bluuebunny/crossref_metadata_2025_split huggingface dataset:
UPDATE - 2022 Italian guidelines on the management of bronchiolitis in infants
Authors: Manti Sara , Staiano Annamaria , Orfeo Luigi , Midulla Fabio , Marseglia Gian Luigi , Ghizzi Chiara , Zampogna Stefania , Carnielli Virgilio Paolo , Favilli Silvia , Ruggieri Martino , Perri Domenico , Di Mauro Giuseppe , Gattinara Guido Castelli , D’Avino Antonio , Becherucci Paolo , Prete Arcangelo , Zampino Giuseppe , Lanari Marcello , Biban Paolo , Manzoni Paolo , Esposito Susanna , Corsello Giovanni , Baraldi Eugenio 
Published: February 2023

AbstractBronchiolitis is an acute respiratory illness that is the leading cause of hospitalization in young children. This document aims to update the consensus document published in 2014 to provide guidance on the current best practices for managing bronchiolitis in infants. The document addresses care in both hospitals and primary care. The diagnosis of bronchiolitis is based on the clinical history and physical examination. The mainstays of management are largely supportive, consisting of fluid management and respiratory support. Evidence suggests no benefit with the use of salbutamol, glucocorticosteroids and antibiotics with potential risk of harm. Because of the lack of effective treatment, the reduction of morbidity must rely on preventive measures. De-implementation of non-evidence-based interventions is a major goal, and educational interventions for clinicians should be carried out to promote high-value care of infants with bronchiolitis. Well-prepared implementation strategies to standardize care and improve the quality of care are needed to promote adherence to guidelines and discourage non-evidence-based attitudes. In parallel, parents' education will help reduce patient pressure and contribute to inappropriate prescriptions. Infants with pre-existing risk factors (i.e., prematurity, bronchopulmonary dysplasia, congenital heart diseases, immunodeficiency, neuromuscular diseases, cystic fibrosis, Down syndrome) present a significant risk of severe bronchiolitis and should be carefully assessed. This revised document, based on international and national scientific evidence, reinforces the current recommendations and integrates the recent advances for optimal care and prevention of acute bronchiolitis.
SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data
Authors: Macnair Will , Robinson Mark 
Published: February 2023

AbstractQuality control (QC) is a critical component of single-cell RNA-seq (scRNA-seq) processing pipelines. Current approaches to QC implicitly assume that datasets are comprised of one cell type, potentially resulting in biased exclusion of rare cell types. We introduce , which robustly fits a Gaussian mixture model across multiple samples, improves sensitivity, and reduces bias compared to current approaches. We show via simulations that is less susceptible to exclusion of rarer cell types. We also demonstrate on a complex real dataset (867k cells over 172 samples). is general, is implemented in R, and could be applied to other data types.
Proteomic analysis of exosome-like vesicles from Fasciola gigantica adult worm provides support for new vaccine targets against fascioliasis
Authors: Sheng Zhao-An , Wu Cui-Lan , Wang Dong-Ying , Zhong Shu-Hong , Yang Xi , Rao Guo-Shun , Peng Hao , Feng Shi-Wen , Li Jun , Huang Wei-Yi , Luo Hong-Lin 
Published: February 2023

Abstract
Background
Extracellular vesicles (EVs) released by helminths play an important role in parasite-host communication. However, little is known about the characteristics and contents of the EVs of Fasciola gigantica, a parasitic flatworm that causes tropical fascioliasis. A better understanding of EVs released by F. gigantica will help elucidate the mechanism of F. gigantica-host interaction and facilitate the search for new vaccine candidates for the control and treatment of fascioliasis.

Methods
Two different populations of EVs (15k EVs and 100k EVs) were purified from adult F. gigantica culture media by ultracentrifugation. The morphology and size of the purified EVs were determined by transmission electron microscopy (TEM) and by the Zetasizer Nano ZSP high performance particle characterization system. With the aim of identifying diagnostic markers or potential vaccine candidates, proteins within the isolated 100k EVs were analyzed using mass spectrometry-based proteomics (LC–MS/MS). Mice were then vaccinated with excretory/secretory products (ESPs; depleted of EVs), 15k EVs, 100k EVs and recombinant F. gigantica heat shock protein 70 (rFg-HSP70) combined with alum adjuvant followed by challenge infection with F. gigantica metacercariae. Fluke recovery and antibody levels were used as measures of vaccine protection.

