens are still the mainstay of therapy, options have now expanded to include complement-directed treatments and other B-cell-directed or plasma-cell-directed therapies.
Platelet components and bacterial contamination: hospital perspective 2022
Authors: Szczepiorkowski Zbigniew M. , Pagano Monica B. 
Published: December 2022

Abstract
Bacterial contamination of platelet units has been one of the most common transfusion-transmitted infections. Approximately 4 to 7 fatalities are being reported to the US Food and Drug Administration (FDA) annually, which cites bacterially contaminated platelet units as the cause. Over the past 3 decades, different mitigation strategies have been introduced to minimize the risk of morbidity and mortality related to contaminated platelet units. The process of platelet collection and manufacturing as well as storage at 20°C to 24°C contributes to higher prevalence of contaminated units. The risk of transfusing bacterially contaminated platelets can be lowered using different types of interventions. Prevention of bacterial contamination can be done by strict adherence to techniques that minimize contamination during unit collection. The detection of bacteria in platelet products can be improved with a combination of rapid testing and bacterial cultures that involve large volume and delayed sampling. Finally, pathogen reduction can inactivate bacteria or other pathogens present in the unit.
This article describes different strategies that blood centers and transfusion services have undertaken since October 2021 to meet FDA guidance requirements. Market forces as well as feasibility of different FDA-proposed approaches have limited the number of practical solutions to just a few. In addition, the blood product availability required hospitals to adopt more progressive strategies to provide patients with needed platelet products.
Automatic identifying and counting blood cells in smear images by using single shot detector and Taguchi method
Authors: Chen Yao-Mei , Tsai Jinn-Tsong , Ho Wen-Hsien 
Published: December 2022

Abstract
Background
Researchers have tried to identify and count different blood cells in microscopic smear images by using deep learning methods of artificial intelligence to solve the highly time-consuming problem.

Results
The three types of blood cells are platelets, red blood cells, and white blood cells. This study used the Resnet50 network as a backbone network of the single shot detector (SSD) for automatically identifying and counting different blood cells and, meanwhile, proposed a systematic method to find a better combination of algorithm hyperparameters of the Resnet50 network for promoting accuracy for identifying and counting blood cells. The Resnet50 backbone network of the SSD with its optimized algorithm hyperparameters, which is called the Resnet50-SSD model, was developed to enhance the feature extraction ability for identifying and counting blood cells. Furthermore, the algorithm hyperparameters of Resnet50 backbone networks of the SSD were optimized by the Taguchi experimental method for promoting detection accuracy of the Resnet50-SSD model. The experimental result shows that the detection accuracy of the Resnet50-SSD model with 512 × 512 × 3 input images was better than that of the Resnet50-SSD model with 300 × 300 × 3 input images on the test set of blood cells images. Additionally, the detection accuracy of the Resnet50-SSD model using the combination of algorithm hyperparameters got by the Taguchi method was better than that of the Resnet50-SSD model using the combination of algorithm hyperparameters given by the Matlab example.

Conclusion
In blood cell images acquired from the BCCD dataset, the proposed Resnet50-SSD model had higher accuracy in identifying and counting blood cells, especially white blood cells and red blood cells.
amica: an interactive and user-friendly web-platform for the analysis of proteomics data
Authors: Didusch Sebastian , Madern Moritz , Hartl Markus , Baccarini Manuela 
Published: December 2022

Abstract
Background
Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis.

Results
In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources. amica provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica’s query interface interactively to compare multiple conditions and rapidly identify enriched or depleted proteins. They can visualize their results using customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application.

Conclusions
The strong emphasis on dynamic user interactions, the integration of various databases and the option to download processed data, facilitate the analysis of complex proteomic data for both first-time users and experienced bioinformaticians. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica.
Outcome prediction for patients assessed by the medical emergency team: a retrospective cohort study
Authors: Adielsson Anna , Danielsson Christian , Forkman Pontus , Karlsson Thomas , Pettersson Linda , Herlitz Johan , Lundin Stefan 
Published: December 2022

Abstract
Background
Medical emergency teams (METs) have been implemented to reduce hospital mortality by the early recognition and treatment of potentially life-threatening conditions. The objective of this study was to establish a clinically useful association between clinical variables and mortality risk, among patients assessed by the MET, and further to design an easy-to-use risk score for the prediction of death within 30 days.