Results
TEM analysis and nanoparticle tracking analysis indicated the successful isolation of two subpopulations of EVs (15k EVs and 100k EVs) from adult F. gigantica culture supernatants using differential centrifugation. A total of 755 proteins were identified in the 100k EVs. Exosome biogenesis or vesicle trafficking proteins, ESCRT (endosomal sorting complex required for transport) pathway proteins and exosome markers, heat shock proteins and 14-3-3 proteins were identified in the 100k EVs. These results indicate that the isolated 100k EVs were exosome-like vesicles. The functions of the identified proteins may be associated with immune regulation, immune evasion and virulence. Mice immunized with F. gigantica ESPs, 15k EVs, 100k EVs and rFg-HSP70 exhibited a reduction in fluke burden of 67.90%, 60.38%, 37.73% and 56.6%, respectively, compared with the adjuvant control group. The vaccination of mice with F. gigantica 100k EVs, 15k EVs, ESP and rFg-HSP70 induced significant production of specific immunoglobulins in sera, namely IgG, IgG1 and IgG2a.

Conclusion
The results of this study suggest that proteins within the exosome-like vesicles of F. gigantica have immunomodulatory, immune evasion and virulence functions. This knowledge may lead to new strategies for immunotherapy, vaccination and the diagnosis of fascioliasis.

Graphical Abstract
Extramedullary relapse of Immunoglobulin A-kappa myeloma manifesting as plasmacytoma of the pleura without bone marrow involvement and following autologous bone marrow transplant: a case report
Authors: Rezvani Alireza , Shahriarirad Reza , Fallahi Mohammad Javad , Zeighami Ali 
Published: February 2023

Abstract
Background
Recurrence of multiple myeloma is among the most challenging issues for patients and treating physicians reported after autologous stem cell transplantation. However, extramedullary involvement after chemotherapy and transplantation has been rarely reported, especially as pleural manifestations. Protein electrophoresis indicated immunoglobulin A monoclonal kappa plasma cell neoplasm in our case.

Case presentation
A 48-year-old middle-eastern man was referred to our clinic with cough, dyspnea, fever, and left side pleural effusion. A year after chemotherapy and autologous bone marrow transplantation, the patient presented with features in favor of pleural relapse, without bone marrow involvement. Protein electrophoresis demonstrated immunoglobulin A monoclonal kappa plasma cell neoplasm in our case. The patient was effectively treated with dexamethasone, thalidomide, cisplatin, doxorubicin, cyclophosphamide, and etoposide with no notable adverse effects.

Conclusion
Physicians should be aware of various presentations of multiple myeloma relapse, especially in autologous stem cell transplantation patients. Atypical and unique presentations such as the pleural involvement warrant further reporting of evidence to provide early management and treatment options.
ICU patients with infectious complications after abdominopelvic surgery: Is thoracic CT in addition to abdominal CT helpful?
Authors: Nebelung Heiner , Wotschel Natalie , Held Hanns-Christoph , Kirchberg Johanna , Weitz Jürgen , Radosa Christoph Georg , Laniado Michael , Hoffmann Ralf-Thorsten , Plodeck Verena 
Published: February 2023

Abstract
Background
The aim of this study was to assess the usefulness of adding thoracic CT to abdominal CT in intensive care unit (ICU) patients with signs of infection after abdominopelvic surgery.

Methods
143 thoracoabdominal CTs of ICU patients with signs of infection after abdominopelvic surgery were retrospectively reviewed for thoracic pathologies. It was determined if pathologic findings were visible only on thoracic CT above the diaphragmatic dome or also on abdominal CT up to the diaphragmatic dome. All thoracic pathologies visible only above the diaphragmatic dome were retrospectively analyzed by an ICU physician in terms of clinical relevance. Diagnostic and therapeutic efficacy of thoracic CT were assessed with regard to an infectious focus and to other pathologic findings.

Results
297 pathologic thoracic findings were recorded. 26 of the 297 findings could only be detected on images obtained above the diaphragmatic dome (in 23 of 143 CTs). A change in patient management was initiated due to only one of the 26 supradiaphragmatic findings. Diagnostic efficacy of thoracic CT in addition to abdominal CT to identify an infectious focus was 3.5% (95%-CI: 0.5–6.5%) and therapeutic efficacy was 0.7% (95%-CI: 0–2.1%). With regard to all pathologic thoracic findings, diagnostic efficacy was 16.1% (95%-CI: 10.1–22.1%) and therapeutic efficacy remained at 0.7%.

Conclusions
Additional thoracic CT to detect an infectious focus in ICU patients after abdominopelvic surgery leads to identification of the focus in only 3.5% and to changes in patient management in only 0.7%. Other relevant findings are more common (16.1%), but very rarely affect patient management.
Privacy-preserving cloud-edge collaborative learning without trusted third-party coordinator
Authors: Yu Xiaopeng , Tang Dianhua , Zhao Wei 
Published: February 2023

AbstractCloud-edge collaborative learning has received considerable attention recently, which is an emerging distributed machine learning (ML) architecture for improving the performance of model training among cloud center and edge nodes. However, existing cloud-edge collaborative learning schemes cannot efficiently train high-performance models on large-scale sparse samples, and have the potential risk of revealing the privacy of sensitive data. In this paper, adopting homomorphic encryption (HE) cryptographic technique, we present a privacy-preserving cloud-edge collaborative learning over vertically partitioned data, which allows cloud center and edge node to securely train a shared model without a third-party coordinator, and thus greatly reduces the system complexity. Furthermore, the proposed scheme adopts the batching technique and single instruction multiple data (SIMD) to achieve parallel processing. Finally, the evaluation results show that the proposed scheme improves the model performance and reduces the training time compared with the existing methods; the security analysis indicates that our scheme can guarantee the security in semi-honest model.
SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation
Authors: de Sainte Agathe Jean-Madeleine , Filser Mathilde , Isidor Bertrand , Besnard Thomas , Gueguen Paul , Perrin Aurélien , Van Goethem Charles , Verebi Camille , Masingue Marion , Rendu John , Cossée Mireille , Bergougnoux Anne , Frobert Laurent , Buratti Julien , Lejeune Élodie , Le Guern Éric , Pasquier Florence , Clot Fabienne , Kalatzis Vasiliki , Roux Anne-Françoise , Cogné Benjamin , Baux David 
Published: February 2023

Abstract
SpliceAI is an open-source deep learning splicing prediction algorithm that has demonstrated in the past few years its high ability to predict splicing defects caused by DNA variations. However, its outputs present several drawbacks: (1) although the numerical values are very convenient for batch filtering, their precise interpretation can be difficult, (2) the outputs are delta scores which can sometimes mask a severe consequence, and (3) complex delins are most often not handled. We present here SpliceAI-visual, a free online tool based on the SpliceAI algorithm, and show how it complements the traditional SpliceAI analysis. First, SpliceAI-visual manipulates raw scores and not delta scores, as the latter can be misleading in certain circumstances. Second, the outcome of SpliceAI-visual is user-friendly thanks to the graphical presentation. Third, SpliceAI-visual is currently one of the only SpliceAI-derived implementations able to annotate complex variants (e.g., complex delins). We report here the benefits of using SpliceAI-visual and demonstrate its relevance in the assessment/modulation of the PVS1 classification criteria. We also show how SpliceAI-visual can elucidate several complex splicing defects taken from the literature but also from unpublished cases. SpliceAI-visual is available as a Google Colab notebook and has also been fully integrated in a free online variant interpretation tool, MobiDetails (https://mobidetails.iurc.montp.inserm.fr/MD).