Methods
Observational retrospective register study in a tertiary university hospital in Sweden, comprising 2,601 patients, assessed by the MET from 2010 to 2015. Patient registry data at the time of MET assessment was analysed from an epidemiological perspective, using univariable and multivariable analyses with death within 30 days as the outcome variable. Predictors of outcome were defined from age, gender, type of ward for admittance, previous medical history, acute medical condition, vital parameters and laboratory biomarkers. Identified factors independently associated with mortality were then used to develop a prognostic risk score for mortality.

Results
The overall 30-day mortality was high (29.0%). We identified thirteen factors independently associated with 30-day mortality concerning; age, type of ward for admittance, vital parameters, laboratory biomarkers, previous medical history and acute medical condition. A MET risk score for mortality based on the impact of these individual thirteen factors in the model yielded a median (range) AUC of 0.780 (0.774–0.785) with good calibration. When corrected for optimism by internal validation, the score yielded a median (range) AUC of 0.768 (0.762–0.773).

Conclusions
Among clinical variables available at the time of MET assessment, thirteen factors were found to be independently associated with 30-day mortality. By applying a simple risk scoring system based on these individual factors, patients at higher risk of dying within 30 days after the MET assessment may be identified and treated earlier in the process.
Accuracy of noninvasive methods for the diagnosis of liver fibrosis in children with chronic viral hepatitis
Authors: ElShahawy A , El-Raziky MS , Sharaf SA , Elsharkawy A , Enayet A , Taher H 
Published: December 2022

Abstract
Background
Liver biopsy is the reference standard for assessing liver fibrosis. Moreover, it is an invasive procedure. Transient elastography (TE) is an accurate, noninvasive method for evaluating liver stiffness as a surrogate of liver fibrosis. The aspartate aminotransferase to platelet ratio index (APRI) and Hyaluronic acid (HA) are noninvasive alternatives to liver biopsy for detecting hepatic fibrosis. This study aimed to identify the accuracy of APRI, HA, and TE concerning liver biopsy in children with chronic viral hepatitis.

Methods
This cross-sectional study included 50 children, 5–18 years with chronic viral hepatitis B (HBV) or hepatitis C (HCV) who underwent liver biopsy within nine months of laboratory tests, determining APRI & performing TE. Twenty healthy children of age and sex-matching patients were included as a control group for the serum HA levels.

Results
The histopathological findings of the studied cases showed seven cases with (F0) fibrosis, 36 cases with mild (F1,2), two children with moderate (F3,4), and five children with severe (F5,6). The median (IQR) of steatosis was 4 (three had HCV). When correlating TE, APRI, and HA values in all cases with their laboratory data, there was a positive correlation between ALT and APRI values (P-value = 0.000), a positive correlation between AST and HA values (P-value = 0.02), and a negative correlation between stiffness and APRI.
The sensitivity of HA, APRI, and TE compared to fibrosis detected by histopathology was 60.5, 65.1, and 60.5%, and their specificity was 71.4, 57.1, and 85.7%, respectively. TE was significantly higher in a group with (moderate to severe) fibrosis.

Conclusion
APRI, HA, and TE are good indicators of the presence of fibrosis almost with the same accuracy. TE is the only method to differentiate mild cases from those with significant fibrosis.
Informing the development of an outcome set and banks of items to measure mobility among individuals with acquired brain injury using natural language processing
Authors: Alhasani Rehab , Godbout Mathieu , Durand Audrey , Auger Claudine , Lamontagne Anouk , Ahmed Sara 
Published: December 2022