Graphical abstract
A courtly brocade belt belonging to Qajar period (1789–1925), Iran
Authors: Koochakzaei Alireza , Oudbashi Omid 
Published: February 2023

Abstract
This paper identifies the materials used to make a brocade belt belonging to the Qajar courtiers in Iran. This belt consists of two fabric types: red support and golden brocade. Accordingly, this paper examined the skin and tannin type, fiber types, dyeing agents, mordant, and metal wrapping of brocade yarns and metal buckle. Technical imaging, ESI–MS, FORS, FTIR and SEM–EDS were used to identify the materials. Multi-band imaging methods included Vis, UVL, IRR, and UVR, in which UVFC and IRFC images were obtained after processing. The results showed that cotton yarn was used in both fabrics. The red fabric yarns were dyed using cochineal and alum mordant. Also, the yellow brocade yarns were dyed using catechins-rich plants, and in this dyeing process, polyphenols and alum have been as mordant. Madder-dyed yarns are also found in parts of the belt. Examination of the metal wrapping of brocade yarns suggests using strips of copper-nickel alloy with a thin layer of gold-silver alloy. This secondary coating protects the copper-nickel strips and increases their golden luster. The leather analysis of the leather parts also indicated the using cattle/calfskin tanned with gallotannins. Belt buckle analysis also shows the use of brass alloy with a high percentage of zinc, leading to a golden sheen and the buckle desired strength. The results show the use of low-cost materials in the manufacture of clothing for the lower levels of the Qajar court.
Liquid biopsy-based identification of prognostic and immunotherapeutically relevant gene signatures in lower grade glioma
Authors: Wu Changwu , Long Wenyong , Qin Chaoying , Wang Xiangyu , Li Yuzhe , Xiao Kai , Li Yue , Liu Qing 
Published: February 2023

Abstract
Background
Recent studies have shown that immunotherapies, including peptide vaccines, remain promising strategies for patients with lower grade glioma (LGG); however new biomarkers need to be developed to identify patients who may benefit from therapy. We aimed to investigate the feasibility of liquid biopsy-based gene signatures in predicting the prognosis of LGG patients, as well as the benefits of immunotherapy.

Methods
We evaluated the association between circulating immune cells and treatment response by analyzing peripheral blood mononuclear cell (PBMC) samples from LGG patients receiving peptide vaccine immunotherapy, identified response-related genes (RRGs), and constructed RRG-related Response Score. In addition, RRG-related RiskScore was constructed in LGG tumor samples based on RRGs; association analysis for RiskScore and characteristics of TME as well as patient prognosis were performed in two LGG tumor datasets. The predictive power of RiskScore for immunotherapy benefits was analyzed in an anti-PD-1 treatment cohort.

Results
This study demonstrated the importance of circulating immune cells, including monocytes, in the immunotherapeutic response and prognosis of patients with LGG. Overall, 43 significant RRGs were identified, and three clusters with different characteristics were identified in PBMC samples based on RRGs. The constructed RRG-related Response Score could identify patients who produced a complete response to peptide vaccine immunotherapy and could predict prognosis. Additionally, three subtypes were identified in LGG tumors based on RRGs, with subtype 2 being an immune “hot” phenotype suitable for immune checkpoint therapy. The constructed RRG-related RiskScore was significantly positively correlated with the level of tumor immune cell infiltration. Patients with high RiskScore had a worse prognosis and were more likely to respond to immune checkpoint therapy. The therapeutic advantage and clinical benefits of patients with a high RiskScore were confirmed in an anti-PD-1 treatment cohort.

Conclusion
This study confirmed the potential of liquid biopsy for individualized treatment selection in LGG patients and determined the feasibility of circulating immune cells as biomarkers for LGG. Scoring systems based on RRGs can predict the benefits of immunotherapy and prognosis in patients with LGG. This work would help to increase our understanding of the clinical significance of liquid biopsy and more effectively guide individualized immunotherapy strategies.
Design, development and performance analysis of cognitive assisting aid with multi sensor fused navigation for visually impaired people
Authors: Bala Myneni Madhu , Vasundhara D. N. , Haritha Akkineni , Moorthy CH. V. K. N. S. N. 
Published: February 2023

AbstractThe research and innovations in the field of wearable auxiliary devices for visually impaired and blind people are playing a vital role towards improving their quality of life. However, in spite of the promising research outcomes, the existing wearable aids has several weaknesses such as more weight, limitations in the number of features and cost. The main objective of this manuscript is to provide the detailed design of a novel lightweight wearable aid with higher number of features for visually impaired and blind people. The proposed research aims to design a cognitive assistant that will guide the blind people for walking by detecting the environment around them. The framework include a Multi-Sensor Fused Navigation system comprises of a sensor-based, vision-based, and cognitive (intelligent/smart) application. The visual features for the design include obstacle detection, uneven surface detection, slope and downward steps detection, pothole detection and hallow object detection; location tracking, walking guide, image capturing and video recording. This prototype is named as Blind’s Apron based on its appearance. The invention focusses on parameters like reduction on size (quite handy) and light weight (comfortable to wear), higher number of detection features, and minimum user intervention (high end operations like switching on and off). All user interactions are friendly and affordable to everyone. The results obtained in this research lead to a high end technical intervention with ease of use. Finally, the performance of the proposed cognitive assistant is tested with a user study in real-time. The feedback and corresponding results establish the effective outcome of the proposed invention which is a light weight and feature enhanced device with easily understandable instructions.
Geography, rurality, and community distress: deaths due to suicide, alcohol-use, and drug-use among Colorado Veterans
Authors: Spark Talia L. , Reid Colleen E. , Adams Rachel Sayko , Schneider Alexandra L. , Forster Jeri , Denneson Lauren M. , Bollinger Mary , Brenner Lisa A. 
Published: February 2023

Abstract
Background
In the USA, deaths due to suicide, alcohol, or drug-related causes (e.g., alcohol-related liver disease, overdose) have doubled since 2002. Veterans appear disproportionately impacted by growing trends. Limited research has been conducted regarding the relationship between community-level factors (e.g., rurality, community distress resulting from economic conditions) and the presence of spatial clustering of suicide, alcohol-related, or drug-related deaths. We explored community-level relationships in Colorado Veterans and compared suicide, alcohol-, and drug-related death rates between the Colorado adult population and Veterans.

Methods
2009–2020 suicide, alcohol-related, and/or drug-related deaths were identified using qualifying multiple cause-of-death International Classification of Disease (ICD)-10 codes in CDC WONDER for the general adult population and Colorado death data for Veteran populations. Age and race adjusted rates were calculated to compare risk overall and by mortality type (i.e., suicide, alcohol-related, drug-related). In Veteran decedents, age-adjusted rates were stratified by rurality and community distress, measured by the Distressed Communities Index. Standardized mortality ratios were calculated to measure spatial autocorrelation and identify clusters using global and local Moran’s I, respectively.

Results
6.4% of Colorado Veteran deaths (n = 6948) were identified as being related to suicide, alcohol, or drugs. Compared to rates in the general population of Colorado adults, Veterans had 1.8 times higher rates of such deaths overall (2.1 times higher for suicide, 1.8 times higher for alcohol-related, 1.3 times higher for drug-related). Among Veterans, community distress was associated with an increased risk of alcohol-related [age-adjusted rate per 100,000 (95% CI) = 129.6 (89.9–193.1)] and drug-related deaths [95.0 (48.6–172.0)]. This same significant association was not identified among those that died by suicide. Rurality was not associated with risk for any of the deaths of interest. There was significant spatial clustering for alcohol-related deaths in southeast Colorado.

Conclusions
Colorado Veterans have higher rates of deaths due to suicide, alcohol-related, and drug-related causes compared to members of the general adult population. Upstream prevention efforts, such as community-based interventions targeting alcohol-use and community economic distress, are warranted. More research is also needed to understand how community distress and other social determinants of health impact the community burden of suicide, alcohol-related, and drug-related mortality.