AbstractBackgroundThe sheer number of measures evaluating mobility and inconsistencies in terminology make it challenging to extract potential core domains and items. Automating a portion of the data synthesis would allow us to cover a much larger volume of studies and databases in a smaller fraction of the time compared to the usual process. Thus, the objective of this study was to identify a comprehensive outcome set and develop preliminary banks of items of mobility among individuals with acquired brain injury (ABI) using Natural Language Processing (NLP).MethodsAn umbrella review of 47 reviews evaluating the content of mobility measures among individuals with ABI was conducted. A search was performed on 5 databases between 2000 and 2020. Two independent reviewers retrieved copies of the measures and extracted mobility domains and items. A pre-trained BERT model (state-of-the-art model for NLP) provided vector representations for each sentence. Using the International Classification of Functioning, Disability, and Health Framework (ICF) ontology as a guide for clustering, ak-means algorithm was used to retrieve clusters of similar sentences from their embeddings. The resulting embedding clusters were evaluated using the Silhouette score and fine-tuned according to expert input.ResultsThe study identified 246 mobility measures, including 474 domains and 2109 items. Encoding the clusters using the ICF ontology and expert knowledge helped in regrouping the items in a way that is more closely related to mobility terminology. Our best results identified banks of items that were used to create a 24 comprehensive outcome sets of mobility, including Upper Extremity Mobility, Emotional Function, Balance, Motor Control, Self-care, Social Life and Relationships, Cognition, Walking, Postural Transition, Recreation, and Leisure Activities, Activities of Daily Living, Physical Functioning, Communication, Work/Study, Climbing, Sensory Functions, General Health, Fatigue, Functional Independence, Pain, Alcohol and Drugs Use, Transportation, Sleeping, and Finances.ConclusionThe banks of items of mobility domains represent a first step toward establishing a comprehensive outcome set and a common language of mobility to develop the ontology. It enables researchers and healthcare professionals to begin exposing the content of mobility measures as a way to assess mobility comprehensively.
A novel TTR mutation (p.Ala65Val) underlying late-onset hereditary transthyretin (ATTRv) amyloidosis with mixed cardiac and neuropathic phenotype: a case report
Authors: Thimm Andreas , Oubari Sara , Hoffmann Julia , Carpinteiro Alexander , Papathanasiou Maria , Luedike Peter , Kessler Lukas , Rischpler Christoph , Röcken Christoph , Diebold Isabel , Rassaf Tienush , Schmidt Hartmut , Kleinschnitz Christoph , Hagenacker Tim 
Published: December 2022

Abstract
Background
Hereditary transthyretin (ATTRv) amyloidosis is a rare, genetically heterogeneous and phenotypically variable systemic disease characterized by deposition of misfolded transthyretin fibrils in various tissues. ATTRv cardiomyopathy and progressive axonal polyneuropathy are the most common manifestations, leading to severe disability and ultimately death within approximately ten years. As disease-modifying treatment options evolve, timely diagnosis and treatment initiation are crucial to prevent rapid disease progression.

Case presentation
Here, we report on a 73-year old patient initially diagnosed with cardiac wild-type ATTR (ATTRwt) amyloidosis by endomyocardial biopsy. Molecular genetic analysis revealed a novel TTR sequence variant (p.Ala65Val) that is highly likely to be amyloidogenic in light of previously reported TTR mutations and the patient’s clinical presentation and family history.

Conclusions
Our findings expand the spectrum of known pathogenic TTR mutations and underline the importance of a thorough diagnostic workup in amyloidosis patients including careful genetic testing to avoid misdiagnosis and missing of treatment opportunities and to enable cascade testing and tracking of carriers.
Effects of individualized PEEP on postoperative delirium among older patients in prone position: study protocol for a prospective randomized controlled trial
Authors: Zhang Wenchao , Han Shuang , Li Jianli 
Published: December 2022

AbstractBackgroundPostoperative delirium (POD) is an acute mental disorder that often occurs in the elderly after surgery. It can delay functional recovery, extend hospital stay, and increase 1-year mortality and financial costs. Studies have shown that inflammation and cerebral desaturation are the potential pathogenesis of postoperative delirium. Prone-position surgery increases peak airway pressure and decreases lung compliance, exacerbating ventilator-induced inflammation response, as well as the decrease of the patient's cerebral oxygen saturation. Recent studies demonstrated that lung-protective ventilation strategy could reduce inflammatory response and improve cerebral oxygen saturation (rSO2) to prevent POD. In this trial, we aim to investigate the effect of the individualized PEEP on postoperative delirium in elderly patients during prone position.MethodsA prospective, randomized clinical trial will be performed in Hebei General Hospital. 106 patients undergoing elective surgery in prone position will be randomly divided into controlled group (group C) and individualized PEEP group (group I). Lung-protective ventilation with tidal volume of 6ml/kg predictive body weight (PBW) and positive end-expiratory pressure (PEEP) of 5 cm H2O will be applied to patients in group C. Patients in group I will receive the same tidal volume as described in group C plus individualized PEEP corresponding to the maximum dynamic compliance (Cdyn) in the titration method. Our primary endpoint is the prevalence of postoperative delirium based on the Confusion Assessment Method (CAM) until postoperative day 3. Secondary endpoints include the intraoperative rSO2, respiratory variables, arterial blood gases, lung ultrasound score (LUS), postoperative VAS score, and plasma concentrations of IL-6, IL-1β and neuron-specific enolase (NSE).DiscussionThe results of the current protocol might provide evidence for individualized PEEP to prevent POD among older surgical patients in prone position.Trial registrationChinese Clinical Trial Registry (ChiCTR2200056001). Registered 2022 January 30,http://www.chictr.org.cn/index.aspx.